channel_count
int64 1
1
| characteristics_ch1
stringlengths 6
9.77k
| contact_address
stringlengths 1
229
| contact_city
stringlengths 1
47
| contact_country
stringclasses 71
values | contact_institute
stringlengths 2
128
| contact_name
stringlengths 4
74
| contact_zip
stringclasses 1
value | data_processing
stringlengths 4
10.6k
| extract_protocol_ch1
stringlengths 6
14.3k
| geo_accession
stringlengths 9
10
| instrument_model
stringclasses 13
values | last_update_date
stringlengths 11
11
| library_selection
stringclasses 6
values | library_source
stringclasses 5
values | library_strategy
stringclasses 1
value | molecule_ch1
stringclasses 7
values | organism_ch1
stringclasses 1
value | platform_id
stringclasses 13
values | relation
stringlengths 0
2.61k
| sample
stringlengths 9
10
| series_id
stringlengths 8
29
| singlecellprobability
float64 0
1
| source_name_ch1
stringlengths 1
253
| status
stringlengths 21
21
| submission_date
stringlengths 11
11
| taxid_ch1
stringclasses 1
value | title
stringlengths 1
120
| type
stringclasses 1
value | sra
stringlengths 47
49
⌀ | biosample
stringlengths 51
51
⌀ |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | cell type: pancreatic progenitors cells | 82 Walnut St. Unit 3 | Brookline | USA | Harvard Medical School | Yuting,,Liu | All obtained reads from each sample were mapped against the human genome (hg19 build) with Bowtie/Tophat v2.0.2 which allows mapping across splice sites by reads segmentation (Trapnell et al., 2012). All programs were performed with default setting (unless otherwise specified).,The unique mapped reads (69-91% of total reads) were subsequently assembled into transcripts guided by reference annotation (Gencode v14 and Refseq gene models) with Cufflinks v2.0.2 (Trapnell et al., 2012). Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).,For the analyses of lncRNAs, cufflinks was used to estimate the transcript level FPKM values with the Gencode v14 lincRNA annotation (Derrien et al., 2012), and human body map lincRNA annotations (Cabili et al., 2011).,processed data file for protein-coding genes:,processed_FPKM_genes_human_pancreatic_lineage_140112.txt,processed data file for lncRNAs:,processed_FPKM_lncRNAs_human_pancreatic_lineage_140112.txt,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample. | Total RNA was purified from 1,000 sorted cells using ZR RNA microprep kit (Zymo Research, UAS). The cDNA synthesis and amplification was performed with the SMARTer ultra-low input RNA kit (Clontech, US).,The amplified cDNA (10-40 ng) was then fragmented by Covaris S2 sonicator (Covaris, US) and converted to sequencing libraries following the Illuminaâs construction protocol for low input DNA (Illumina, US). Barcoded libraries were pooled and sequenced in Illumina Hiseq 2000 instrument (pair-end 100bp). | GSM1093232 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248487,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974785 | GSM1093232 | GSE44875 | 0.558144 | pancreatic progenitors cells | Public on Jun 01 2014 | Mar 05 2013 | 9606 | PP1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248487 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974785 |
|
1 | cell type: pancreatic progenitors cells | 82 Walnut St. Unit 3 | Brookline | USA | Harvard Medical School | Yuting,,Liu | All obtained reads from each sample were mapped against the human genome (hg19 build) with Bowtie/Tophat v2.0.2 which allows mapping across splice sites by reads segmentation (Trapnell et al., 2012). All programs were performed with default setting (unless otherwise specified).,The unique mapped reads (69-91% of total reads) were subsequently assembled into transcripts guided by reference annotation (Gencode v14 and Refseq gene models) with Cufflinks v2.0.2 (Trapnell et al., 2012). Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).,For the analyses of lncRNAs, cufflinks was used to estimate the transcript level FPKM values with the Gencode v14 lincRNA annotation (Derrien et al., 2012), and human body map lincRNA annotations (Cabili et al., 2011).,processed data file for protein-coding genes:,processed_FPKM_genes_human_pancreatic_lineage_140112.txt,processed data file for lncRNAs:,processed_FPKM_lncRNAs_human_pancreatic_lineage_140112.txt,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample. | Total RNA was purified from 1,000 sorted cells using ZR RNA microprep kit (Zymo Research, UAS). The cDNA synthesis and amplification was performed with the SMARTer ultra-low input RNA kit (Clontech, US).,The amplified cDNA (10-40 ng) was then fragmented by Covaris S2 sonicator (Covaris, US) and converted to sequencing libraries following the Illuminaâs construction protocol for low input DNA (Illumina, US). Barcoded libraries were pooled and sequenced in Illumina Hiseq 2000 instrument (pair-end 100bp). | GSM1093233 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248488,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974786 | GSM1093233 | GSE44875 | 0.15643 | pancreatic progenitors cells | Public on Jun 01 2014 | Mar 05 2013 | 9606 | PP2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248488 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974786 |
|
1 | cell type: human pancreatic alpha cells | 82 Walnut St. Unit 3 | Brookline | USA | Harvard Medical School | Yuting,,Liu | All obtained reads from each sample were mapped against the human genome (hg19 build) with Bowtie/Tophat v2.0.2 which allows mapping across splice sites by reads segmentation (Trapnell et al., 2012). All programs were performed with default setting (unless otherwise specified).,The unique mapped reads (69-91% of total reads) were subsequently assembled into transcripts guided by reference annotation (Gencode v14 and Refseq gene models) with Cufflinks v2.0.2 (Trapnell et al., 2012). Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).,For the analyses of lncRNAs, cufflinks was used to estimate the transcript level FPKM values with the Gencode v14 lincRNA annotation (Derrien et al., 2012), and human body map lincRNA annotations (Cabili et al., 2011).,processed data file for protein-coding genes:,processed_FPKM_genes_human_pancreatic_lineage_140112.txt,processed data file for lncRNAs:,processed_FPKM_lncRNAs_human_pancreatic_lineage_140112.txt,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample. | Total RNA was purified from 1,000 sorted cells using ZR RNA microprep kit (Zymo Research, UAS). The cDNA synthesis and amplification was performed with the SMARTer ultra-low input RNA kit (Clontech, US).,The amplified cDNA (10-40 ng) was then fragmented by Covaris S2 sonicator (Covaris, US) and converted to sequencing libraries following the Illuminaâs construction protocol for low input DNA (Illumina, US). Barcoded libraries were pooled and sequenced in Illumina Hiseq 2000 instrument (pair-end 100bp). | GSM1093235 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248490,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974788 | GSM1093235 | GSE44875 | 0.527332 | human pancreatic alpha cells | Public on Jun 01 2014 | Mar 05 2013 | 9606 | alpha1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248490 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974788 |
|
1 | cell type: human pancreatic alpha cells | 82 Walnut St. Unit 3 | Brookline | USA | Harvard Medical School | Yuting,,Liu | All obtained reads from each sample were mapped against the human genome (hg19 build) with Bowtie/Tophat v2.0.2 which allows mapping across splice sites by reads segmentation (Trapnell et al., 2012). All programs were performed with default setting (unless otherwise specified).,The unique mapped reads (69-91% of total reads) were subsequently assembled into transcripts guided by reference annotation (Gencode v14 and Refseq gene models) with Cufflinks v2.0.2 (Trapnell et al., 2012). Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).,For the analyses of lncRNAs, cufflinks was used to estimate the transcript level FPKM values with the Gencode v14 lincRNA annotation (Derrien et al., 2012), and human body map lincRNA annotations (Cabili et al., 2011).,processed data file for protein-coding genes:,processed_FPKM_genes_human_pancreatic_lineage_140112.txt,processed data file for lncRNAs:,processed_FPKM_lncRNAs_human_pancreatic_lineage_140112.txt,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample. | Total RNA was purified from 1,000 sorted cells using ZR RNA microprep kit (Zymo Research, UAS). The cDNA synthesis and amplification was performed with the SMARTer ultra-low input RNA kit (Clontech, US).,The amplified cDNA (10-40 ng) was then fragmented by Covaris S2 sonicator (Covaris, US) and converted to sequencing libraries following the Illuminaâs construction protocol for low input DNA (Illumina, US). Barcoded libraries were pooled and sequenced in Illumina Hiseq 2000 instrument (pair-end 100bp). | GSM1093236 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248491,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974789 | GSM1093236 | GSE44875 | 0.734671 | human pancreatic alpha cells | Public on Jun 01 2014 | Mar 05 2013 | 9606 | alpha2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248491 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974789 |
|
1 | cell type: human pancreatic beta cells | 82 Walnut St. Unit 3 | Brookline | USA | Harvard Medical School | Yuting,,Liu | All obtained reads from each sample were mapped against the human genome (hg19 build) with Bowtie/Tophat v2.0.2 which allows mapping across splice sites by reads segmentation (Trapnell et al., 2012). All programs were performed with default setting (unless otherwise specified).,The unique mapped reads (69-91% of total reads) were subsequently assembled into transcripts guided by reference annotation (Gencode v14 and Refseq gene models) with Cufflinks v2.0.2 (Trapnell et al., 2012). Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).,For the analyses of lncRNAs, cufflinks was used to estimate the transcript level FPKM values with the Gencode v14 lincRNA annotation (Derrien et al., 2012), and human body map lincRNA annotations (Cabili et al., 2011).,processed data file for protein-coding genes:,processed_FPKM_genes_human_pancreatic_lineage_140112.txt,processed data file for lncRNAs:,processed_FPKM_lncRNAs_human_pancreatic_lineage_140112.txt,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample. | Total RNA was purified from 1,000 sorted cells using ZR RNA microprep kit (Zymo Research, UAS). The cDNA synthesis and amplification was performed with the SMARTer ultra-low input RNA kit (Clontech, US).,The amplified cDNA (10-40 ng) was then fragmented by Covaris S2 sonicator (Covaris, US) and converted to sequencing libraries following the Illuminaâs construction protocol for low input DNA (Illumina, US). Barcoded libraries were pooled and sequenced in Illumina Hiseq 2000 instrument (pair-end 100bp). | GSM1093237 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248492,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974790 | GSM1093237 | GSE44875 | 0.519434 | human pancreatic beta cells | Public on Jun 01 2014 | Mar 05 2013 | 9606 | beta1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248492 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974790 |
|
1 | cell type: human pancreatic beta cells | 82 Walnut St. Unit 3 | Brookline | USA | Harvard Medical School | Yuting,,Liu | All obtained reads from each sample were mapped against the human genome (hg19 build) with Bowtie/Tophat v2.0.2 which allows mapping across splice sites by reads segmentation (Trapnell et al., 2012). All programs were performed with default setting (unless otherwise specified).,The unique mapped reads (69-91% of total reads) were subsequently assembled into transcripts guided by reference annotation (Gencode v14 and Refseq gene models) with Cufflinks v2.0.2 (Trapnell et al., 2012). Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).,For the analyses of lncRNAs, cufflinks was used to estimate the transcript level FPKM values with the Gencode v14 lincRNA annotation (Derrien et al., 2012), and human body map lincRNA annotations (Cabili et al., 2011).,processed data file for protein-coding genes:,processed_FPKM_genes_human_pancreatic_lineage_140112.txt,processed data file for lncRNAs:,processed_FPKM_lncRNAs_human_pancreatic_lineage_140112.txt,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample. | Total RNA was purified from 1,000 sorted cells using ZR RNA microprep kit (Zymo Research, UAS). The cDNA synthesis and amplification was performed with the SMARTer ultra-low input RNA kit (Clontech, US).,The amplified cDNA (10-40 ng) was then fragmented by Covaris S2 sonicator (Covaris, US) and converted to sequencing libraries following the Illuminaâs construction protocol for low input DNA (Illumina, US). Barcoded libraries were pooled and sequenced in Illumina Hiseq 2000 instrument (pair-end 100bp). | GSM1093238 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248493,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974791 | GSM1093238 | GSE44875 | 0.422463 | human pancreatic beta cells | Public on Jun 01 2014 | Mar 05 2013 | 9606 | beta2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248493 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974791 |
|
1 | cell type: human embryonic kidney (HEK) 293 T-REx Flp-In cell lines,rna subset: poly A RNA | WiesenstraÃe 14 | GieÃen | Germany | Technische Hochschule MIttelhessen | Andreas,,Gogol-Döring | RNA-seq reads were mapped with at most two mismatches to the human genome reference and a set of sequences consisting of all possible junctions between the exons of each Refseq gene. For each exon E of a RefSeq gene, we computed the number of reads which could only be mapped to E or exon junctions containing E with an overlap of at least 6bp ("spliced-in" event), and the number of reads which could be mapped only to exon junctions skipping E and overlap with both exons by at least 6bp ("spliced-out" event).,processed data files format and content: The .tab.txt files contain the number of reads supporting splicing-in and splicing-out events of exons. Each row of the table represents a single exon of a RefSeq gene. The columns of the list contains the chromosome ("chrom"), the starting position of the exon ("begin", 0-based), the ending position of the exon ("end", 0 based position of the first base after the exon), the name of the gene ("name"), a number which uniquely labels the exon within the gene ("exon"), the definition of the strand ("strand", either "+" or "-"), the number of reads supporting a splicing-in event ("in"), and the number of reads supporting a splicing-out event ("out"). Note that the first 3 columns conform to the bed file format.,Base calling was done on the Illumina HiSeq 2000 machine using RTA 1.12. We kept only reads passing the filtering.,Genome_build: hg19 | For RNA-Seq, total RNA was extracted using Trizol reagent and poly A RNA was isolated from 1 ug of total RNA for sequencing libraries construction.,RNA-Seq libraries were prepared following Illumina TruSeq RNA Sample Prep Kit protocol. | GSM1095127 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248556,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974931 | GSM1095127 | GSE44976 | 0.035638 | Ctrl_RBM10.KD.24h_RNA-Seq | Public on Sep 03 2013 | Mar 08 2013 | 9606 | Ctrl_RBM10.KD.24h_RNA-Seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248556 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974931 |
|
1 | cell type: human embryonic kidney (HEK) 293 T-REx Flp-In cell lines,stable cell line: stable cell lines inducibly expressing FLAG/HA-tagged RBM10,rna subset: poly A RNA | WiesenstraÃe 14 | GieÃen | Germany | Technische Hochschule MIttelhessen | Andreas,,Gogol-Döring | RNA-seq reads were mapped with at most two mismatches to the human genome reference and a set of sequences consisting of all possible junctions between the exons of each Refseq gene. For each exon E of a RefSeq gene, we computed the number of reads which could only be mapped to E or exon junctions containing E with an overlap of at least 6bp ("spliced-in" event), and the number of reads which could be mapped only to exon junctions skipping E and overlap with both exons by at least 6bp ("spliced-out" event).,processed data files format and content: The .tab.txt files contain the number of reads supporting splicing-in and splicing-out events of exons. Each row of the table represents a single exon of a RefSeq gene. The columns of the list contains the chromosome ("chrom"), the starting position of the exon ("begin", 0-based), the ending position of the exon ("end", 0 based position of the first base after the exon), the name of the gene ("name"), a number which uniquely labels the exon within the gene ("exon"), the definition of the strand ("strand", either "+" or "-"), the number of reads supporting a splicing-in event ("in"), and the number of reads supporting a splicing-out event ("out"). Note that the first 3 columns conform to the bed file format.,Base calling was done on the Illumina HiSeq 2000 machine using RTA 1.12. We kept only reads passing the filtering.,Genome_build: hg19 | For RNA-Seq, total RNA was extracted using Trizol reagent and poly A RNA was isolated from 1 ug of total RNA for sequencing libraries construction.,RNA-Seq libraries were prepared following Illumina TruSeq RNA Sample Prep Kit protocol. | GSM1095131 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248560,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974939 | GSM1095131 | GSE44976 | 0.001174 | Ctrl_RBM10.OE.1_RNA-Seq | Public on Sep 03 2013 | Mar 08 2013 | 9606 | Ctrl_RBM10.OE.1_RNA-Seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248560 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974939 |
|
1 | cell type: human embryonic kidney (HEK) 293 T-REx Flp-In cell lines,stable cell line: stable cell lines inducibly expressing FLAG/HA-tagged RBM10,rna subset: poly A RNA | WiesenstraÃe 14 | GieÃen | Germany | Technische Hochschule MIttelhessen | Andreas,,Gogol-Döring | RNA-seq reads were mapped with at most two mismatches to the human genome reference and a set of sequences consisting of all possible junctions between the exons of each Refseq gene. For each exon E of a RefSeq gene, we computed the number of reads which could only be mapped to E or exon junctions containing E with an overlap of at least 6bp ("spliced-in" event), and the number of reads which could be mapped only to exon junctions skipping E and overlap with both exons by at least 6bp ("spliced-out" event).,processed data files format and content: The .tab.txt files contain the number of reads supporting splicing-in and splicing-out events of exons. Each row of the table represents a single exon of a RefSeq gene. The columns of the list contains the chromosome ("chrom"), the starting position of the exon ("begin", 0-based), the ending position of the exon ("end", 0 based position of the first base after the exon), the name of the gene ("name"), a number which uniquely labels the exon within the gene ("exon"), the definition of the strand ("strand", either "+" or "-"), the number of reads supporting a splicing-in event ("in"), and the number of reads supporting a splicing-out event ("out"). Note that the first 3 columns conform to the bed file format.,Base calling was done on the Illumina HiSeq 2000 machine using RTA 1.12. We kept only reads passing the filtering.,Genome_build: hg19 | For RNA-Seq, total RNA was extracted using Trizol reagent and poly A RNA was isolated from 1 ug of total RNA for sequencing libraries construction.,RNA-Seq libraries were prepared following Illumina TruSeq RNA Sample Prep Kit protocol. | GSM1095132 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248561,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974941 | GSM1095132 | GSE44976 | 0.063725 | Ctrl_RBM10.OE.2_RNA-Seq | Public on Sep 03 2013 | Mar 08 2013 | 9606 | Ctrl_RBM10.OE.2_RNA-Seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248561 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974941 |
|
1 | cell type: human embryonic kidney (HEK) 293 T-REx Flp-In cell lines,rna subset: poly A RNA | WiesenstraÃe 14 | GieÃen | Germany | Technische Hochschule MIttelhessen | Andreas,,Gogol-Döring | RNA-seq reads were mapped with at most two mismatches to the human genome reference and a set of sequences consisting of all possible junctions between the exons of each Refseq gene. For each exon E of a RefSeq gene, we computed the number of reads which could only be mapped to E or exon junctions containing E with an overlap of at least 6bp ("spliced-in" event), and the number of reads which could be mapped only to exon junctions skipping E and overlap with both exons by at least 6bp ("spliced-out" event).,processed data files format and content: The .tab.txt files contain the number of reads supporting splicing-in and splicing-out events of exons. Each row of the table represents a single exon of a RefSeq gene. The columns of the list contains the chromosome ("chrom"), the starting position of the exon ("begin", 0-based), the ending position of the exon ("end", 0 based position of the first base after the exon), the name of the gene ("name"), a number which uniquely labels the exon within the gene ("exon"), the definition of the strand ("strand", either "+" or "-"), the number of reads supporting a splicing-in event ("in"), and the number of reads supporting a splicing-out event ("out"). Note that the first 3 columns conform to the bed file format.,Base calling was done on the Illumina HiSeq 2000 machine using RTA 1.12. We kept only reads passing the filtering.,Genome_build: hg19 | For RNA-Seq, total RNA was extracted using Trizol reagent and poly A RNA was isolated from 1 ug of total RNA for sequencing libraries construction.,RNA-Seq libraries were prepared following Illumina TruSeq RNA Sample Prep Kit protocol. | GSM1095133 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248562,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974943 | GSM1095133 | GSE44976 | 0.060617 | RBM10.KD.24h_RNA-Seq | Public on Sep 03 2013 | Mar 08 2013 | 9606 | RBM10.KD.24h_RNA-Seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248562 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974943 |
|
1 | cell type: human embryonic kidney (HEK) 293 T-REx Flp-In cell lines,rna subset: poly A RNA | WiesenstraÃe 14 | GieÃen | Germany | Technische Hochschule MIttelhessen | Andreas,,Gogol-Döring | RNA-seq reads were mapped with at most two mismatches to the human genome reference and a set of sequences consisting of all possible junctions between the exons of each Refseq gene. For each exon E of a RefSeq gene, we computed the number of reads which could only be mapped to E or exon junctions containing E with an overlap of at least 6bp ("spliced-in" event), and the number of reads which could be mapped only to exon junctions skipping E and overlap with both exons by at least 6bp ("spliced-out" event).,processed data files format and content: The .tab.txt files contain the number of reads supporting splicing-in and splicing-out events of exons. Each row of the table represents a single exon of a RefSeq gene. The columns of the list contains the chromosome ("chrom"), the starting position of the exon ("begin", 0-based), the ending position of the exon ("end", 0 based position of the first base after the exon), the name of the gene ("name"), a number which uniquely labels the exon within the gene ("exon"), the definition of the strand ("strand", either "+" or "-"), the number of reads supporting a splicing-in event ("in"), and the number of reads supporting a splicing-out event ("out"). Note that the first 3 columns conform to the bed file format.,Base calling was done on the Illumina HiSeq 2000 machine using RTA 1.12. We kept only reads passing the filtering.,Genome_build: hg19 | For RNA-Seq, total RNA was extracted using Trizol reagent and poly A RNA was isolated from 1 ug of total RNA for sequencing libraries construction.,RNA-Seq libraries were prepared following Illumina TruSeq RNA Sample Prep Kit protocol. | GSM1095134 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248563,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974945 | GSM1095134 | GSE44976 | 0.003833 | RBM10.KD.48h.1_RNA-Seq | Public on Sep 03 2013 | Mar 08 2013 | 9606 | RBM10.KD.48h.1_RNA-Seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248563 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974945 |
|
1 | cell type: human embryonic kidney (HEK) 293 T-REx Flp-In cell lines,rna subset: poly A RNA | WiesenstraÃe 14 | GieÃen | Germany | Technische Hochschule MIttelhessen | Andreas,,Gogol-Döring | RNA-seq reads were mapped with at most two mismatches to the human genome reference and a set of sequences consisting of all possible junctions between the exons of each Refseq gene. For each exon E of a RefSeq gene, we computed the number of reads which could only be mapped to E or exon junctions containing E with an overlap of at least 6bp ("spliced-in" event), and the number of reads which could be mapped only to exon junctions skipping E and overlap with both exons by at least 6bp ("spliced-out" event).,processed data files format and content: The .tab.txt files contain the number of reads supporting splicing-in and splicing-out events of exons. Each row of the table represents a single exon of a RefSeq gene. The columns of the list contains the chromosome ("chrom"), the starting position of the exon ("begin", 0-based), the ending position of the exon ("end", 0 based position of the first base after the exon), the name of the gene ("name"), a number which uniquely labels the exon within the gene ("exon"), the definition of the strand ("strand", either "+" or "-"), the number of reads supporting a splicing-in event ("in"), and the number of reads supporting a splicing-out event ("out"). Note that the first 3 columns conform to the bed file format.,Base calling was done on the Illumina HiSeq 2000 machine using RTA 1.12. We kept only reads passing the filtering.,Genome_build: hg19 | For RNA-Seq, total RNA was extracted using Trizol reagent and poly A RNA was isolated from 1 ug of total RNA for sequencing libraries construction.,RNA-Seq libraries were prepared following Illumina TruSeq RNA Sample Prep Kit protocol. | GSM1095135 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248564,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974947 | GSM1095135 | GSE44976 | 0.037335 | RBM10.KD.48h.2_RNA-Seq | Public on Sep 03 2013 | Mar 08 2013 | 9606 | RBM10.KD.48h.2_RNA-Seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248564 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974947 |
|
1 | cell type: human embryonic kidney (HEK) 293 T-REx Flp-In cell lines,rna subset: poly A RNA | WiesenstraÃe 14 | GieÃen | Germany | Technische Hochschule MIttelhessen | Andreas,,Gogol-Döring | RNA-seq reads were mapped with at most two mismatches to the human genome reference and a set of sequences consisting of all possible junctions between the exons of each Refseq gene. For each exon E of a RefSeq gene, we computed the number of reads which could only be mapped to E or exon junctions containing E with an overlap of at least 6bp ("spliced-in" event), and the number of reads which could be mapped only to exon junctions skipping E and overlap with both exons by at least 6bp ("spliced-out" event).,processed data files format and content: The .tab.txt files contain the number of reads supporting splicing-in and splicing-out events of exons. Each row of the table represents a single exon of a RefSeq gene. The columns of the list contains the chromosome ("chrom"), the starting position of the exon ("begin", 0-based), the ending position of the exon ("end", 0 based position of the first base after the exon), the name of the gene ("name"), a number which uniquely labels the exon within the gene ("exon"), the definition of the strand ("strand", either "+" or "-"), the number of reads supporting a splicing-in event ("in"), and the number of reads supporting a splicing-out event ("out"). Note that the first 3 columns conform to the bed file format.,Base calling was done on the Illumina HiSeq 2000 machine using RTA 1.12. We kept only reads passing the filtering.,Genome_build: hg19 | For RNA-Seq, total RNA was extracted using Trizol reagent and poly A RNA was isolated from 1 ug of total RNA for sequencing libraries construction.,RNA-Seq libraries were prepared following Illumina TruSeq RNA Sample Prep Kit protocol. | GSM1095136 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248565,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974949 | GSM1095136 | GSE44976 | 0.014024 | RBM10.KD.72h_RNA-Seq | Public on Sep 03 2013 | Mar 08 2013 | 9606 | RBM10.KD.72h_RNA-Seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248565 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974949 |
|
1 | cell type: human embryonic kidney (HEK) 293 T-REx Flp-In cell lines,stable cell line: stable cell lines inducibly expressing FLAG/HA-tagged RBM10,rna subset: poly A RNA | WiesenstraÃe 14 | GieÃen | Germany | Technische Hochschule MIttelhessen | Andreas,,Gogol-Döring | RNA-seq reads were mapped with at most two mismatches to the human genome reference and a set of sequences consisting of all possible junctions between the exons of each Refseq gene. For each exon E of a RefSeq gene, we computed the number of reads which could only be mapped to E or exon junctions containing E with an overlap of at least 6bp ("spliced-in" event), and the number of reads which could be mapped only to exon junctions skipping E and overlap with both exons by at least 6bp ("spliced-out" event).,processed data files format and content: The .tab.txt files contain the number of reads supporting splicing-in and splicing-out events of exons. Each row of the table represents a single exon of a RefSeq gene. The columns of the list contains the chromosome ("chrom"), the starting position of the exon ("begin", 0-based), the ending position of the exon ("end", 0 based position of the first base after the exon), the name of the gene ("name"), a number which uniquely labels the exon within the gene ("exon"), the definition of the strand ("strand", either "+" or "-"), the number of reads supporting a splicing-in event ("in"), and the number of reads supporting a splicing-out event ("out"). Note that the first 3 columns conform to the bed file format.,Base calling was done on the Illumina HiSeq 2000 machine using RTA 1.12. We kept only reads passing the filtering.,Genome_build: hg19 | For RNA-Seq, total RNA was extracted using Trizol reagent and poly A RNA was isolated from 1 ug of total RNA for sequencing libraries construction.,RNA-Seq libraries were prepared following Illumina TruSeq RNA Sample Prep Kit protocol. | GSM1095137 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248566,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974951 | GSM1095137 | GSE44976 | 0.005288 | RBM10.OE.1_RNA-Seq | Public on Sep 03 2013 | Mar 08 2013 | 9606 | RBM10.OE.1_RNA-Seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248566 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974951 |
|
1 | cell type: human embryonic kidney (HEK) 293 T-REx Flp-In cell lines,stable cell line: stable cell lines inducibly expressing FLAG/HA-tagged RBM10,rna subset: poly A RNA | WiesenstraÃe 14 | GieÃen | Germany | Technische Hochschule MIttelhessen | Andreas,,Gogol-Döring | RNA-seq reads were mapped with at most two mismatches to the human genome reference and a set of sequences consisting of all possible junctions between the exons of each Refseq gene. For each exon E of a RefSeq gene, we computed the number of reads which could only be mapped to E or exon junctions containing E with an overlap of at least 6bp ("spliced-in" event), and the number of reads which could be mapped only to exon junctions skipping E and overlap with both exons by at least 6bp ("spliced-out" event).,processed data files format and content: The .tab.txt files contain the number of reads supporting splicing-in and splicing-out events of exons. Each row of the table represents a single exon of a RefSeq gene. The columns of the list contains the chromosome ("chrom"), the starting position of the exon ("begin", 0-based), the ending position of the exon ("end", 0 based position of the first base after the exon), the name of the gene ("name"), a number which uniquely labels the exon within the gene ("exon"), the definition of the strand ("strand", either "+" or "-"), the number of reads supporting a splicing-in event ("in"), and the number of reads supporting a splicing-out event ("out"). Note that the first 3 columns conform to the bed file format.,Base calling was done on the Illumina HiSeq 2000 machine using RTA 1.12. We kept only reads passing the filtering.,Genome_build: hg19 | For RNA-Seq, total RNA was extracted using Trizol reagent and poly A RNA was isolated from 1 ug of total RNA for sequencing libraries construction.,RNA-Seq libraries were prepared following Illumina TruSeq RNA Sample Prep Kit protocol. | GSM1095138 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248567,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974953 | GSM1095138 | GSE44976 | 0 | RBM10.OE.2_RNA-Seq | Public on Sep 03 2013 | Mar 08 2013 | 9606 | RBM10.OE.2_RNA-Seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248567 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974953 |
|
1 | cell type: lymphoblastoid cell lines (LCLs) derived from healthy control,rna subset: poly A RNA | WiesenstraÃe 14 | GieÃen | Germany | Technische Hochschule MIttelhessen | Andreas,,Gogol-Döring | RNA-seq reads were mapped with at most two mismatches to the human genome reference and a set of sequences consisting of all possible junctions between the exons of each Refseq gene. For each exon E of a RefSeq gene, we computed the number of reads which could only be mapped to E or exon junctions containing E with an overlap of at least 6bp ("spliced-in" event), and the number of reads which could be mapped only to exon junctions skipping E and overlap with both exons by at least 6bp ("spliced-out" event).,processed data files format and content: The .tab.txt files contain the number of reads supporting splicing-in and splicing-out events of exons. Each row of the table represents a single exon of a RefSeq gene. The columns of the list contains the chromosome ("chrom"), the starting position of the exon ("begin", 0-based), the ending position of the exon ("end", 0 based position of the first base after the exon), the name of the gene ("name"), a number which uniquely labels the exon within the gene ("exon"), the definition of the strand ("strand", either "+" or "-"), the number of reads supporting a splicing-in event ("in"), and the number of reads supporting a splicing-out event ("out"). Note that the first 3 columns conform to the bed file format.,Base calling was done on the Illumina HiSeq 2000 machine using RTA 1.12. We kept only reads passing the filtering.,Genome_build: hg19 | For RNA-Seq, total RNA was extracted using Trizol reagent and poly A RNA was isolated from 1 ug of total RNA for sequencing libraries construction.,RNA-Seq libraries were prepared following Illumina TruSeq RNA Sample Prep Kit protocol. | GSM1095139 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248568,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974955 | GSM1095139 | GSE44976 | 0.00176 | Normal.2_RNA-Seq | Public on Sep 03 2013 | Mar 08 2013 | 9606 | Normal.2_RNA-Seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248568 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974955 |
|
1 | cell type: lymphoblastoid cell lines (LCLs) derived from patient,rna subset: poly A RNA | WiesenstraÃe 14 | GieÃen | Germany | Technische Hochschule MIttelhessen | Andreas,,Gogol-Döring | RNA-seq reads were mapped with at most two mismatches to the human genome reference and a set of sequences consisting of all possible junctions between the exons of each Refseq gene. For each exon E of a RefSeq gene, we computed the number of reads which could only be mapped to E or exon junctions containing E with an overlap of at least 6bp ("spliced-in" event), and the number of reads which could be mapped only to exon junctions skipping E and overlap with both exons by at least 6bp ("spliced-out" event).,processed data files format and content: The .tab.txt files contain the number of reads supporting splicing-in and splicing-out events of exons. Each row of the table represents a single exon of a RefSeq gene. The columns of the list contains the chromosome ("chrom"), the starting position of the exon ("begin", 0-based), the ending position of the exon ("end", 0 based position of the first base after the exon), the name of the gene ("name"), a number which uniquely labels the exon within the gene ("exon"), the definition of the strand ("strand", either "+" or "-"), the number of reads supporting a splicing-in event ("in"), and the number of reads supporting a splicing-out event ("out"). Note that the first 3 columns conform to the bed file format.,Base calling was done on the Illumina HiSeq 2000 machine using RTA 1.12. We kept only reads passing the filtering.,Genome_build: hg19 | For RNA-Seq, total RNA was extracted using Trizol reagent and poly A RNA was isolated from 1 ug of total RNA for sequencing libraries construction.,RNA-Seq libraries were prepared following Illumina TruSeq RNA Sample Prep Kit protocol. | GSM1095141 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248570,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974959 | GSM1095141 | GSE44976 | 0.003275 | Patient_RNA-Seq | Public on Sep 03 2013 | Mar 08 2013 | 9606 | Patient_RNA-Seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248570 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974959 |
|
1 | cell line: CHL-1, DKMG, JURKAT,cancer subtype: CHL-1-melanoma, DKMG-GBM, JURKAT-TALL | 269 Campus Drive (CCSR 3245A) | Stanford | USA | Stanford University | Craig,Patrick,Giacomini | Samples were mapped to the human genome and RefSeq transcriptome using ELAND.,A custom C# script was used to extract all mate pairs with one read mapping to the candidate rearranged gene (identified by breakpoint analysis) and the other read mapping to a separate genomic locus.,A separate C# script screened mate pairs for single reads mapping to potential exon-exon fusion junctions of nominated gene fusions.,Genome_build: hg18,Supplementary_files_format_and_content: Our pipeline outputs a single file (GeneFusions.txt) after all samples are run through our pipeline. This file is a tab delimited text file with the first column representing the gene fusion name, the second column includes the sample from which the gene fusion was identified, the third column includes the chromosome of the 5' partner gene, the fourth column includes the chromosome of the 3' partner gene, the fifth column includes the exon position of the gene fusion junction, and the sixth column includes the number of mate pairs supporting the specific gene fusion. | mRNA Seq-8 Sample Prep Kit (Illumina) | GSM1097789 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248166,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974539 | GSM1097789 | GSE45133,GSE45137 | 0.001798 | Combined human cancer cell lines (CHL-1, DKMG, JURKAT) | Public on May 31 2013 | Mar 13 2013 | 9606 | Multi_C | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248166 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974539 |
|
1 | cell type: CD34+ cells,rna subtype: messenger RNA | Level 2, Lowy Cancer Research Centre, University of New South Wales | Sydney | Australia | UNIVERSITY OF NEW SOUTH WALES | Jason,,Wong | Base-calling: Illumina Real Time Analysis, scoring metric v1.5,Raw reads were prefiltered to remove all reads that have 3 or more bases with a quality score of less than Q13,All provided cleaned data have had adaptors clipped except the small RNA-seq data which still contains 5' adaptor: 5'-TGGAATTCTCGTATGCCGTCTTCTGCTTG,Alignments were all made against hg19. The following aligners were used. ChIP-seq: bwa (version 0.6.1-r104) default parameters , mRNA-seq: tophat (version 1.3.1) -g 25 -r 20 --segment-length 45 -G "hg19_refseq.gtf" --solexa1.3-quals, smallRNA: bowtie (version 0.12.5) -v 2 -m 25 --solexa1.3-quals --best --strata.,Bed files generated from BAM files using bedtools bamtobed (version 2.15.0). For ChIP-seq files, each bed entry is extended to 200bp in length. For RNA-seq the split option was used.,Genome_build: hg19,Supplementary_files_format_and_content: Bed files contain coordinates for all aligned reads | Bone marrow (BM) samples were harvested from normal volunteers with informed consent in accordance with local ethical guidelines. The CD34+ fraction was obtained by magnetic bead separation using an automated CliniMACS cell separation system (Miltenyi Biotec, Cologne). Cell purity was assessed by flow cytometry and was ââ°Â¥ 98%. ChIP assays were performed with 15 x 10^6 per condition. Total RNA extraction and purification was performed using miRNeasy mini kits (QIAGEN). The small RNA fraction (<200nt) was collected in a separate fraction from total RNA, as per manufacturerââ¬â¢s standard instructions. Total RNA was amplified using the Ovation RNA-seq system V2 (NuGEN) prior to sequencing.,For ChIP, cells were harvested and washed with phosphate-buffered saline (PBS), followed by incubation of 1% (w/v) formaldehyde for 10 minutes at room temperature. To terminate the cross-link, cells were incubated with 0.125M glycine for 5 minutes. Cells were washed with PBS and lysed on ice in Cell lysis buffer (10mM Tris [pH 8.0], 10mM NaCl, 0.2% NP-40) for 10 minutes to recover nuclei. After centrifugation at 1500xg for 5 minutes, nuclei were lysed in Nucleus lysis buffer (50 mM Tris, 10mM EDTA, 1% SDS [pH 8.0]) on ice for 10 minutes. The lysate was diluted in IP dilution buffer (20mM Tris [pH 8.0], 2mM EDTA, 150mM NaCl, 1% Triton-X100, 0.01% SDS) and sonicated (Settings: High, 30sec pulses) using BioRuptor® sonicator (Diagenode, Liège, Belgium) to yield an average fragmentation size of approximately 200bp. The chromatin was pre-cleared with 100?g rabbit IgG for 1 hour followed by incubation with 100?l protein-G-agarose (Roche Applied Science, Penzberg, Germany) for 2 hours. For each sample, 300?l pre-cleared chromatin was removed (input for the subsequent qRT-PCR analysis) and the remaining chromatin was aliquoted, and incubated with the indicated antibody for 18 hours at 4°C. To collect immune complexes, 50?l protein G-agarose was added to the chromatin and incubated for additional 2 hours at 4°C. Protein-G-agarose pellets were washed at 5000xg; twice with 500?l IP wash buffer 1 (20mM Tris [pH 8.0], 2mM EDTAm 50mM NaCl, 1% Triton-X100, 0.1% SDS), once with IP wash buffer 2 (10mM Tris [pH 8.0], 1mM EDTA, 0.25M LiCl, 1% NP-40, 1% Sodium deoxycholate) and twice with TE (10mM Tris, 1mM EDTA [pH8.0]). Immuno-precipitated chromatin was eluted in 300?l Elution Buffer (100mM NaHCO3, 1% SDS) and reverse-cross link was obtained by incubation with RNase A and NaCl (0.3M final concentration) at 67°C for 18 hours followed by treatment with Proteinase K at 45°C for 2 hours. Input DNA (pre-cleared chromatin) was treated with RNase A and Proteinase K simultaneously.,Library construction was performed as per Illumina protocol Rev A 11257047 | GSM1097887 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248938,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01975666 | GSM1097887 | GSE45144 | 0.001978 | CD34+ cells | Public on Sep 03 2013 | Mar 13 2013 | 9606 | CD34_mRNA-seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248938 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01975666 |
|
1 | knockdown chemistry: Gapmer,knockdown target: Scramble,cell line: HeLa | 733 N. Broadway Avenue | Baltimore | USA | Johns Hopkins University | Loyal,A,Goff | Basecalls were performed using CASAVA 1.8,Reads were aligned using Tophat2 with default options,Expression quantification and differential analysis was done using Cuffdiff2 using UCSC reference transcriptome .gtf files (mouse or human) and Tophat2 aligned reads as input and default options.,Cuffdiff output files were processed using cummeRbund for indexing, exploration, and visualization of results.,Genome_build: hg19 | 1ml of Trizol and 200μl of chloroform were added and the mix was centrifuged at 4°C at 13,000 rpm for 15 minutes. The aqueous layer was cleaned and DNase treated on RNeasy Mini columns.,Illumina TruSeq RNA | GSM1098180 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249074,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01977945 | GSM1098180 | GSE45157 | 0.004565 | HeLa Cells | Public on Jun 01 2013 | Mar 14 2013 | 9606 | HeLa_Control_Gapmer_1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249074 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01977945 |
|
1 | knockdown chemistry: Gapmer,knockdown target: Scramble,cell line: HeLa | 733 N. Broadway Avenue | Baltimore | USA | Johns Hopkins University | Loyal,A,Goff | Basecalls were performed using CASAVA 1.8,Reads were aligned using Tophat2 with default options,Expression quantification and differential analysis was done using Cuffdiff2 using UCSC reference transcriptome .gtf files (mouse or human) and Tophat2 aligned reads as input and default options.,Cuffdiff output files were processed using cummeRbund for indexing, exploration, and visualization of results.,Genome_build: hg19 | 1ml of Trizol and 200μl of chloroform were added and the mix was centrifuged at 4°C at 13,000 rpm for 15 minutes. The aqueous layer was cleaned and DNase treated on RNeasy Mini columns.,Illumina TruSeq RNA | GSM1098181 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249075,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01977946 | GSM1098181 | GSE45157 | 0.003822 | HeLa Cells | Public on Jun 01 2013 | Mar 14 2013 | 9606 | HeLa_Control_Gapmer_2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249075 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01977946 |
|
1 | knockdown chemistry: Gapmer,knockdown target: linc-FIRRE,cell line: HeLa | 733 N. Broadway Avenue | Baltimore | USA | Johns Hopkins University | Loyal,A,Goff | Basecalls were performed using CASAVA 1.8,Reads were aligned using Tophat2 with default options,Expression quantification and differential analysis was done using Cuffdiff2 using UCSC reference transcriptome .gtf files (mouse or human) and Tophat2 aligned reads as input and default options.,Cuffdiff output files were processed using cummeRbund for indexing, exploration, and visualization of results.,Genome_build: hg19 | 1ml of Trizol and 200μl of chloroform were added and the mix was centrifuged at 4°C at 13,000 rpm for 15 minutes. The aqueous layer was cleaned and DNase treated on RNeasy Mini columns.,Illumina TruSeq RNA | GSM1098183 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249077,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01977948 | GSM1098183 | GSE45157 | 0.003421 | HeLa Cells | Public on Jun 01 2013 | Mar 14 2013 | 9606 | HeLa_FIRRE_Gapmer_2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249077 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01977948 |
|
1 | knockdown chemistry: Gapmer,knockdown target: linc-FIRRE,cell line: HeLa | 733 N. Broadway Avenue | Baltimore | USA | Johns Hopkins University | Loyal,A,Goff | Basecalls were performed using CASAVA 1.8,Reads were aligned using Tophat2 with default options,Expression quantification and differential analysis was done using Cuffdiff2 using UCSC reference transcriptome .gtf files (mouse or human) and Tophat2 aligned reads as input and default options.,Cuffdiff output files were processed using cummeRbund for indexing, exploration, and visualization of results.,Genome_build: hg19 | 1ml of Trizol and 200μl of chloroform were added and the mix was centrifuged at 4°C at 13,000 rpm for 15 minutes. The aqueous layer was cleaned and DNase treated on RNeasy Mini columns.,Illumina TruSeq RNA | GSM1098184 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249078,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01977949 | GSM1098184 | GSE45157 | 0.004334 | HeLa Cells | Public on Jun 01 2013 | Mar 14 2013 | 9606 | HeLa_FIRRE_Gapmer_3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249078 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01977949 |
|
1 | knockdown chemistry: Gapmer,knockdown target: linc-FIRRE,cell line: HeLa | 733 N. Broadway Avenue | Baltimore | USA | Johns Hopkins University | Loyal,A,Goff | Basecalls were performed using CASAVA 1.8,Reads were aligned using Tophat2 with default options,Expression quantification and differential analysis was done using Cuffdiff2 using UCSC reference transcriptome .gtf files (mouse or human) and Tophat2 aligned reads as input and default options.,Cuffdiff output files were processed using cummeRbund for indexing, exploration, and visualization of results.,Genome_build: hg19 | 1ml of Trizol and 200μl of chloroform were added and the mix was centrifuged at 4°C at 13,000 rpm for 15 minutes. The aqueous layer was cleaned and DNase treated on RNeasy Mini columns.,Illumina TruSeq RNA | GSM1098185 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249079,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01977950 | GSM1098185 | GSE45157 | 0 | HeLa Cells | Public on Jun 01 2013 | Mar 14 2013 | 9606 | HeLa_FIRRE_Gapmer_4 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249079 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01977950 |
|
1 | knockdown chemistry: siRNA,knockdown target: Scramble,cell line: HeLa | 733 N. Broadway Avenue | Baltimore | USA | Johns Hopkins University | Loyal,A,Goff | Basecalls were performed using CASAVA 1.8,Reads were aligned using Tophat2 with default options,Expression quantification and differential analysis was done using Cuffdiff2 using UCSC reference transcriptome .gtf files (mouse or human) and Tophat2 aligned reads as input and default options.,Cuffdiff output files were processed using cummeRbund for indexing, exploration, and visualization of results.,Genome_build: hg19 | 1ml of Trizol and 200μl of chloroform were added and the mix was centrifuged at 4°C at 13,000 rpm for 15 minutes. The aqueous layer was cleaned and DNase treated on RNeasy Mini columns.,Illumina TruSeq RNA | GSM1098186 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249080,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01977951 | GSM1098186 | GSE45157 | 0.003661 | HeLa Cells | Public on Jun 01 2013 | Mar 14 2013 | 9606 | HeLa_Scramble_siRNA_1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249080 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01977951 |
|
1 | knockdown chemistry: siRNA,knockdown target: Scramble,cell line: HeLa | 733 N. Broadway Avenue | Baltimore | USA | Johns Hopkins University | Loyal,A,Goff | Basecalls were performed using CASAVA 1.8,Reads were aligned using Tophat2 with default options,Expression quantification and differential analysis was done using Cuffdiff2 using UCSC reference transcriptome .gtf files (mouse or human) and Tophat2 aligned reads as input and default options.,Cuffdiff output files were processed using cummeRbund for indexing, exploration, and visualization of results.,Genome_build: hg19 | 1ml of Trizol and 200μl of chloroform were added and the mix was centrifuged at 4°C at 13,000 rpm for 15 minutes. The aqueous layer was cleaned and DNase treated on RNeasy Mini columns.,Illumina TruSeq RNA | GSM1098187 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249081,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01977952 | GSM1098187 | GSE45157 | 0.003158 | HeLa Cells | Public on Jun 01 2013 | Mar 14 2013 | 9606 | HeLa_Scramble_siRNA_2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249081 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01977952 |
|
1 | knockdown chemistry: siRNA,knockdown target: hnRNPU,cell line: HeLa | 733 N. Broadway Avenue | Baltimore | USA | Johns Hopkins University | Loyal,A,Goff | Basecalls were performed using CASAVA 1.8,Reads were aligned using Tophat2 with default options,Expression quantification and differential analysis was done using Cuffdiff2 using UCSC reference transcriptome .gtf files (mouse or human) and Tophat2 aligned reads as input and default options.,Cuffdiff output files were processed using cummeRbund for indexing, exploration, and visualization of results.,Genome_build: hg19 | 1ml of Trizol and 200μl of chloroform were added and the mix was centrifuged at 4°C at 13,000 rpm for 15 minutes. The aqueous layer was cleaned and DNase treated on RNeasy Mini columns.,Illumina TruSeq RNA | GSM1098188 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249082,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01977953 | GSM1098188 | GSE45157 | 0.002428 | HeLa Cells | Public on Jun 01 2013 | Mar 14 2013 | 9606 | HeLa_hnRNPU_siRNA_1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249082 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01977953 |
|
1 | knockdown chemistry: siRNA,knockdown target: hnRNPU,cell line: HeLa | 733 N. Broadway Avenue | Baltimore | USA | Johns Hopkins University | Loyal,A,Goff | Basecalls were performed using CASAVA 1.8,Reads were aligned using Tophat2 with default options,Expression quantification and differential analysis was done using Cuffdiff2 using UCSC reference transcriptome .gtf files (mouse or human) and Tophat2 aligned reads as input and default options.,Cuffdiff output files were processed using cummeRbund for indexing, exploration, and visualization of results.,Genome_build: hg19 | 1ml of Trizol and 200μl of chloroform were added and the mix was centrifuged at 4°C at 13,000 rpm for 15 minutes. The aqueous layer was cleaned and DNase treated on RNeasy Mini columns.,Illumina TruSeq RNA | GSM1098189 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249083,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01977954 | GSM1098189 | GSE45157 | 0.003661 | HeLa Cells | Public on Jun 01 2013 | Mar 14 2013 | 9606 | HeLa_hnRNPU_siRNA_2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249083 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01977954 |
|
1 | age: 59,tissue: adipose tissue,log10 body mass index: 1.436353766,log10 basal metabolic rate (kcal): 1830,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.352532716,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.635899375,plasma free fatty acids under the curve ogtt (mmol/l * min): 23.7,fat mass (%): 22,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.491853096,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 132,log10 homair (insulin resistance index based on homa): 0.499381564,log10 homais (insulin secretion index based on homa): 2.316269962,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.60162548,insgenin (insulinogenic index): 2.017791932,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.470116353,log10 matsuda insulin sensitivity index: 0.608904289,muscle mass (%): 47.5,lg10 serum c-reactive protein (mg/l): 0.074450719,lg10 plasma adiponectin (mg/l): 0.799340549,ogtt fasting plasma free fatty acid (mmol/l): 0.39,ogtt 30 min plasma free fatty acid (mmol/l): 0.26,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 4.9,ogtt 30 min plasma glucose (mmol/l): 7.1,ogtt 120 min plasma glucose (mmol/l): 4.9,log10 il1 receptor antagonist (pg/ml): 2.186730376,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 1.161368002,ogtt 30 min plasma insulin (mu/l): 1.721810615,ogtt 120 min plasma insulin (mu/l): 1.862727528,log10 ogtt fasting plasma proinsulin (pm/l): 1.187520721,ogtt 30 min plasma proinsulin (pm/l): 1.383815366,ogtt 120 min plasma proinsulin (pm/l): 1.804139432,log10 bioimpedance: Resistance: 2.679427897,log10 bioimpedance (reactance): 1.819543936,waist to hip ratio: 0.985,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.447158031,log10 creatinine (umol/l): 1.944482672,log10 total cholesterol (mmol/l): 0.733197265,log10 ldl cholesterol (mmol/l): 0.5774918,log10 hdl cholesterol (mmol/l): 0.029383778,log10 total triglycerides (mmol/l): 0,log10 serum apoa1 (g/l): 0.096910013,log10 serum apob (g/l): 0.079181246,log10 urinary albumin excretion rate (ug/min): 0.726998728 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098196 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249095,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978023 | GSM1098196 | GSE45159 | 0.255963 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM388 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249095 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978023 |
|
1 | age: 60,tissue: adipose tissue,log10 body mass index: 1.350674814,log10 basal metabolic rate (kcal): 2236,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.527231569,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.552601458,plasma free fatty acids under the curve ogtt (mmol/l * min): 25.95,fat mass (%): 15.7,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.518653156,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 109.5,log10 homair (insulin resistance index based on homa): 0.06279083,log10 homais (insulin secretion index based on homa): 1.769551079,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.278319089,insgenin (insulinogenic index): 1.917580524,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.186984572,log10 matsuda insulin sensitivity index: 1.01207028,muscle mass (%): 61.8,lg10 serum c-reactive protein (mg/l): -0.308918508,lg10 plasma adiponectin (mg/l): 1.068185862,ogtt fasting plasma free fatty acid (mmol/l): 0.38,ogtt 30 min plasma free fatty acid (mmol/l): 0.3,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5.2,ogtt 30 min plasma glucose (mmol/l): 8,ogtt 120 min plasma glucose (mmol/l): 3.9,log10 il1 receptor antagonist (pg/ml): 1.87517706,log10 il1 beta (pg/ml): -0.494850022,log10 ogtt fasting plasma insulin (mu/l): 0.698970004,ogtt 30 min plasma insulin (mu/l): 1.639486489,ogtt 120 min plasma insulin (mu/l): 1.021189299,log10 ogtt fasting plasma proinsulin (pm/l): 1.056904851,ogtt 30 min plasma proinsulin (pm/l): 1.442479769,ogtt 120 min plasma proinsulin (pm/l): 1.494154594,log10 bioimpedance: Resistance: 2.688419822,log10 bioimpedance (reactance): 2.049218023,waist to hip ratio: 0.93814433,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.230448921,log10 creatinine (umol/l): 1.897627091,log10 total cholesterol (mmol/l): 0.759667845,log10 ldl cholesterol (mmol/l): 0.591064607,log10 hdl cholesterol (mmol/l): 0.204119983,log10 total triglycerides (mmol/l): 0.250420002,log10 serum apoa1 (g/l): 0.260071388,log10 serum apob (g/l): 0.11058971,log10 urinary albumin excretion rate (ug/min): 0.602059991 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098197 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249096,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978024 | GSM1098197 | GSE45159 | 0.340697 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM473 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249096 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978024 |
|
1 | age: 50,tissue: adipose tissue,log10 body mass index: 1.403499536,log10 basal metabolic rate (kcal): 1650,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.623318869,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.887438141,plasma free fatty acids under the curve ogtt (mmol/l * min): 15.75,fat mass (%): 21.1,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.63481105,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 135,log10 homair (insulin resistance index based on homa): 0.361308025,log10 homais (insulin secretion index based on homa): 1.973127854,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.70981249,insgenin (insulinogenic index): 2.36361198,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.648320972,log10 matsuda insulin sensitivity index: 0.62415725,muscle mass (%): 45.1,lg10 serum c-reactive protein (mg/l): -0.122628654,lg10 plasma adiponectin (mg/l): 1.1430148,ogtt fasting plasma free fatty acid (mmol/l): 0.25,ogtt 30 min plasma free fatty acid (mmol/l): 0.17,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 5.5,ogtt 30 min plasma glucose (mmol/l): 7.9,ogtt 120 min plasma glucose (mmol/l): 5.3,log10 il1 receptor antagonist (pg/ml): 2.276714495,log10 il1 beta (pg/ml): -0.698970004,log10 ogtt fasting plasma insulin (mu/l): 0.973127854,ogtt 30 min plasma insulin (mu/l): 2.007747778,ogtt 120 min plasma insulin (mu/l): 1.707570176,log10 ogtt fasting plasma proinsulin (pm/l): 1.113943352,ogtt 30 min plasma proinsulin (pm/l): 1.436162647,ogtt 120 min plasma proinsulin (pm/l): 1.525044807,log10 bioimpedance: Resistance: 2.717670503,log10 bioimpedance (reactance): 1.755874856,waist to hip ratio: 0.96969697,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.62324929,log10 creatinine (umol/l): 1.886490725,log10 total cholesterol (mmol/l): 0.804820679,log10 ldl cholesterol (mmol/l): 0.667452953,log10 hdl cholesterol (mmol/l): 0.164352856,log10 total triglycerides (mmol/l): 0.269512944,log10 serum apoa1 (g/l): 0.204119983,log10 serum apob (g/l): 0.167317335,log10 urinary albumin excretion rate (ug/min): 0.810417027 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098198 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249097,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978025 | GSM1098198 | GSE45159 | 0.363363 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM482 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249097 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978025 |
|
1 | age: 58,tissue: adipose tissue,log10 body mass index: 1.487384452,log10 basal metabolic rate (kcal): 1562,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.376566407,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.749816692,plasma free fatty acids under the curve ogtt (mmol/l * min): 20.4,fat mass (%): 25,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.610102063,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 145.5,log10 homair (insulin resistance index based on homa): 0.104487111,log10 homais (insulin secretion index based on homa): 1.77815125,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.587508921,insgenin (insulinogenic index): 2.150466011,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.541504359,log10 matsuda insulin sensitivity index: 0.834858425,muscle mass (%): 41.3,lg10 serum c-reactive protein (mg/l): -0.097997109,lg10 plasma adiponectin (mg/l): 0.954242509,ogtt fasting plasma free fatty acid (mmol/l): 0.44,ogtt 30 min plasma free fatty acid (mmol/l): 0.2,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 5.3,ogtt 30 min plasma glucose (mmol/l): 9,ogtt 120 min plasma glucose (mmol/l): 3.6,log10 il1 receptor antagonist (pg/ml): 2.234162819,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.73239376,ogtt 30 min plasma insulin (mu/l): 1.966610987,ogtt 120 min plasma insulin (mu/l): 1.255272505,log10 ogtt fasting plasma proinsulin (pm/l): 1.167317335,ogtt 30 min plasma proinsulin (pm/l): 1.494154594,ogtt 120 min plasma proinsulin (pm/l): 1.588831726,log10 bioimpedance: Resistance: 2.671172843,log10 bioimpedance (reactance): 1.672097858,waist to hip ratio: 1.034825871,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.505149978,log10 creatinine (umol/l): 1.939519253,log10 total cholesterol (mmol/l): 0.69019608,log10 ldl cholesterol (mmol/l): 0.530199698,log10 hdl cholesterol (mmol/l): 0.220108088,log10 total triglycerides (mmol/l): 0.045322979,log10 serum apoa1 (g/l): 0.187520721,log10 serum apob (g/l): 0.021189299,log10 urinary albumin excretion rate (ug/min): 0.949661017 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098199 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249098,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978026 | GSM1098199 | GSE45159 | 0.156395 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM490 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249098 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978026 |
|
1 | age: 53,tissue: adipose tissue,log10 body mass index: 1.389436069,log10 basal metabolic rate (kcal): 1758,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.365129111,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.730864987,plasma free fatty acids under the curve ogtt (mmol/l * min): 16.65,fat mass (%): 20.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.485829309,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 105,log10 homair (insulin resistance index based on homa): 0.045583738,log10 homais (insulin secretion index based on homa): 1.787106093,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.142326883,insgenin (insulinogenic index): 1.719505737,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.01494035,log10 matsuda insulin sensitivity index: 1.069394356,muscle mass (%): 44.9,lg10 serum c-reactive protein (mg/l): 0.173477643,lg10 plasma adiponectin (mg/l): 0.857332496,ogtt fasting plasma free fatty acid (mmol/l): 0.3,ogtt 30 min plasma free fatty acid (mmol/l): 0.18,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.1,ogtt 30 min plasma glucose (mmol/l): 7,ogtt 120 min plasma glucose (mmol/l): 4.9,log10 il1 receptor antagonist (pg/ml): 2.129077324,log10 il1 beta (pg/ml): -0.853871964,log10 ogtt fasting plasma insulin (mu/l): 0.69019608,ogtt 30 min plasma insulin (mu/l): 1.33243846,ogtt 120 min plasma insulin (mu/l): 1.324282455,log10 ogtt fasting plasma proinsulin (pm/l): 1.053078443,ogtt 30 min plasma proinsulin (pm/l): 1.26245109,ogtt 120 min plasma proinsulin (pm/l): 1.428134794,log10 bioimpedance: Resistance: 2.705007959,log10 bioimpedance (reactance): 1.698970004,waist to hip ratio: 0.970588235,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.176091259,log10 creatinine (umol/l): 1.949390007,log10 total cholesterol (mmol/l): 0.767155866,log10 ldl cholesterol (mmol/l): 0.604226053,log10 hdl cholesterol (mmol/l): 0.176091259,log10 total triglycerides (mmol/l): -0.065501549,log10 serum apoa1 (g/l): 0.217483944,log10 serum apob (g/l): 0.064457989,log10 urinary albumin excretion rate (ug/min): 0.687029885 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098200 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249099,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978027 | GSM1098200 | GSE45159 | 0.258982 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM492 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249099 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978027 |
|
1 | age: 55,tissue: adipose tissue,log10 body mass index: 1.373285187,log10 basal metabolic rate (kcal): 1546,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.373093233,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.455462055,plasma free fatty acids under the curve ogtt (mmol/l * min): 40.2,fat mass (%): 16.7,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.16616308,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 453,log10 homair (insulin resistance index based on homa): -0.032452024,log10 homais (insulin secretion index based on homa): 1.49560466,log10 insulin area under the curve (ogtt) (pmol/l * min): 3.807332039,insgenin (insulinogenic index): 0.963483166,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 3.582631439,log10 matsuda insulin sensitivity index: 1.190338397,muscle mass (%): 45.9,lg10 serum c-reactive protein (mg/l): -0.559090918,lg10 plasma adiponectin (mg/l): 1.053078443,ogtt fasting plasma free fatty acid (mmol/l): 0.67,ogtt 30 min plasma free fatty acid (mmol/l): 0.39,ogtt 120 min plasma free fatty acid (mmol/l): 0.15,ogtt fasting plasma glucose (mmol/l): 5.8,ogtt 30 min plasma glucose (mmol/l): 12,ogtt 120 min plasma glucose (mmol/l): 7.6,log10 il1 receptor antagonist (pg/ml): 2.099231615,log10 il1 beta (pg/ml): -0.958607315,log10 ogtt fasting plasma insulin (mu/l): 0.556302501,ogtt 30 min plasma insulin (mu/l): 1.117271296,ogtt 120 min plasma insulin (mu/l): 0.707570176,log10 ogtt fasting plasma proinsulin (pm/l): 0.86923172,ogtt 30 min plasma proinsulin (pm/l): 1.176091259,ogtt 120 min plasma proinsulin (pm/l): 1.385606274,log10 bioimpedance: Resistance: 2.691081492,log10 bioimpedance (reactance): 1.662757832,waist to hip ratio: 0.984536082,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.255272505,log10 creatinine (umol/l): 1.944482672,log10 total cholesterol (mmol/l): 0.774516966,log10 ldl cholesterol (mmol/l): 0.572871602,log10 hdl cholesterol (mmol/l): 0.359835482,log10 total triglycerides (mmol/l): -0.148741651,log10 serum apoa1 (g/l): 0.264817823,log10 serum apob (g/l): -0.045757491,log10 urinary albumin excretion rate (ug/min): 0.646581935 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098201 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249100,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978028 | GSM1098201 | GSE45159 | 0.176817 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM520 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249100 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978028 |
|
1 | age: 58,tissue: adipose tissue,log10 body mass index: 1.406329326,log10 basal metabolic rate (kcal): 1726,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.230109829,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.46745006,plasma free fatty acids under the curve ogtt (mmol/l * min): 18.15,fat mass (%): 16.5,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.080817528,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): -22.5,log10 homair (insulin resistance index based on homa): -0.217686662,log10 homais (insulin secretion index based on homa): 1.684246748,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.372875197,insgenin (insulinogenic index): NA,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.33264041,log10 matsuda insulin sensitivity index: 1.164045038,muscle mass (%): 47.1,lg10 serum c-reactive protein (mg/l): 0.140508043,lg10 plasma adiponectin (mg/l): 0.826074803,ogtt fasting plasma free fatty acid (mmol/l): 0.28,ogtt 30 min plasma free fatty acid (mmol/l): 0.21,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 4.7,ogtt 30 min plasma glucose (mmol/l): 4.7,ogtt 120 min plasma glucose (mmol/l): 4.2,log10 il1 receptor antagonist (pg/ml): 2.099646117,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.462397998,ogtt 30 min plasma insulin (mu/l): 1.754348336,ogtt 120 min plasma insulin (mu/l): 1.029383778,log10 ogtt fasting plasma proinsulin (pm/l): 1.033423755,ogtt 30 min plasma proinsulin (pm/l): 1.437750563,ogtt 120 min plasma proinsulin (pm/l): 1.46834733,log10 bioimpedance: Resistance: 2.617000341,log10 bioimpedance (reactance): 1.602059991,waist to hip ratio: 0.917525773,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.531478917,log10 creatinine (umol/l): 1.977723605,log10 total cholesterol (mmol/l): 0.795880017,log10 ldl cholesterol (mmol/l): 0.646403726,log10 hdl cholesterol (mmol/l): 0.212187604,log10 total triglycerides (mmol/l): 0.10720997,log10 serum apoa1 (g/l): 0.167317335,log10 serum apob (g/l): 0.075546961,log10 urinary albumin excretion rate (ug/min): 0.572096768 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098202 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249101,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978029 | GSM1098202 | GSE45159 | 0.183983 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM522 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249101 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978029 |
|
1 | age: 60,tissue: adipose tissue,log10 body mass index: 1.478333113,log10 basal metabolic rate (kcal): 1630,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.202747826,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.508748397,plasma free fatty acids under the curve ogtt (mmol/l * min): 20.1,fat mass (%): 22.7,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.769837844,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 201,log10 homair (insulin resistance index based on homa): 0.215549444,log10 homais (insulin secretion index based on homa): 1.798354636,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.341632336,insgenin (insulinogenic index): 1.854539596,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.235730397,log10 matsuda insulin sensitivity index: 0.850912144,muscle mass (%): 44,lg10 serum c-reactive protein (mg/l): 0.213783299,lg10 plasma adiponectin (mg/l): 0.568201724,ogtt fasting plasma free fatty acid (mmol/l): 0.31,ogtt 30 min plasma free fatty acid (mmol/l): 0.22,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 8.2,ogtt 120 min plasma glucose (mmol/l): 6.6,log10 il1 receptor antagonist (pg/ml): 1.935104021,log10 il1 beta (pg/ml): -0.537602002,log10 ogtt fasting plasma insulin (mu/l): 0.819543936,ogtt 30 min plasma insulin (mu/l): 1.575187845,ogtt 120 min plasma insulin (mu/l): 1.462397998,log10 ogtt fasting plasma proinsulin (pm/l): 0.991226076,ogtt 30 min plasma proinsulin (pm/l): 1.243038049,ogtt 120 min plasma proinsulin (pm/l): 1.495544338,log10 bioimpedance: Resistance: 2.63748973,log10 bioimpedance (reactance): 1.681241237,waist to hip ratio: 1.028846154,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.342422681,log10 creatinine (umol/l): 1.982271233,log10 total cholesterol (mmol/l): 0.680335513,log10 ldl cholesterol (mmol/l): 0.509202522,log10 hdl cholesterol (mmol/l): 0.012837225,log10 total triglycerides (mmol/l): 0.240549248,log10 serum apoa1 (g/l): 0.075546961,log10 serum apob (g/l): 0.08278537,log10 urinary albumin excretion rate (ug/min): 1.245070488 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098203 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249102,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978030 | GSM1098203 | GSE45159 | 0.211758 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM575 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249102 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978030 |
|
1 | age: 55,tissue: adipose tissue,log10 body mass index: 1.393928211,log10 basal metabolic rate (kcal): 1730,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.639220552,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.842943832,plasma free fatty acids under the curve ogtt (mmol/l * min): 24.75,fat mass (%): 19,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.701306462,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 196.5,log10 homair (insulin resistance index based on homa): 0.142945363,log10 homais (insulin secretion index based on homa): 1.816609502,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.196037941,insgenin (insulinogenic index): 1.60159773,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.059070913,log10 matsuda insulin sensitivity index: 0.990185811,muscle mass (%): 46.9,lg10 serum c-reactive protein (mg/l): 0.308777774,lg10 plasma adiponectin (mg/l): 1.133538908,ogtt fasting plasma free fatty acid (mmol/l): 0.38,ogtt 30 min plasma free fatty acid (mmol/l): 0.22,ogtt 120 min plasma free fatty acid (mmol/l): 0.13,ogtt fasting plasma glucose (mmol/l): 5.3,ogtt 30 min plasma glucose (mmol/l): 10,ogtt 120 min plasma glucose (mmol/l): 3.4,log10 il1 receptor antagonist (pg/ml): 2.073351702,log10 il1 beta (pg/ml): -1,log10 ogtt fasting plasma insulin (mu/l): 0.770852012,ogtt 30 min plasma insulin (mu/l): 1.57054294,ogtt 120 min plasma insulin (mu/l): 0.819543936,log10 ogtt fasting plasma proinsulin (pm/l): 0.792391689,ogtt 30 min plasma proinsulin (pm/l): 1.204119983,ogtt 120 min plasma proinsulin (pm/l): 1.152288344,log10 bioimpedance: Resistance: 2.684845362,log10 bioimpedance (reactance): 1.72427587,waist to hip ratio: 0.917525773,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.397940009,log10 creatinine (umol/l): 1.875061263,log10 total cholesterol (mmol/l): 0.693726949,log10 ldl cholesterol (mmol/l): 0.477121255,log10 hdl cholesterol (mmol/l): 0.238046103,log10 total triglycerides (mmol/l): -0.080921908,log10 serum apoa1 (g/l): 0.173186268,log10 serum apob (g/l): -0.050609993,log10 urinary albumin excretion rate (ug/min): 1.044812344 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098204 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249103,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978031 | GSM1098204 | GSE45159 | 0.066173 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM598 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249103 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978031 |
|
1 | age: 54,tissue: adipose tissue,log10 body mass index: 1.465206508,log10 basal metabolic rate (kcal): 1713,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.475855676,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.886433506,plasma free fatty acids under the curve ogtt (mmol/l * min): 31.65,fat mass (%): 24.5,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.981567282,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 303,log10 homair (insulin resistance index based on homa): 0.49785074,log10 homais (insulin secretion index based on homa): 2,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.714966482,insgenin (insulinogenic index): 2.158814647,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.635845508,log10 matsuda insulin sensitivity index: 0.50747184,muscle mass (%): 43.8,lg10 serum c-reactive protein (mg/l): 0.29841638,lg10 plasma adiponectin (mg/l): 0.799340549,ogtt fasting plasma free fatty acid (mmol/l): 0.65,ogtt 30 min plasma free fatty acid (mmol/l): 0.29,ogtt 120 min plasma free fatty acid (mmol/l): 0.1,ogtt fasting plasma glucose (mmol/l): 5.9,ogtt 30 min plasma glucose (mmol/l): 9.9,ogtt 120 min plasma glucose (mmol/l): 7.3,log10 il1 receptor antagonist (pg/ml): 2.045714059,log10 il1 beta (pg/ml): -0.853871964,log10 ogtt fasting plasma insulin (mu/l): 1.079181246,ogtt 30 min plasma insulin (mu/l): 2.033825694,ogtt 120 min plasma insulin (mu/l): 1.643452676,log10 ogtt fasting plasma proinsulin (pm/l): 1.340444115,ogtt 30 min plasma proinsulin (pm/l): 1.870988814,ogtt 120 min plasma proinsulin (pm/l): 1.968482949,log10 bioimpedance: Resistance: 2.686636269,log10 bioimpedance (reactance): 1.763427994,waist to hip ratio: 1.014851485,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.612783857,log10 creatinine (umol/l): 1.919078092,log10 total cholesterol (mmol/l): 0.792391689,log10 ldl cholesterol (mmol/l): 0.369215857,log10 hdl cholesterol (mmol/l): 0.033423755,log10 total triglycerides (mmol/l): 0.883093359,log10 serum apoa1 (g/l): 0.120573931,log10 serum apob (g/l): 0.071882007,log10 urinary albumin excretion rate (ug/min): 0.87185875 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098205 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249104,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978032 | GSM1098205 | GSE45159 | 0.113722 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM783 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249104 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978032 |
|
1 | age: 51,tissue: adipose tissue,log10 body mass index: 1.48669827,log10 basal metabolic rate (kcal): 1676,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.069738097,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.600171425,plasma free fatty acids under the curve ogtt (mmol/l * min): 27.75,fat mass (%): 22.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.904634622,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 238.5,log10 homair (insulin resistance index based on homa): 0.543240028,log10 homais (insulin secretion index based on homa): 2.020361283,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.629287245,insgenin (insulinogenic index): 1.980003372,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.520562131,log10 matsuda insulin sensitivity index: 0.524273321,muscle mass (%): 43.3,lg10 serum c-reactive protein (mg/l): -0.152427341,lg10 plasma adiponectin (mg/l): 0.672097858,ogtt fasting plasma free fatty acid (mmol/l): 0.58,ogtt 30 min plasma free fatty acid (mmol/l): 0.25,ogtt 120 min plasma free fatty acid (mmol/l): 0.09,ogtt fasting plasma glucose (mmol/l): 6,ogtt 30 min plasma glucose (mmol/l): 9.6,ogtt 120 min plasma glucose (mmol/l): 6.5,log10 il1 receptor antagonist (pg/ml): 2.261619677,log10 il1 beta (pg/ml): 0.021189299,log10 ogtt fasting plasma insulin (mu/l): 1.117271296,ogtt 30 min plasma insulin (mu/l): 1.847572659,ogtt 120 min plasma insulin (mu/l): 1.774516966,log10 ogtt fasting plasma proinsulin (pm/l): 0.903089987,ogtt 30 min plasma proinsulin (pm/l): 1.305351369,ogtt 120 min plasma proinsulin (pm/l): 1.692846919,log10 bioimpedance: Resistance: 2.605305046,log10 bioimpedance (reactance): 1.602059991,waist to hip ratio: 0.976303318,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.531478917,log10 creatinine (umol/l): 2.029383778,log10 total cholesterol (mmol/l): 0.648360011,log10 ldl cholesterol (mmol/l): 0.456366033,log10 hdl cholesterol (mmol/l): 0.089905111,log10 total triglycerides (mmol/l): 0.152288344,log10 serum apoa1 (g/l): 0.089905111,log10 serum apob (g/l): -0.026872146,log10 urinary albumin excretion rate (ug/min): 1.134546163 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098206 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249105,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978033 | GSM1098206 | GSE45159 | 0.280541 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM803 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249105 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978033 |
|
1 | age: 57,tissue: adipose tissue,log10 body mass index: 1.327687058,log10 basal metabolic rate (kcal): 1553,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.584945002,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.437725264,plasma free fatty acids under the curve ogtt (mmol/l * min): 25.95,fat mass (%): 11.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.439830884,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 46.5,log10 homair (insulin resistance index based on homa): -0.101274818,log10 homais (insulin secretion index based on homa): 1.540790335,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.057704132,insgenin (insulinogenic index): 1.586265724,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 3.956408571,log10 matsuda insulin sensitivity index: 1.170063428,muscle mass (%): 49.7,lg10 serum c-reactive protein (mg/l): -0.583359493,lg10 plasma adiponectin (mg/l): 0.770852012,ogtt fasting plasma free fatty acid (mmol/l): 0.46,ogtt 30 min plasma free fatty acid (mmol/l): 0.28,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5.4,ogtt 30 min plasma glucose (mmol/l): 6.1,ogtt 120 min plasma glucose (mmol/l): 5.5,log10 il1 receptor antagonist (pg/ml): 2.045362103,log10 il1 beta (pg/ml): -0.568636236,log10 ogtt fasting plasma insulin (mu/l): 0.51851394,ogtt 30 min plasma insulin (mu/l): 0.892094603,ogtt 120 min plasma insulin (mu/l): 1.488550717,log10 ogtt fasting plasma proinsulin (pm/l): 0.995635195,ogtt 30 min plasma proinsulin (pm/l): 1.017033339,ogtt 120 min plasma proinsulin (pm/l): 1.390935107,log10 bioimpedance: Resistance: 2.679427897,log10 bioimpedance (reactance): 1.662757832,waist to hip ratio: 0.840659341,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 0.903089987,log10 creatinine (umol/l): 1.886490725,log10 total cholesterol (mmol/l): 0.750508395,log10 ldl cholesterol (mmol/l): 0.53529412,log10 hdl cholesterol (mmol/l): 0.307496038,log10 total triglycerides (mmol/l): -0.091514981,log10 serum apoa1 (g/l): 0.204119983,log10 serum apob (g/l): -0.031517051,log10 urinary albumin excretion rate (ug/min): 0.508676069 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098207 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249106,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978034 | GSM1098207 | GSE45159 | 0.187657 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM817 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249106 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978034 |
|
1 | age: 52,tissue: adipose tissue,log10 body mass index: 1.517036236,log10 basal metabolic rate (kcal): 1684,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.611832412,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.11805107,plasma free fatty acids under the curve ogtt (mmol/l * min): 14.7,fat mass (%): 24.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.515699838,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 84,log10 homair (insulin resistance index based on homa): 0.261024834,log10 homais (insulin secretion index based on homa): 1.903089987,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.4954472,insgenin (insulinogenic index): 2.385118576,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.411973058,log10 matsuda insulin sensitivity index: 0.783578563,muscle mass (%): 42.7,lg10 serum c-reactive protein (mg/l): 0.241795431,lg10 plasma adiponectin (mg/l): 0.612783857,ogtt fasting plasma free fatty acid (mmol/l): 0.25,ogtt 30 min plasma free fatty acid (mmol/l): 0.16,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.4,ogtt 30 min plasma glucose (mmol/l): 6.5,ogtt 120 min plasma glucose (mmol/l): 5.8,log10 il1 receptor antagonist (pg/ml): 2.337738717,log10 il1 beta (pg/ml): -0.552841969,log10 ogtt fasting plasma insulin (mu/l): 0.880813592,ogtt 30 min plasma insulin (mu/l): 1.716837723,ogtt 120 min plasma insulin (mu/l): 1.64246452,log10 ogtt fasting plasma proinsulin (pm/l): 1.245512668,ogtt 30 min plasma proinsulin (pm/l): 1.666517981,ogtt 120 min plasma proinsulin (pm/l): 1.909556029,log10 bioimpedance: Resistance: 2.603144373,log10 bioimpedance (reactance): 1.633468456,waist to hip ratio: 0.990909091,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.556302501,log10 creatinine (umol/l): 1.886490725,log10 total cholesterol (mmol/l): 0.693726949,log10 ldl cholesterol (mmol/l): 0.50242712,log10 hdl cholesterol (mmol/l): 0.056904851,log10 total triglycerides (mmol/l): 0.318063335,log10 serum apoa1 (g/l): 0.100370545,log10 serum apob (g/l): 0.025305865,log10 urinary albumin excretion rate (ug/min): 0.922510263 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098208 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249107,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978035 | GSM1098208 | GSE45159 | 0.323616 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM833 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249107 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978035 |
|
1 | age: 56,tissue: adipose tissue,log10 body mass index: 1.396552355,log10 basal metabolic rate (kcal): 1663,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.485385281,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.705854221,plasma free fatty acids under the curve ogtt (mmol/l * min): 29.7,fat mass (%): 21.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.04028972,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 333,log10 homair (insulin resistance index based on homa): 0.610660163,log10 homais (insulin secretion index based on homa): 2.087781418,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.808730734,insgenin (insulinogenic index): 2.151817564,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.72722396,log10 matsuda insulin sensitivity index: 0.385433076,muscle mass (%): 45,lg10 serum c-reactive protein (mg/l): -0.53313238,lg10 plasma adiponectin (mg/l): 0.414973348,ogtt fasting plasma free fatty acid (mmol/l): 0.34,ogtt 30 min plasma free fatty acid (mmol/l): 0.35,ogtt 120 min plasma free fatty acid (mmol/l): 0.08,ogtt fasting plasma glucose (mmol/l): 6,ogtt 30 min plasma glucose (mmol/l): 9.9,ogtt 120 min plasma glucose (mmol/l): 8.2,log10 il1 receptor antagonist (pg/ml): 2.269466243,log10 il1 beta (pg/ml): -0.568636236,log10 ogtt fasting plasma insulin (mu/l): 1.184691431,ogtt 30 min plasma insulin (mu/l): 2.031408464,ogtt 120 min plasma insulin (mu/l): 1.954242509,log10 ogtt fasting plasma proinsulin (pm/l): 1.298853076,ogtt 30 min plasma proinsulin (pm/l): 1.688419822,ogtt 120 min plasma proinsulin (pm/l): 1.849419414,log10 bioimpedance: Resistance: 2.728353782,log10 bioimpedance (reactance): 1.763427994,waist to hip ratio: 1.01025641,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.568201724,log10 creatinine (umol/l): 1.913813852,log10 total cholesterol (mmol/l): 0.580924976,log10 ldl cholesterol (mmol/l): 0.267171728,log10 hdl cholesterol (mmol/l): 0.068185862,log10 total triglycerides (mmol/l): 0.475671188,log10 serum apoa1 (g/l): 0.139879086,log10 serum apob (g/l): -0.022276395,log10 urinary albumin excretion rate (ug/min): 1.007061855 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098209 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249108,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978036 | GSM1098209 | GSE45159 | 0.149286 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM844 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249108 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978036 |
|
1 | age: 55,tissue: adipose tissue,log10 body mass index: 1.472965295,log10 basal metabolic rate (kcal): 1577,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.450543015,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.820917525,plasma free fatty acids under the curve ogtt (mmol/l * min): 18,fat mass (%): 23.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.587777516,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 97.5,log10 homair (insulin resistance index based on homa): 0.068103367,log10 homais (insulin secretion index based on homa): 1.650908559,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.321411998,insgenin (insulinogenic index): 2.007320953,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.244944753,log10 matsuda insulin sensitivity index: 0.964545375,muscle mass (%): 42.1,lg10 serum c-reactive protein (mg/l): 0.574841195,lg10 plasma adiponectin (mg/l): 0.880813592,ogtt fasting plasma free fatty acid (mmol/l): 0.38,ogtt 30 min plasma free fatty acid (mmol/l): 0.19,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 7.6,ogtt 120 min plasma glucose (mmol/l): 5.1,log10 il1 receptor antagonist (pg/ml): 2.070665753,log10 il1 beta (pg/ml): -0.769551079,log10 ogtt fasting plasma insulin (mu/l): 0.672097858,ogtt 30 min plasma insulin (mu/l): 1.586587305,ogtt 120 min plasma insulin (mu/l): 1.390935107,log10 ogtt fasting plasma proinsulin (pm/l): 1.033423755,ogtt 30 min plasma proinsulin (pm/l): 1.338456494,ogtt 120 min plasma proinsulin (pm/l): 1.633468456,log10 bioimpedance: Resistance: 2.652246341,log10 bioimpedance (reactance): 1.633468456,waist to hip ratio: 1.014354067,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.361727836,log10 creatinine (umol/l): 1.924279286,log10 total cholesterol (mmol/l): 0.71432976,log10 ldl cholesterol (mmol/l): 0.494154594,log10 hdl cholesterol (mmol/l): 0.217483944,log10 total triglycerides (mmol/l): 0.053078443,log10 serum apoa1 (g/l): 0.220108088,log10 serum apob (g/l): 0,log10 urinary albumin excretion rate (ug/min): 0.647287531 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098210 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249109,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978037 | GSM1098210 | GSE45159 | 0.226469 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM874 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249109 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978037 |
|
1 | age: 57,tissue: adipose tissue,log10 body mass index: 1.430991056,log10 basal metabolic rate (kcal): 1436,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.20051725,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.26100052,plasma free fatty acids under the curve ogtt (mmol/l * min): 22.95,fat mass (%): 21,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.714245518,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 264,log10 homair (insulin resistance index based on homa): -0.068881289,log10 homais (insulin secretion index based on homa): 1.789146635,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.568717876,insgenin (insulinogenic index): 2.0678017,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.533568713,log10 matsuda insulin sensitivity index: 0.898372406,muscle mass (%): 44.5,lg10 serum c-reactive protein (mg/l): 0.707825568,lg10 plasma adiponectin (mg/l): 1.045322979,ogtt fasting plasma free fatty acid (mmol/l): 0.38,ogtt 30 min plasma free fatty acid (mmol/l): 0.25,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 4.8,ogtt 30 min plasma glucose (mmol/l): 7.7,ogtt 120 min plasma glucose (mmol/l): 6.8,log10 il1 receptor antagonist (pg/ml): 2.219767845,log10 il1 beta (pg/ml): -0.102372909,log10 ogtt fasting plasma insulin (mu/l): 0.602059991,ogtt 30 min plasma insulin (mu/l): 1.781755375,ogtt 120 min plasma insulin (mu/l): 1.741939078,log10 ogtt fasting plasma proinsulin (pm/l): 1,ogtt 30 min plasma proinsulin (pm/l): 1.423245874,ogtt 120 min plasma proinsulin (pm/l): 1.776701184,log10 bioimpedance: Resistance: 2.705007959,log10 bioimpedance (reactance): 1.755874856,waist to hip ratio: 1.010752688,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.544068044,log10 creatinine (umol/l): 1.986771734,log10 total cholesterol (mmol/l): 0.877946952,log10 ldl cholesterol (mmol/l): 0.730782276,log10 hdl cholesterol (mmol/l): 0.240549248,log10 total triglycerides (mmol/l): -0.148741651,log10 serum apoa1 (g/l): 0.247973266,log10 serum apob (g/l): 0.170261715,log10 urinary albumin excretion rate (ug/min): 0.575642049 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098211 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249110,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978038 | GSM1098211 | GSE45159 | 0.237078 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM888 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249110 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978038 |
|
1 | age: 52,tissue: adipose tissue,log10 body mass index: 1.414995599,log10 basal metabolic rate (kcal): 1754,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.389519992,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.635899375,plasma free fatty acids under the curve ogtt (mmol/l * min): 17.4,fat mass (%): 17.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.714245518,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 180,log10 homair (insulin resistance index based on homa): -0.120458135,log10 homais (insulin secretion index based on homa): 1.491361694,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.198024426,insgenin (insulinogenic index): 1.583576586,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.131779009,log10 matsuda insulin sensitivity index: 1.106043024,muscle mass (%): 48.8,lg10 serum c-reactive protein (mg/l): -0.573488739,lg10 plasma adiponectin (mg/l): 1.243038049,ogtt fasting plasma free fatty acid (mmol/l): 0.22,ogtt 30 min plasma free fatty acid (mmol/l): 0.22,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.5,ogtt 30 min plasma glucose (mmol/l): 9.1,ogtt 120 min plasma glucose (mmol/l): 4.7,log10 il1 receptor antagonist (pg/ml): 2.19002338,log10 il1 beta (pg/ml): -0.356547324,log10 ogtt fasting plasma insulin (mu/l): 0.491361694,ogtt 30 min plasma insulin (mu/l): 1.416640507,ogtt 120 min plasma insulin (mu/l): 1.354108439,log10 ogtt fasting plasma proinsulin (pm/l): 0.991226076,ogtt 30 min plasma proinsulin (pm/l): 1.357934847,ogtt 120 min plasma proinsulin (pm/l): 1.672097858,log10 bioimpedance: Resistance: 2.62838893,log10 bioimpedance (reactance): 1.698970004,waist to hip ratio: 0.904761905,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.322219295,log10 creatinine (umol/l): 1.944482672,log10 total cholesterol (mmol/l): 0.797959644,log10 ldl cholesterol (mmol/l): 0.550228353,log10 hdl cholesterol (mmol/l): 0.419955748,log10 total triglycerides (mmol/l): -0.075720714,log10 serum apoa1 (g/l): 0.342422681,log10 serum apob (g/l): -0.013228266,log10 urinary albumin excretion rate (ug/min): 1.078012216 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098212 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249111,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978039 | GSM1098212 | GSE45159 | 0.254287 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM906 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249111 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978039 |
|
1 | age: 54,tissue: adipose tissue,log10 body mass index: 1.423812763,log10 basal metabolic rate (kcal): 1629,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.084411853,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.302689358,plasma free fatty acids under the curve ogtt (mmol/l * min): 12.45,fat mass (%): 20.1,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.714245518,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 192,log10 homair (insulin resistance index based on homa): 0.504062883,log10 homais (insulin secretion index based on homa): 2.146128036,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.808609287,insgenin (insulinogenic index): 2.158362492,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.738645811,log10 matsuda insulin sensitivity index: 0.474421526,muscle mass (%): 46.8,lg10 serum c-reactive protein (mg/l): -0.067019178,lg10 plasma adiponectin (mg/l): 0.832508913,ogtt fasting plasma free fatty acid (mmol/l): 0.17,ogtt 30 min plasma free fatty acid (mmol/l): 0.15,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.4,ogtt 30 min plasma glucose (mmol/l): 8,ogtt 120 min plasma glucose (mmol/l): 6.2,log10 il1 receptor antagonist (pg/ml): 2.857784651,log10 il1 beta (pg/ml): 0.152288344,log10 ogtt fasting plasma insulin (mu/l): 1.123851641,ogtt 30 min plasma insulin (mu/l): 1.87909588,ogtt 120 min plasma insulin (mu/l): 2.123851641,log10 ogtt fasting plasma proinsulin (pm/l): 1.127104798,ogtt 30 min plasma proinsulin (pm/l): 1.383815366,ogtt 120 min plasma proinsulin (pm/l): 1.81756537,log10 bioimpedance: Resistance: 2.678518379,log10 bioimpedance (reactance): 1.763427994,waist to hip ratio: 1.041884817,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.770852012,log10 creatinine (umol/l): 2.021189299,log10 total cholesterol (mmol/l): 0.706717782,log10 ldl cholesterol (mmol/l): 0.5132176,log10 hdl cholesterol (mmol/l): 0.133538908,log10 total triglycerides (mmol/l): 0.240549248,log10 serum apoa1 (g/l): 0.184691431,log10 serum apob (g/l): 0.064457989,log10 urinary albumin excretion rate (ug/min): 0.794995807 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098213 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249112,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978040 | GSM1098213 | GSE45159 | 0.169843 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM908 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249112 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978040 |
|
1 | age: 55,tissue: adipose tissue,log10 body mass index: 1.429511788,log10 basal metabolic rate (kcal): 1492,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.511090418,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.6875184,plasma free fatty acids under the curve ogtt (mmol/l * min): 19.8,fat mass (%): 20.9,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.900112063,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 319.5,log10 homair (insulin resistance index based on homa): 0.258584077,log10 homais (insulin secretion index based on homa): 1.932248216,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.586902223,insgenin (insulinogenic index): 1.950781977,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.519618012,log10 matsuda insulin sensitivity index: 0.701131284,muscle mass (%): 43.2,lg10 serum c-reactive protein (mg/l): -0.044793462,lg10 plasma adiponectin (mg/l): 0.968482949,ogtt fasting plasma free fatty acid (mmol/l): 0.4,ogtt 30 min plasma free fatty acid (mmol/l): 0.2,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 5.3,ogtt 30 min plasma glucose (mmol/l): 9.5,ogtt 120 min plasma glucose (mmol/l): 6.8,log10 il1 receptor antagonist (pg/ml): 1.772321707,log10 il1 beta (pg/ml): -0.356547324,log10 ogtt fasting plasma insulin (mu/l): 0.886490725,ogtt 30 min plasma insulin (mu/l): 1.846337112,ogtt 120 min plasma insulin (mu/l): 1.671172843,log10 ogtt fasting plasma proinsulin (pm/l): 1.029383778,ogtt 30 min plasma proinsulin (pm/l): 1.534026106,ogtt 120 min plasma proinsulin (pm/l): 1.689308859,log10 bioimpedance: Resistance: 2.685741739,log10 bioimpedance (reactance): 1.662757832,waist to hip ratio: 1.026737968,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.491361694,log10 creatinine (umol/l): 1.908485019,log10 total cholesterol (mmol/l): 0.761927838,log10 ldl cholesterol (mmol/l): 0.559906625,log10 hdl cholesterol (mmol/l): 0.209515015,log10 total triglycerides (mmol/l): 0.278753601,log10 serum apoa1 (g/l): 0.227886705,log10 serum apob (g/l): 0.086359831,log10 urinary albumin excretion rate (ug/min): 0.681241237 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098214 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249113,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978041 | GSM1098214 | GSE45159 | 0.009933 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM951 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249113 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978041 |
|
1 | age: 52,tissue: adipose tissue,log10 body mass index: 1.340452376,log10 basal metabolic rate (kcal): 1556,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.723610629,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.694080445,plasma free fatty acids under the curve ogtt (mmol/l * min): 8.4,fat mass (%): 17.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.482807957,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 67.5,log10 homair (insulin resistance index based on homa): -0.172630727,log10 homais (insulin secretion index based on homa): 1.469434426,log10 insulin area under the curve (ogtt) (pmol/l * min): 3.982813762,insgenin (insulinogenic index): 1.640978057,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 3.880584956,log10 matsuda insulin sensitivity index: 1.274560314,muscle mass (%): 47.4,lg10 serum c-reactive protein (mg/l): -0.404503778,lg10 plasma adiponectin (mg/l): 0.892094603,ogtt fasting plasma free fatty acid (mmol/l): 0.1,ogtt 30 min plasma free fatty acid (mmol/l): 0.1,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.4,ogtt 30 min plasma glucose (mmol/l): 7.8,ogtt 120 min plasma glucose (mmol/l): 3.7,log10 il1 receptor antagonist (pg/ml): 1.736635498,log10 il1 beta (pg/ml): -0.744727495,log10 ogtt fasting plasma insulin (mu/l): 0.447158031,ogtt 30 min plasma insulin (mu/l): 1.307496038,ogtt 120 min plasma insulin (mu/l): 0.880813592,log10 ogtt fasting plasma proinsulin (pm/l): 0.954242509,ogtt 30 min plasma proinsulin (pm/l): 1.336459734,ogtt 120 min plasma proinsulin (pm/l): 1.413299764,log10 bioimpedance: Resistance: 2.764176132,log10 bioimpedance (reactance): 1.812913357,waist to hip ratio: 0.924731183,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.301029996,log10 creatinine (umol/l): 1.857332496,log10 total cholesterol (mmol/l): 0.827369273,log10 ldl cholesterol (mmol/l): 0.648360011,log10 hdl cholesterol (mmol/l): 0.298853076,log10 total triglycerides (mmol/l): 0.041392685,log10 serum apoa1 (g/l): 0.260071388,log10 serum apob (g/l): 0.093421685,log10 urinary albumin excretion rate (ug/min): 0.739313246 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098215 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249114,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978042 | GSM1098215 | GSE45159 | 0.276479 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM964 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249114 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978042 |
|
1 | age: 53,tissue: adipose tissue,log10 body mass index: 1.409596272,log10 basal metabolic rate (kcal): 1779,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.58477133,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.879855404,plasma free fatty acids under the curve ogtt (mmol/l * min): 47.85,fat mass (%): 20.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.794415866,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 264,log10 homair (insulin resistance index based on homa): -0.131029196,log10 homais (insulin secretion index based on homa): 1.575731053,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.154545692,insgenin (insulinogenic index): 1.522650109,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.07809415,log10 matsuda insulin sensitivity index: 1.123009983,muscle mass (%): 46.8,lg10 serum c-reactive protein (mg/l): 0.823082797,lg10 plasma adiponectin (mg/l): 0.763427994,ogtt fasting plasma free fatty acid (mmol/l): 0.82,ogtt 30 min plasma free fatty acid (mmol/l): 0.51,ogtt 120 min plasma free fatty acid (mmol/l): 0.11,ogtt fasting plasma glucose (mmol/l): 5.2,ogtt 30 min plasma glucose (mmol/l): 9,ogtt 120 min plasma glucose (mmol/l): 6,log10 il1 receptor antagonist (pg/ml): 2.219348717,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.505149978,ogtt 30 min plasma insulin (mu/l): 1.385606274,ogtt 120 min plasma insulin (mu/l): 1.28780173,log10 ogtt fasting plasma proinsulin (pm/l): 0.934498451,ogtt 30 min plasma proinsulin (pm/l): 1.247973266,ogtt 120 min plasma proinsulin (pm/l): 1.505149978,log10 bioimpedance: Resistance: 2.682145076,log10 bioimpedance (reactance): 1.748188027,waist to hip ratio: 0.95049505,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.342422681,log10 creatinine (umol/l): 1.892094603,log10 total cholesterol (mmol/l): 0.809559715,log10 ldl cholesterol (mmol/l): 0.617000341,log10 hdl cholesterol (mmol/l): 0.198657087,log10 total triglycerides (mmol/l): -0.346787486,log10 serum apoa1 (g/l): 0.173186268,log10 serum apob (g/l): 0.053078443,log10 urinary albumin excretion rate (ug/min): 1.06694679 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098216 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249115,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978043 | GSM1098216 | GSE45159 | 0.307238 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1019 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249115 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978043 |
|
1 | age: 53,tissue: adipose tissue,log10 body mass index: 1.390438731,log10 basal metabolic rate (kcal): 1641,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.542620469,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.74798165,plasma free fatty acids under the curve ogtt (mmol/l * min): 13.05,fat mass (%): 19.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.651051691,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 132,log10 homair (insulin resistance index based on homa): 0.369133362,log10 homais (insulin secretion index based on homa): 1.951938555,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.585990584,insgenin (insulinogenic index): 2.216045882,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.502140227,log10 matsuda insulin sensitivity index: 0.671973688,muscle mass (%): 45.5,lg10 serum c-reactive protein (mg/l): 0.421932813,lg10 plasma adiponectin (mg/l): 0.707570176,ogtt fasting plasma free fatty acid (mmol/l): 0.25,ogtt 30 min plasma free fatty acid (mmol/l): 0.14,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 7.8,ogtt 120 min plasma glucose (mmol/l): 5.6,log10 il1 receptor antagonist (pg/ml): 2.044735697,log10 il1 beta (pg/ml): -0.795880017,log10 ogtt fasting plasma insulin (mu/l): 0.973127854,ogtt 30 min plasma insulin (mu/l): 1.843232778,ogtt 120 min plasma insulin (mu/l): 1.669316881,log10 ogtt fasting plasma proinsulin (pm/l): 1.025305865,ogtt 30 min plasma proinsulin (pm/l): 1.584331224,ogtt 120 min plasma proinsulin (pm/l): 1.796574333,log10 bioimpedance: Resistance: 2.712649702,log10 bioimpedance (reactance): 1.73239376,waist to hip ratio: 0.916256158,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.397940009,log10 creatinine (umol/l): 1.903089987,log10 total cholesterol (mmol/l): 0.725911632,log10 ldl cholesterol (mmol/l): 0.519827994,log10 hdl cholesterol (mmol/l): 0.130333768,log10 total triglycerides (mmol/l): 0.004321374,log10 serum apoa1 (g/l): 0.155336037,log10 serum apob (g/l): -0.022276395,log10 urinary albumin excretion rate (ug/min): 1.245923737 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098217 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249116,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978044 | GSM1098217 | GSE45159 | 0.023671 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1086 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249116 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978044 |
|
1 | age: 57,tissue: adipose tissue,log10 body mass index: 1.427737755,log10 basal metabolic rate (kcal): 1605,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.480201657,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.671088803,plasma free fatty acids under the curve ogtt (mmol/l * min): 15.45,fat mass (%): 17.1,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.45224124,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 64.5,log10 homair (insulin resistance index based on homa): -0.180748617,log10 homais (insulin secretion index based on homa): 1.492915522,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.419922721,insgenin (insulinogenic index): 2.440909082,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.385284455,log10 matsuda insulin sensitivity index: 1.075030415,muscle mass (%): 45.5,lg10 serum c-reactive protein (mg/l): 0.244771761,lg10 plasma adiponectin (mg/l): 0.531478917,ogtt fasting plasma free fatty acid (mmol/l): 0.45,ogtt 30 min plasma free fatty acid (mmol/l): 0.13,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.3,ogtt 30 min plasma glucose (mmol/l): 6.6,ogtt 120 min plasma glucose (mmol/l): 5,log10 il1 receptor antagonist (pg/ml): 2.06669855,log10 il1 beta (pg/ml): -0.853871964,log10 ogtt fasting plasma insulin (mu/l): 0.447158031,ogtt 30 min plasma insulin (mu/l): 1.796574333,ogtt 120 min plasma insulin (mu/l): 1.113943352,log10 ogtt fasting plasma proinsulin (pm/l): 0.72427587,ogtt 30 min plasma proinsulin (pm/l): 1.495544338,ogtt 120 min plasma proinsulin (pm/l): 1.534026106,log10 bioimpedance: Resistance: 2.603144373,log10 bioimpedance (reactance): 1.556302501,waist to hip ratio: 0.897959184,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.342422681,log10 creatinine (umol/l): 1.913813852,log10 total cholesterol (mmol/l): 0.568201724,log10 ldl cholesterol (mmol/l): 0.365487985,log10 hdl cholesterol (mmol/l): -0.013228266,log10 total triglycerides (mmol/l): -0.102372909,log10 serum apoa1 (g/l): 0.017033339,log10 serum apob (g/l): -0.148741651,log10 urinary albumin excretion rate (ug/min): 0.599768195 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098218 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249117,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978045 | GSM1098218 | GSE45159 | 0.229011 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1092 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249117 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978045 |
|
1 | age: 54,tissue: adipose tissue,log10 body mass index: 1.387714902,log10 basal metabolic rate (kcal): 1650,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.496036167,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.622149964,plasma free fatty acids under the curve ogtt (mmol/l * min): 26.4,fat mass (%): 15.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.13378441,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 415.5,log10 homair (insulin resistance index based on homa): 0.293730757,log10 homais (insulin secretion index based on homa): 1.795880017,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.612062965,insgenin (insulinogenic index): 1.810922422,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.550619653,log10 matsuda insulin sensitivity index: 0.619624223,muscle mass (%): 47.9,lg10 serum c-reactive protein (mg/l): -0.510041521,lg10 plasma adiponectin (mg/l): 0.672097858,ogtt fasting plasma free fatty acid (mmol/l): 0.55,ogtt 30 min plasma free fatty acid (mmol/l): 0.28,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.9,ogtt 30 min plasma glucose (mmol/l): 9.6,ogtt 120 min plasma glucose (mmol/l): 10.2,log10 il1 receptor antagonist (pg/ml): 1.777716739,log10 il1 beta (pg/ml): -0.585026652,log10 ogtt fasting plasma insulin (mu/l): 0.875061263,ogtt 30 min plasma insulin (mu/l): 1.675778342,ogtt 120 min plasma insulin (mu/l): 1.933993164,log10 ogtt fasting plasma proinsulin (pm/l): 1.075546961,ogtt 30 min plasma proinsulin (pm/l): 1.654176542,ogtt 120 min plasma proinsulin (pm/l): 1.879669206,log10 bioimpedance: Resistance: 2.636487896,log10 bioimpedance (reactance): 1.633468456,waist to hip ratio: 0.928205128,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.447158031,log10 creatinine (umol/l): 1.913813852,log10 total cholesterol (mmol/l): 0.571708832,log10 ldl cholesterol (mmol/l): 0.298853076,log10 hdl cholesterol (mmol/l): 0.117271296,log10 total triglycerides (mmol/l): 0.245512668,log10 serum apoa1 (g/l): 0.133538908,log10 serum apob (g/l): -0.102372909,log10 urinary albumin excretion rate (ug/min): 0.713910354 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098219 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249118,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978046 | GSM1098219 | GSE45159 | 0.251424 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1111 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249118 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978046 |
|
1 | age: 57,tissue: adipose tissue,log10 body mass index: 1.463304683,log10 basal metabolic rate (kcal): 1468,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.673759129,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.856303676,plasma free fatty acids under the curve ogtt (mmol/l * min): 34.2,fat mass (%): 22.9,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.03617361,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 222,log10 homair (insulin resistance index based on homa): 0.468937806,log10 homais (insulin secretion index based on homa): 1.751822312,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.525951341,insgenin (insulinogenic index): 1.739233184,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.425827564,log10 matsuda insulin sensitivity index: 0.57716663,muscle mass (%): 42.1,lg10 serum c-reactive protein (mg/l): 0.27392678,lg10 plasma adiponectin (mg/l): 0.380211242,ogtt fasting plasma free fatty acid (mmol/l): 0.65,ogtt 30 min plasma free fatty acid (mmol/l): 0.37,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 6.9,ogtt 30 min plasma glucose (mmol/l): 9.7,ogtt 120 min plasma glucose (mmol/l): 8.1,log10 il1 receptor antagonist (pg/ml): 2.348285388,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.982271233,ogtt 30 min plasma insulin (mu/l): 1.546542663,ogtt 120 min plasma insulin (mu/l): 1.870403905,log10 ogtt fasting plasma proinsulin (pm/l): 1.149219113,ogtt 30 min plasma proinsulin (pm/l): 1.447158031,ogtt 120 min plasma proinsulin (pm/l): 1.84260924,log10 bioimpedance: Resistance: 2.678518379,log10 bioimpedance (reactance): 1.672097858,waist to hip ratio: 0.94,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.591064607,log10 creatinine (umol/l): 1.86332286,log10 total cholesterol (mmol/l): 0.791690649,log10 ldl cholesterol (mmol/l): 0.57634135,log10 hdl cholesterol (mmol/l): 0.250420002,log10 total triglycerides (mmol/l): 0.123851641,log10 serum apoa1 (g/l): 0.220108088,log10 serum apob (g/l): 0.045322979,log10 urinary albumin excretion rate (ug/min): 0.700546393 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098220 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249119,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978047 | GSM1098220 | GSE45159 | 0.320832 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1160 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249119 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978047 |
|
1 | age: 56,tissue: adipose tissue,log10 body mass index: 1.283277711,log10 basal metabolic rate (kcal): 1607,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.367816206,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.251302989,plasma free fatty acids under the curve ogtt (mmol/l * min): 20.25,fat mass (%): 12.1,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.653740779,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 217.5,log10 homair (insulin resistance index based on homa): -0.281775196,log10 homais (insulin secretion index based on homa): 1.535113202,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.264510876,insgenin (insulinogenic index): 1.70410412,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.221648928,log10 matsuda insulin sensitivity index: 1.171841611,muscle mass (%): 50,lg10 serum c-reactive protein (mg/l): -0.853871964,lg10 plasma adiponectin (mg/l): 0.832508913,ogtt fasting plasma free fatty acid (mmol/l): 0.33,ogtt 30 min plasma free fatty acid (mmol/l): 0.24,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 4.9,ogtt 30 min plasma glucose (mmol/l): 8.6,ogtt 120 min plasma glucose (mmol/l): 4.8,log10 il1 receptor antagonist (pg/ml): 2.226728757,log10 il1 beta (pg/ml): -0.769551079,log10 ogtt fasting plasma insulin (mu/l): 0.380211242,ogtt 30 min plasma insulin (mu/l): 1.526339277,ogtt 120 min plasma insulin (mu/l): 1.352182518,log10 ogtt fasting plasma proinsulin (pm/l): 0.819543936,ogtt 30 min plasma proinsulin (pm/l): 1.1430148,ogtt 120 min plasma proinsulin (pm/l): 1.600972896,log10 bioimpedance: Resistance: 2.754348336,log10 bioimpedance (reactance): 1.755874856,waist to hip ratio: 0.869565217,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 0.954242509,log10 creatinine (umol/l): 1.944482672,log10 total cholesterol (mmol/l): 0.691965103,log10 ldl cholesterol (mmol/l): 0.498310554,log10 hdl cholesterol (mmol/l): 0.222716471,log10 total triglycerides (mmol/l): -0.124938737,log10 serum apoa1 (g/l): 0.068185862,log10 serum apob (g/l): -0.142667504,log10 urinary albumin excretion rate (ug/min): 0.49785074 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098221 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249120,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978048 | GSM1098221 | GSE45159 | 0.239579 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1162 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249120 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978048 |
|
1 | age: 56,tissue: adipose tissue,log10 body mass index: 1.490049526,log10 basal metabolic rate (kcal): 1504,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.977929407,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.289010918,plasma free fatty acids under the curve ogtt (mmol/l * min): 31.05,fat mass (%): 25,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.04028972,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 405,log10 homair (insulin resistance index based on homa): 0.602927713,log10 homais (insulin secretion index based on homa): 2.244992866,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.83943405,insgenin (insulinogenic index): 1.951013539,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.756400263,log10 matsuda insulin sensitivity index: 0.360849371,muscle mass (%): 40.4,lg10 serum c-reactive protein (mg/l): 0.244771761,lg10 plasma adiponectin (mg/l): 0.740362689,ogtt fasting plasma free fatty acid (mmol/l): 0.56,ogtt 30 min plasma free fatty acid (mmol/l): 0.34,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5.4,ogtt 30 min plasma glucose (mmol/l): 9,ogtt 120 min plasma glucose (mmol/l): 9.6,log10 il1 receptor antagonist (pg/ml): 2.578536067,log10 il1 beta (pg/ml): -0.283996656,log10 ogtt fasting plasma insulin (mu/l): 1.222716471,ogtt 30 min plasma insulin (mu/l): 1.846955325,ogtt 120 min plasma insulin (mu/l): 2.194791758,log10 ogtt fasting plasma proinsulin (pm/l): 1.103803721,ogtt 30 min plasma proinsulin (pm/l): 1.307496038,ogtt 120 min plasma proinsulin (pm/l): 1.750508395,log10 bioimpedance: Resistance: 2.669316881,log10 bioimpedance (reactance): 1.633468456,waist to hip ratio: 1.014150943,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.431363764,log10 creatinine (umol/l): 1.785329835,log10 total cholesterol (mmol/l): 0.725911632,log10 ldl cholesterol (mmol/l): 0.549003262,log10 hdl cholesterol (mmol/l): 0.093421685,log10 total triglycerides (mmol/l): 0.204119983,log10 serum apoa1 (g/l): 0.093421685,log10 serum apob (g/l): 0.045322979,log10 urinary albumin excretion rate (ug/min): 0.768391413 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098222 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249121,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978049 | GSM1098222 | GSE45159 | 0.314603 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1165 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249121 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978049 |
|
1 | age: 56,tissue: adipose tissue,log10 body mass index: 1.319423937,log10 basal metabolic rate (kcal): 1483,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.898000295,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.710734607,plasma free fatty acids under the curve ogtt (mmol/l * min): 13.5,fat mass (%): 14.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.533329732,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 129,log10 homair (insulin resistance index based on homa): -0.076410618,log10 homais (insulin secretion index based on homa): 1.665111737,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.101918834,insgenin (insulinogenic index): 1.598267002,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 3.999174056,log10 matsuda insulin sensitivity index: 1.146953948,muscle mass (%): 47.4,lg10 serum c-reactive protein (mg/l): -0.003050752,lg10 plasma adiponectin (mg/l): 0.740362689,ogtt fasting plasma free fatty acid (mmol/l): 0.24,ogtt 30 min plasma free fatty acid (mmol/l): 0.15,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.1,ogtt 30 min plasma glucose (mmol/l): 7.4,ogtt 120 min plasma glucose (mmol/l): 4.9,log10 il1 receptor antagonist (pg/ml): 2.157758886,log10 il1 beta (pg/ml): -0.920818754,log10 ogtt fasting plasma insulin (mu/l): 0.568201724,ogtt 30 min plasma insulin (mu/l): 1.276461804,ogtt 120 min plasma insulin (mu/l): 1.309630167,log10 ogtt fasting plasma proinsulin (pm/l): 1,ogtt 30 min plasma proinsulin (pm/l): 1.11058971,ogtt 120 min plasma proinsulin (pm/l): 1.348304863,log10 bioimpedance: Resistance: 2.748188027,log10 bioimpedance (reactance): 1.73239376,waist to hip ratio: 0.928961749,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.431363764,log10 creatinine (umol/l): 1.806179974,log10 total cholesterol (mmol/l): 0.704150517,log10 ldl cholesterol (mmol/l): 0.511883361,log10 hdl cholesterol (mmol/l): 0.181843588,log10 total triglycerides (mmol/l): -0.180456064,log10 serum apoa1 (g/l): 0.117271296,log10 serum apob (g/l): -0.080921908,log10 urinary albumin excretion rate (ug/min): 0.783903579 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098223 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249122,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978050 | GSM1098223 | GSE45159 | 0.257102 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1167 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249122 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978050 |
|
1 | age: 54,tissue: adipose tissue,log10 body mass index: 1.465941054,log10 basal metabolic rate (kcal): 1624,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.149075129,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.507046139,plasma free fatty acids under the curve ogtt (mmol/l * min): 21.15,fat mass (%): 27.6,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.946906274,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 267,log10 homair (insulin resistance index based on homa): 0.174156759,log10 homais (insulin secretion index based on homa): 1.651278014,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.386730765,insgenin (insulinogenic index): 1.703430064,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.30815874,log10 matsuda insulin sensitivity index: 0.818178344,muscle mass (%): 40.1,lg10 serum c-reactive protein (mg/l): -0.232844134,lg10 plasma adiponectin (mg/l): 0.755874856,ogtt fasting plasma free fatty acid (mmol/l): 0.36,ogtt 30 min plasma free fatty acid (mmol/l): 0.24,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 6,ogtt 30 min plasma glucose (mmol/l): 9.1,ogtt 120 min plasma glucose (mmol/l): 7.8,log10 il1 receptor antagonist (pg/ml): 2.398356731,log10 il1 beta (pg/ml): 0.100370545,log10 ogtt fasting plasma insulin (mu/l): 0.748188027,ogtt 30 min plasma insulin (mu/l): 1.501059262,ogtt 120 min plasma insulin (mu/l): 1.663700925,log10 ogtt fasting plasma proinsulin (pm/l): 1.123851641,ogtt 30 min plasma proinsulin (pm/l): 1.367355921,ogtt 120 min plasma proinsulin (pm/l): 1.674861141,log10 bioimpedance: Resistance: 2.619093331,log10 bioimpedance (reactance): 1.633468456,waist to hip ratio: 0.957746479,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.204119983,log10 creatinine (umol/l): 2.004321374,log10 total cholesterol (mmol/l): 0.592176757,log10 ldl cholesterol (mmol/l): 0.357934847,log10 hdl cholesterol (mmol/l): 0.037426498,log10 total triglycerides (mmol/l): 0,log10 serum apoa1 (g/l): 0.004321374,log10 serum apob (g/l): -0.214670165,log10 urinary albumin excretion rate (ug/min): 0.90045523 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098224 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249123,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978051 | GSM1098224 | GSE45159 | 0.166311 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1180 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249123 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978051 |
|
1 | age: 51,tissue: adipose tissue,log10 body mass index: 1.378213836,log10 basal metabolic rate (kcal): 1510,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.339395984,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.423859499,plasma free fatty acids under the curve ogtt (mmol/l * min): 20.25,fat mass (%): 18.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.632086413,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 145.5,log10 homair (insulin resistance index based on homa): 0.57333584,log10 homais (insulin secretion index based on homa): 2.215400993,log10 insulin area under the curve (ogtt) (pmol/l * min): 5.206804296,insgenin (insulinogenic index): 2.870571102,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 5.175395831,log10 matsuda insulin sensitivity index: 0.282185572,muscle mass (%): 45.9,lg10 serum c-reactive protein (mg/l): 0.529173603,lg10 plasma adiponectin (mg/l): 0.662757832,ogtt fasting plasma free fatty acid (mmol/l): 0.35,ogtt 30 min plasma free fatty acid (mmol/l): 0.22,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 5.4,ogtt 30 min plasma glucose (mmol/l): 8.2,ogtt 120 min plasma glucose (mmol/l): 4.9,log10 il1 receptor antagonist (pg/ml): 2.484641445,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 1.193124598,ogtt 30 min plasma insulin (mu/l): 2.558708571,ogtt 120 min plasma insulin (mu/l): 2.035029282,log10 ogtt fasting plasma proinsulin (pm/l): 1.103803721,ogtt 30 min plasma proinsulin (pm/l): 1.759667845,ogtt 120 min plasma proinsulin (pm/l): 1.808885867,log10 bioimpedance: Resistance: 2.73479983,log10 bioimpedance (reactance): 1.770852012,waist to hip ratio: 1.016042781,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.477121255,log10 creatinine (umol/l): 1.959041392,log10 total cholesterol (mmol/l): 0.744292983,log10 ldl cholesterol (mmol/l): 0.394451681,log10 hdl cholesterol (mmol/l): 0.029383778,log10 total triglycerides (mmol/l): 0.758911892,log10 serum apoa1 (g/l): 0.220108088,log10 serum apob (g/l): 0.235528447,log10 urinary albumin excretion rate (ug/min): 0.95248423 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098225 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249124,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978052 | GSM1098225 | GSE45159 | 0.200507 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1223 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249124 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978052 |
|
1 | age: 55,tissue: adipose tissue,log10 body mass index: 1.475868926,log10 basal metabolic rate (kcal): 1738,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 5.971589741,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.51279523,plasma free fatty acids under the curve ogtt (mmol/l * min): 18.6,fat mass (%): 22.9,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.35645197,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 67.5,log10 homair (insulin resistance index based on homa): -0.360956442,log10 homais (insulin secretion index based on homa): 1.455931956,log10 insulin area under the curve (ogtt) (pmol/l * min): 3.990072335,insgenin (insulinogenic index): 1.922206277,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 3.920853496,log10 matsuda insulin sensitivity index: 1.390450291,muscle mass (%): 43.3,lg10 serum c-reactive protein (mg/l): 0.682325619,lg10 plasma adiponectin (mg/l): 1.187520721,ogtt fasting plasma free fatty acid (mmol/l): 0.2,ogtt 30 min plasma free fatty acid (mmol/l): 0.2,ogtt 120 min plasma free fatty acid (mmol/l): 0.08,ogtt fasting plasma glucose (mmol/l): 4.9,ogtt 30 min plasma glucose (mmol/l): 6.4,ogtt 120 min plasma glucose (mmol/l): 4.4,log10 il1 receptor antagonist (pg/ml): 2.091209565,log10 il1 beta (pg/ml): -0.602059991,log10 ogtt fasting plasma insulin (mu/l): 0.301029996,ogtt 30 min plasma insulin (mu/l): 1.359835482,ogtt 120 min plasma insulin (mu/l): 0.698970004,log10 ogtt fasting plasma proinsulin (pm/l): 0.924279286,ogtt 30 min plasma proinsulin (pm/l): 1.100370545,ogtt 120 min plasma proinsulin (pm/l): 1.149219113,log10 bioimpedance: Resistance: 2.62324929,log10 bioimpedance (reactance): 1.62324929,waist to hip ratio: 0.930555556,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.041392685,log10 creatinine (umol/l): 2.049218023,log10 total cholesterol (mmol/l): 0.692846919,log10 ldl cholesterol (mmol/l): 0.450249108,log10 hdl cholesterol (mmol/l): 0.247973266,log10 total triglycerides (mmol/l): -0.119186408,log10 serum apoa1 (g/l): 0.152288344,log10 serum apob (g/l): -0.102372909,log10 urinary albumin excretion rate (ug/min): 0.752552832 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098226 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249125,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978053 | GSM1098226 | GSE45159 | 0.26757 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1228 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249125 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978053 |
|
1 | age: 55,tissue: adipose tissue,log10 body mass index: 1.446063944,log10 basal metabolic rate (kcal): 1828,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.68421978,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.031315588,plasma free fatty acids under the curve ogtt (mmol/l * min): 11.25,fat mass (%): 19,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.401946124,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 16.5,log10 homair (insulin resistance index based on homa): 0.187520721,log10 homais (insulin secretion index based on homa): 1.799340549,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.571032996,insgenin (insulinogenic index): 2.51243325,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.514627432,log10 matsuda insulin sensitivity index: 0.826593247,muscle mass (%): 47,lg10 serum c-reactive protein (mg/l): 0.35545152,lg10 plasma adiponectin (mg/l): 0.819543936,ogtt fasting plasma free fatty acid (mmol/l): 0.16,ogtt 30 min plasma free fatty acid (mmol/l): 0.08,ogtt 120 min plasma free fatty acid (mmol/l): 0.09,ogtt fasting plasma glucose (mmol/l): 5.5,ogtt 30 min plasma glucose (mmol/l): 7.2,ogtt 120 min plasma glucose (mmol/l): 3.6,log10 il1 receptor antagonist (pg/ml): 2.047664195,log10 il1 beta (pg/ml): -0.522878745,log10 ogtt fasting plasma insulin (mu/l): 0.799340549,ogtt 30 min plasma insulin (mu/l): 1.99343623,ogtt 120 min plasma insulin (mu/l): 0.653212514,log10 ogtt fasting plasma proinsulin (pm/l): 1.08278537,ogtt 30 min plasma proinsulin (pm/l): 1.357934847,ogtt 120 min plasma proinsulin (pm/l): 1.133538908,log10 bioimpedance: Resistance: 2.592176757,log10 bioimpedance (reactance): 1.62324929,waist to hip ratio: 0.888888889,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.322219295,log10 creatinine (umol/l): 1.86332286,log10 total cholesterol (mmol/l): 0.665580991,log10 ldl cholesterol (mmol/l): 0.450249108,log10 hdl cholesterol (mmol/l): 0.204119983,log10 total triglycerides (mmol/l): -0.086186148,log10 serum apoa1 (g/l): 0.158362492,log10 serum apob (g/l): -0.086186148,log10 urinary albumin excretion rate (ug/min): 1.164264052 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098227 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249126,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978054 | GSM1098227 | GSE45159 | 0.221683 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1247 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249126 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978054 |
|
1 | age: 56,tissue: adipose tissue,log10 body mass index: 1.517639221,log10 basal metabolic rate (kcal): 1710,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.526495272,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.167338599,plasma free fatty acids under the curve ogtt (mmol/l * min): 29.55,fat mass (%): 26.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.949097156,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 280.5,log10 homair (insulin resistance index based on homa): 0.683487317,log10 homais (insulin secretion index based on homa): 2.185636577,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.937282125,insgenin (insulinogenic index): 2.171726454,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.865133598,log10 matsuda insulin sensitivity index: 0.281999031,muscle mass (%): 39.9,lg10 serum c-reactive protein (mg/l): -0.209714836,lg10 plasma adiponectin (mg/l): 0.86923172,ogtt fasting plasma free fatty acid (mmol/l): 0.46,ogtt 30 min plasma free fatty acid (mmol/l): 0.34,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5.9,ogtt 30 min plasma glucose (mmol/l): 8.7,ogtt 120 min plasma glucose (mmol/l): 8.4,log10 il1 receptor antagonist (pg/ml): 2.211200662,log10 il1 beta (pg/ml): -0.619788758,log10 ogtt fasting plasma insulin (mu/l): 1.264817823,ogtt 30 min plasma insulin (mu/l): 1.942999593,ogtt 120 min plasma insulin (mu/l): 2.2955671,log10 ogtt fasting plasma proinsulin (pm/l): 1.46834733,ogtt 30 min plasma proinsulin (pm/l): 1.706717782,ogtt 120 min plasma proinsulin (pm/l): 1.980457892,log10 bioimpedance: Resistance: 2.62324929,log10 bioimpedance (reactance): 1.568201724,waist to hip ratio: 1.018181818,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.681241237,log10 creatinine (umol/l): 1.903089987,log10 total cholesterol (mmol/l): 0.630427875,log10 ldl cholesterol (mmol/l): 0.382017043,log10 hdl cholesterol (mmol/l): 0.190331698,log10 total triglycerides (mmol/l): 0.08278537,log10 serum apoa1 (g/l): 0.184691431,log10 serum apob (g/l): -0.113509275,log10 urinary albumin excretion rate (ug/min): 0.798602876 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098228 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249127,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978055 | GSM1098228 | GSE45159 | 0.467875 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1263 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249127 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978055 |
|
1 | age: 53,tissue: adipose tissue,log10 body mass index: 1.441288134,log10 basal metabolic rate (kcal): 1833,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.171115448,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.602931318,plasma free fatty acids under the curve ogtt (mmol/l * min): 17.4,fat mass (%): 21.9,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.430452552,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 42,log10 homair (insulin resistance index based on homa): 0.104487111,log10 homais (insulin secretion index based on homa): 1.746552264,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.779213971,insgenin (insulinogenic index): 2.629965318,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.750747461,log10 matsuda insulin sensitivity index: 0.76782338,muscle mass (%): 46.6,lg10 serum c-reactive protein (mg/l): 0.124830149,lg10 plasma adiponectin (mg/l): 0.832508913,ogtt fasting plasma free fatty acid (mmol/l): 0.34,ogtt 30 min plasma free fatty acid (mmol/l): 0.16,ogtt 120 min plasma free fatty acid (mmol/l): 0.06,ogtt fasting plasma glucose (mmol/l): 5.4,ogtt 30 min plasma glucose (mmol/l): 7.6,ogtt 120 min plasma glucose (mmol/l): 3.4,log10 il1 receptor antagonist (pg/ml): 2.067554377,log10 il1 beta (pg/ml): -0.657577319,log10 ogtt fasting plasma insulin (mu/l): 0.72427587,ogtt 30 min plasma insulin (mu/l): 2.20871002,ogtt 120 min plasma insulin (mu/l): 0.73239376,log10 ogtt fasting plasma proinsulin (pm/l): 0.924279286,ogtt 30 min plasma proinsulin (pm/l): 1.589949601,ogtt 120 min plasma proinsulin (pm/l): 1.298853076,log10 bioimpedance: Resistance: 2.662757832,log10 bioimpedance (reactance): 1.763427994,waist to hip ratio: 0.954545455,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.322219295,log10 creatinine (umol/l): 2,log10 total cholesterol (mmol/l): 0.814913181,log10 ldl cholesterol (mmol/l): 0.652246341,log10 hdl cholesterol (mmol/l): 0.149219113,log10 total triglycerides (mmol/l): 0.26245109,log10 serum apoa1 (g/l): 0.245512668,log10 serum apob (g/l): 0.146128036,log10 urinary albumin excretion rate (ug/min): 0.304490528 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098229 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249128,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978056 | GSM1098229 | GSE45159 | 0.25875 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1264 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249128 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978056 |
|
1 | age: 56,tissue: adipose tissue,log10 body mass index: 1.41701389,log10 basal metabolic rate (kcal): 1670,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.656291109,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.800841523,plasma free fatty acids under the curve ogtt (mmol/l * min): 12.6,fat mass (%): 18.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.811374694,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 202.5,log10 homair (insulin resistance index based on homa): 0.151608165,log10 homais (insulin secretion index based on homa): 1.679664849,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.23482088,insgenin (insulinogenic index): 1.577236408,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.120968565,log10 matsuda insulin sensitivity index: 0.951756747,muscle mass (%): 47.3,lg10 serum c-reactive protein (mg/l): -0.54515514,lg10 plasma adiponectin (mg/l): 0.832508913,ogtt fasting plasma free fatty acid (mmol/l): 0.31,ogtt 30 min plasma free fatty acid (mmol/l): 0.11,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.8,ogtt 30 min plasma glucose (mmol/l): 11.2,ogtt 120 min plasma glucose (mmol/l): 3.1,log10 il1 receptor antagonist (pg/ml): 2.313761796,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.740362689,ogtt 30 min plasma insulin (mu/l): 1.596597096,ogtt 120 min plasma insulin (mu/l): 0.959041392,log10 ogtt fasting plasma proinsulin (pm/l): 0.880813592,ogtt 30 min plasma proinsulin (pm/l): 1.170261715,ogtt 120 min plasma proinsulin (pm/l): 1.257678575,log10 bioimpedance: Resistance: 2.645422269,log10 bioimpedance (reactance): 1.69019608,waist to hip ratio: 1,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.230448921,log10 creatinine (umol/l): 1.86923172,log10 total cholesterol (mmol/l): 0.691965103,log10 ldl cholesterol (mmol/l): 0.471291711,log10 hdl cholesterol (mmol/l): 0.222716471,log10 total triglycerides (mmol/l): -0.107905397,log10 serum apoa1 (g/l): 0.195899652,log10 serum apob (g/l): -0.060480747,log10 urinary albumin excretion rate (ug/min): 0.551754873 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098230 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249129,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978057 | GSM1098230 | GSE45159 | 0.07069 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1303 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249129 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978057 |
|
1 | age: 54,tissue: adipose tissue,log10 body mass index: 1.373741634,log10 basal metabolic rate (kcal): 1582,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.359654801,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.416505697,plasma free fatty acids under the curve ogtt (mmol/l * min): 29.1,fat mass (%): 14.9,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.742309436,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 256.5,log10 homair (insulin resistance index based on homa): -0.08501079,log10 homais (insulin secretion index based on homa): 1.693140461,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.295281141,insgenin (insulinogenic index): 1.782950133,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.23230984,log10 matsuda insulin sensitivity index: 1.046350387,muscle mass (%): 48,lg10 serum c-reactive protein (mg/l): -0.554395797,lg10 plasma adiponectin (mg/l): 0.72427587,ogtt fasting plasma free fatty acid (mmol/l): 0.66,ogtt 30 min plasma free fatty acid (mmol/l): 0.29,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 5,ogtt 30 min plasma glucose (mmol/l): 8.6,ogtt 120 min plasma glucose (mmol/l): 5.9,log10 il1 receptor antagonist (pg/ml): 2.167346878,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.568201724,ogtt 30 min plasma insulin (mu/l): 1.603144373,ogtt 120 min plasma insulin (mu/l): 1.264817823,log10 ogtt fasting plasma proinsulin (pm/l): 0.880813592,ogtt 30 min plasma proinsulin (pm/l): 1.307496038,ogtt 120 min plasma proinsulin (pm/l): 1.426511261,log10 bioimpedance: Resistance: 2.661812686,log10 bioimpedance (reactance): 1.662757832,waist to hip ratio: 0.955555556,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.662757832,log10 creatinine (umol/l): 1.949390007,log10 total cholesterol (mmol/l): 0.6599162,log10 ldl cholesterol (mmol/l): 0.354108439,log10 hdl cholesterol (mmol/l): 0.334453751,log10 total triglycerides (mmol/l): -0.214670165,log10 serum apoa1 (g/l): 0.227886705,log10 serum apob (g/l): -0.187086643,log10 urinary albumin excretion rate (ug/min): 0.454106891 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098231 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249130,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978058 | GSM1098231 | GSE45159 | 0.2848 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1343 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249130 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978058 |
|
1 | age: 51,tissue: adipose tissue,log10 body mass index: 1.396434654,log10 basal metabolic rate (kcal): 1503,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.553885977,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.619779709,plasma free fatty acids under the curve ogtt (mmol/l * min): 34.05,fat mass (%): 18.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.842350343,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 186,log10 homair (insulin resistance index based on homa): 0.114388554,log10 homais (insulin secretion index based on homa): 1.567297885,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.374363358,insgenin (insulinogenic index): 1.813128834,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.305845582,log10 matsuda insulin sensitivity index: 0.87703081,muscle mass (%): 46.1,lg10 serum c-reactive protein (mg/l): 0.550350672,lg10 plasma adiponectin (mg/l): 0.556302501,ogtt fasting plasma free fatty acid (mmol/l): 0.39,ogtt 30 min plasma free fatty acid (mmol/l): 0.41,ogtt 120 min plasma free fatty acid (mmol/l): 0.08,ogtt fasting plasma glucose (mmol/l): 6.1,ogtt 30 min plasma glucose (mmol/l): 9.2,ogtt 120 min plasma glucose (mmol/l): 6.1,log10 il1 receptor antagonist (pg/ml): 2.317917154,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.681241237,ogtt 30 min plasma insulin (mu/l): 1.584331224,ogtt 120 min plasma insulin (mu/l): 1.542825427,log10 ogtt fasting plasma proinsulin (pm/l): 1.053078443,ogtt 30 min plasma proinsulin (pm/l): 1.257678575,ogtt 120 min plasma proinsulin (pm/l): 1.615950052,log10 bioimpedance: Resistance: 2.696356389,log10 bioimpedance (reactance): 1.72427587,waist to hip ratio: 1.027322404,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.51851394,log10 creatinine (umol/l): 1.903089987,log10 total cholesterol (mmol/l): 0.726727209,log10 ldl cholesterol (mmol/l): 0.561101384,log10 hdl cholesterol (mmol/l): 0.086359831,log10 total triglycerides (mmol/l): -0.036212173,log10 serum apoa1 (g/l): 0.11058971,log10 serum apob (g/l): 0.004321374,log10 urinary albumin excretion rate (ug/min): 0.86923172 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098232 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249131,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978059 | GSM1098232 | GSE45159 | 0.226614 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1353 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249131 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978059 |
|
1 | age: 55,tissue: adipose tissue,log10 body mass index: 1.466297045,log10 basal metabolic rate (kcal): 1691,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.392120527,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.738230244,plasma free fatty acids under the curve ogtt (mmol/l * min): 23.7,fat mass (%): 22.6,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.940313597,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 226.5,log10 homair (insulin resistance index based on homa): 0.605520523,log10 homais (insulin secretion index based on homa): 2.012234456,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.529545843,insgenin (insulinogenic index): 1.779235632,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.370716589,log10 matsuda insulin sensitivity index: 0.532221588,muscle mass (%): 45,lg10 serum c-reactive protein (mg/l): 0.301029996,lg10 plasma adiponectin (mg/l): 0.612783857,ogtt fasting plasma free fatty acid (mmol/l): 0.42,ogtt 30 min plasma free fatty acid (mmol/l): 0.23,ogtt 120 min plasma free fatty acid (mmol/l): 0.08,ogtt fasting plasma glucose (mmol/l): 6.3,ogtt 30 min plasma glucose (mmol/l): 10.3,ogtt 120 min plasma glucose (mmol/l): 6,log10 il1 receptor antagonist (pg/ml): 2.60148417,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 1.158362492,ogtt 30 min plasma insulin (mu/l): 1.736396502,ogtt 120 min plasma insulin (mu/l): 1.680335513,log10 ogtt fasting plasma proinsulin (pm/l): 1.152288344,ogtt 30 min plasma proinsulin (pm/l): 1.318063335,ogtt 120 min plasma proinsulin (pm/l): 1.51851394,log10 bioimpedance: Resistance: 2.651278014,log10 bioimpedance (reactance): 1.72427587,waist to hip ratio: 1.02,log10 serum bilirubin (umol/l): NA,log10 serum alanine aminotransfrase (u/l): 1.579783597,log10 creatinine (umol/l): 1.939519253,log10 total cholesterol (mmol/l): 0.749736316,log10 ldl cholesterol (mmol/l): 0.640481437,log10 hdl cholesterol (mmol/l): -0.036212173,log10 total triglycerides (mmol/l): 0.309630167,log10 serum apoa1 (g/l): 0.071882007,log10 serum apob (g/l): 0.130333768,log10 urinary albumin excretion rate (ug/min): 0.712884519 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098233 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249132,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978060 | GSM1098233 | GSE45159 | 0.184536 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1366 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249132 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978060 |
|
1 | age: 56,tissue: adipose tissue,log10 body mass index: 1.4863247,log10 basal metabolic rate (kcal): 1636,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.748807692,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.144046278,plasma free fatty acids under the curve ogtt (mmol/l * min): 28.35,fat mass (%): 22.7,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.703903573,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 150,log10 homair (insulin resistance index based on homa): 0.385963571,log10 homais (insulin secretion index based on homa): 1.940878548,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.608804064,insgenin (insulinogenic index): 2.191768133,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.527810282,log10 matsuda insulin sensitivity index: 0.668479802,muscle mass (%): 42.2,lg10 serum c-reactive protein (mg/l): -0.160521953,lg10 plasma adiponectin (mg/l): 0.698970004,ogtt fasting plasma free fatty acid (mmol/l): 0.45,ogtt 30 min plasma free fatty acid (mmol/l): 0.3,ogtt 120 min plasma free fatty acid (mmol/l): 0.08,ogtt fasting plasma glucose (mmol/l): 5.7,ogtt 30 min plasma glucose (mmol/l): 9.4,ogtt 120 min plasma glucose (mmol/l): 4.1,log10 il1 receptor antagonist (pg/ml): 2.395169075,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.982271233,ogtt 30 min plasma insulin (mu/l): 2.02325246,ogtt 120 min plasma insulin (mu/l): 0.819543936,log10 ogtt fasting plasma proinsulin (pm/l): 1.086359831,ogtt 30 min plasma proinsulin (pm/l): 1.645422269,ogtt 120 min plasma proinsulin (pm/l): 1.403120521,log10 bioimpedance: Resistance: 2.609594409,log10 bioimpedance (reactance): 1.568201724,waist to hip ratio: 1.028571429,log10 serum bilirubin (umol/l): 1.544068044,log10 serum alanine aminotransfrase (u/l): 1.681241237,log10 creatinine (umol/l): 1.84509804,log10 total cholesterol (mmol/l): 0.655138435,log10 ldl cholesterol (mmol/l): 0.480006943,log10 hdl cholesterol (mmol/l): 0.056904851,log10 total triglycerides (mmol/l): 0.164352856,log10 serum apoa1 (g/l): 0.068185862,log10 serum apob (g/l): 0.012837225,log10 urinary albumin excretion rate (ug/min): 0.934498451 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098234 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249133,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978061 | GSM1098234 | GSE45159 | 0.358195 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1452 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249133 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978061 |
|
1 | age: 59,tissue: adipose tissue,log10 body mass index: 1.38474035,log10 basal metabolic rate (kcal): 1576,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.278526307,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.251888771,plasma free fatty acids under the curve ogtt (mmol/l * min): 15.45,fat mass (%): 12.7,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.582141982,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 58.5,log10 homair (insulin resistance index based on homa): 0.218010043,log10 homais (insulin secretion index based on homa): 1.720159303,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.389449613,insgenin (insulinogenic index): 2.086359831,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.300595484,log10 matsuda insulin sensitivity index: 0.871543768,muscle mass (%): 49.2,lg10 serum c-reactive protein (mg/l): -0.368556231,lg10 plasma adiponectin (mg/l): 0.763427994,ogtt fasting plasma free fatty acid (mmol/l): 0.41,ogtt 30 min plasma free fatty acid (mmol/l): 0.14,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.9,ogtt 30 min plasma glucose (mmol/l): 8.6,ogtt 120 min plasma glucose (mmol/l): 3.6,log10 il1 receptor antagonist (pg/ml): 2.20199762,log10 il1 beta (pg/ml): 0.799340549,log10 ogtt fasting plasma insulin (mu/l): 0.799340549,ogtt 30 min plasma insulin (mu/l): 1.786751422,ogtt 120 min plasma insulin (mu/l): 0.851258349,log10 ogtt fasting plasma proinsulin (pm/l): 0.929418926,ogtt 30 min plasma proinsulin (pm/l): 1.392696953,ogtt 120 min plasma proinsulin (pm/l): 1.488550717,log10 bioimpedance: Resistance: 2.609594409,log10 bioimpedance (reactance): 1.602059991,waist to hip ratio: 0.896907216,log10 serum bilirubin (umol/l): 1.079181246,log10 serum alanine aminotransfrase (u/l): 1.176091259,log10 creatinine (umol/l): 1.963787827,log10 total cholesterol (mmol/l): 0.750508395,log10 ldl cholesterol (mmol/l): 0.563481085,log10 hdl cholesterol (mmol/l): 0.173186268,log10 total triglycerides (mmol/l): 0.037426498,log10 serum apoa1 (g/l): 0.136720567,log10 serum apob (g/l): 0.053078443,log10 urinary albumin excretion rate (ug/min): 1.152118399 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098235 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249134,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978062 | GSM1098235 | GSE45159 | 0.015028 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1483 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249134 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978062 |
|
1 | age: 60,tissue: adipose tissue,log10 body mass index: 1.428052757,log10 basal metabolic rate (kcal): 1622,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.425060246,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.600699475,plasma free fatty acids under the curve ogtt (mmol/l * min): 15.3,fat mass (%): 21.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.839991071,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 256.5,log10 homair (insulin resistance index based on homa): -0.067751784,log10 homais (insulin secretion index based on homa): 1.544068044,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.570402822,insgenin (insulinogenic index): 1.939519253,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.539928788,log10 matsuda insulin sensitivity index: 0.876235596,muscle mass (%): 44.8,lg10 serum c-reactive protein (mg/l): 0.60075515,lg10 plasma adiponectin (mg/l): 0.380211242,ogtt fasting plasma free fatty acid (mmol/l): 0.17,ogtt 30 min plasma free fatty acid (mmol/l): 0.19,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.5,ogtt 30 min plasma glucose (mmol/l): 9.1,ogtt 120 min plasma glucose (mmol/l): 6.4,log10 il1 receptor antagonist (pg/ml): 2.250810204,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.544068044,ogtt 30 min plasma insulin (mu/l): 1.745855195,ogtt 120 min plasma insulin (mu/l): 1.794488047,log10 ogtt fasting plasma proinsulin (pm/l): 1.017033339,ogtt 30 min plasma proinsulin (pm/l): 1.264817823,ogtt 120 min plasma proinsulin (pm/l): 1.648360011,log10 bioimpedance: Resistance: 2.69019608,log10 bioimpedance (reactance): 1.73239376,waist to hip ratio: 1.030612245,log10 serum bilirubin (umol/l): 1.041392685,log10 serum alanine aminotransfrase (u/l): 1.414973348,log10 creatinine (umol/l): 1.924279286,log10 total cholesterol (mmol/l): 0.631443769,log10 ldl cholesterol (mmol/l): 0.440909082,log10 hdl cholesterol (mmol/l): -0.050609993,log10 total triglycerides (mmol/l): -0.060480747,log10 serum apoa1 (g/l): 0.029383778,log10 serum apob (g/l): -0.040958608,log10 urinary albumin excretion rate (ug/min): 0.756156957 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098236 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249135,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978063 | GSM1098236 | GSE45159 | 0.189036 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1504 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249135 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978063 |
|
1 | age: 62,tissue: adipose tissue,log10 body mass index: 1.407947934,log10 basal metabolic rate (kcal): 1420,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.496686471,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.459195841,plasma free fatty acids under the curve ogtt (mmol/l * min): 11.1,fat mass (%): 35,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.491853096,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 84,log10 homair (insulin resistance index based on homa): 0.025305865,log10 homais (insulin secretion index based on homa): 1.698970004,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.288696261,insgenin (insulinogenic index): 1.827070891,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.209515015,log10 matsuda insulin sensitivity index: 1.016750866,muscle mass (%): 39.7,lg10 serum c-reactive protein (mg/l): 0.301029996,lg10 plasma adiponectin (mg/l): 1.004321374,ogtt fasting plasma free fatty acid (mmol/l): 0.2,ogtt 30 min plasma free fatty acid (mmol/l): 0.12,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.3,ogtt 30 min plasma glucose (mmol/l): 7.9,ogtt 120 min plasma glucose (mmol/l): 3.7,log10 il1 receptor antagonist (pg/ml): 2.247899651,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.653212514,ogtt 30 min plasma insulin (mu/l): 1.526339277,ogtt 120 min plasma insulin (mu/l): 1.409933123,log10 ogtt fasting plasma proinsulin (pm/l): 0.919078092,ogtt 30 min plasma proinsulin (pm/l): 1.130333768,ogtt 120 min plasma proinsulin (pm/l): 1.46686762,log10 bioimpedance: Resistance: 2.758154622,log10 bioimpedance (reactance): 1.785329835,waist to hip ratio: 0.989473684,log10 serum bilirubin (umol/l): 1.146128036,log10 serum alanine aminotransfrase (u/l): 1.447158031,log10 creatinine (umol/l): 1.903089987,log10 total cholesterol (mmol/l): 0.791690649,log10 ldl cholesterol (mmol/l): 0.574031268,log10 hdl cholesterol (mmol/l): 0.243038049,log10 total triglycerides (mmol/l): 0.049218023,log10 serum apoa1 (g/l): 0.214843848,log10 serum apob (g/l): 0.053078443,log10 urinary albumin excretion rate (ug/min): 0.562041415 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098237 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249136,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978064 | GSM1098237 | GSE45159 | 0.177973 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1516 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249136 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978064 |
|
1 | age: 52,tissue: adipose tissue,log10 body mass index: 1.465206508,log10 basal metabolic rate (kcal): 1845,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.655647312,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.065821111,plasma free fatty acids under the curve ogtt (mmol/l * min): 12.3,fat mass (%): 24.9,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.747353829,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 103.5,log10 homair (insulin resistance index based on homa): 0.232487866,log10 homais (insulin secretion index based on homa): 1.639201799,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.391675953,insgenin (insulinogenic index): 2.064457989,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.306425028,log10 matsuda insulin sensitivity index: 0.816468919,muscle mass (%): 46.4,lg10 serum c-reactive protein (mg/l): 0.112939976,lg10 plasma adiponectin (mg/l): 0.505149978,ogtt fasting plasma free fatty acid (mmol/l): 0.18,ogtt 30 min plasma free fatty acid (mmol/l): 0.13,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 6.3,ogtt 30 min plasma glucose (mmol/l): 8.1,ogtt 120 min plasma glucose (mmol/l): 6.2,log10 il1 receptor antagonist (pg/ml): 2.138302698,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.785329835,ogtt 30 min plasma insulin (mu/l): 1.611723308,ogtt 120 min plasma insulin (mu/l): 1.540329475,log10 ogtt fasting plasma proinsulin (pm/l): 0.929418926,ogtt 30 min plasma proinsulin (pm/l): 1.201397124,ogtt 120 min plasma proinsulin (pm/l): 1.515873844,log10 bioimpedance: Resistance: 2.695481676,log10 bioimpedance (reactance): 1.875061263,waist to hip ratio: 1.01,log10 serum bilirubin (umol/l): 1.204119983,log10 serum alanine aminotransfrase (u/l): 1.491361694,log10 creatinine (umol/l): 1.875061263,log10 total cholesterol (mmol/l): 0.6599162,log10 ldl cholesterol (mmol/l): 0.488550717,log10 hdl cholesterol (mmol/l): 0.053078443,log10 total triglycerides (mmol/l): 0.025305865,log10 serum apoa1 (g/l): 0.037426498,log10 serum apob (g/l): -0.045757491,log10 urinary albumin excretion rate (ug/min): 0.77003336 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098238 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249137,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978065 | GSM1098238 | GSE45159 | 0.150794 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1518 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249137 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978065 |
|
1 | age: 65,tissue: adipose tissue,log10 body mass index: 1.326961696,log10 basal metabolic rate (kcal): 1199,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.421557173,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 5.877749085,plasma free fatty acids under the curve ogtt (mmol/l * min): 16.95,fat mass (%): 29.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.08081753,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 363,log10 homair (insulin resistance index based on homa): 0.158362492,log10 homais (insulin secretion index based on homa): 1.635483747,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.713305698,insgenin (insulinogenic index): 2.022062253,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.679337031,log10 matsuda insulin sensitivity index: 0.688709281,muscle mass (%): 47.8,lg10 serum c-reactive protein (mg/l): 0.112939976,lg10 plasma adiponectin (mg/l): 1.113943352,ogtt fasting plasma free fatty acid (mmol/l): 0.36,ogtt 30 min plasma free fatty acid (mmol/l): 0.17,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 6,ogtt 30 min plasma glucose (mmol/l): 13.1,ogtt 120 min plasma glucose (mmol/l): 4.6,log10 il1 receptor antagonist (pg/ml): 2.183696809,log10 il1 beta (pg/ml): -0.13667714,log10 ogtt fasting plasma insulin (mu/l): 0.73239376,ogtt 30 min plasma insulin (mu/l): 2.113609151,ogtt 120 min plasma insulin (mu/l): 1.214843848,log10 ogtt fasting plasma proinsulin (pm/l): 0.995635195,ogtt 30 min plasma proinsulin (pm/l): 1.46686762,ogtt 120 min plasma proinsulin (pm/l): 1.411619706,log10 bioimpedance: Resistance: 2.797959644,log10 bioimpedance (reactance): 1.806179974,waist to hip ratio: 0.903225806,log10 serum bilirubin (umol/l): 1.079181246,log10 serum alanine aminotransfrase (u/l): 1.431363764,log10 creatinine (umol/l): 1.919078092,log10 total cholesterol (mmol/l): 0.767155866,log10 ldl cholesterol (mmol/l): 0.507855872,log10 hdl cholesterol (mmol/l): 0.29666519,log10 total triglycerides (mmol/l): 0.267171728,log10 serum apoa1 (g/l): 0.152288344,log10 serum apob (g/l): -0.070581074,log10 urinary albumin excretion rate (ug/min): 0.773742131 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098239 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249138,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978066 | GSM1098239 | GSE45159 | 0.219178 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1574 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249138 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978066 |
|
1 | age: 55,tissue: adipose tissue,log10 body mass index: 1.367376327,log10 basal metabolic rate (kcal): 1545,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.617168971,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.647337353,plasma free fatty acids under the curve ogtt (mmol/l * min): 15.6,fat mass (%): 19.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.849405101,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 214.5,log10 homair (insulin resistance index based on homa): 0.12623967,log10 homais (insulin secretion index based on homa): 1.62838893,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.369549802,insgenin (insulinogenic index): 1.800631173,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.295479133,log10 matsuda insulin sensitivity index: 0.873622119,muscle mass (%): 45.8,lg10 serum c-reactive protein (mg/l): 0.725012725,lg10 plasma adiponectin (mg/l): 1.049218023,ogtt fasting plasma free fatty acid (mmol/l): 0.38,ogtt 30 min plasma free fatty acid (mmol/l): 0.15,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.9,ogtt 30 min plasma glucose (mmol/l): 9.1,ogtt 120 min plasma glucose (mmol/l): 6.4,log10 il1 receptor antagonist (pg/ml): 2.21285319,log10 il1 beta (pg/ml): -0.431798276,log10 ogtt fasting plasma insulin (mu/l): 0.707570176,ogtt 30 min plasma insulin (mu/l): 1.588831726,ogtt 120 min plasma insulin (mu/l): 1.522444234,log10 ogtt fasting plasma proinsulin (pm/l): 1.127104798,ogtt 30 min plasma proinsulin (pm/l): 1.359835482,ogtt 120 min plasma proinsulin (pm/l): 1.646403726,log10 bioimpedance: Resistance: 2.752048448,log10 bioimpedance (reactance): 1.785329835,waist to hip ratio: 0.909090909,log10 serum bilirubin (umol/l): 1.113943352,log10 serum alanine aminotransfrase (u/l): 1.255272505,log10 creatinine (umol/l): 1.880813592,log10 total cholesterol (mmol/l): 0.671172843,log10 ldl cholesterol (mmol/l): 0.338456494,log10 hdl cholesterol (mmol/l): 0.390935107,log10 total triglycerides (mmol/l): -0.207608311,log10 serum apoa1 (g/l): 0.222716471,log10 serum apob (g/l): -0.207608311,log10 urinary albumin excretion rate (ug/min): 0.879860146 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098240 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249139,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978067 | GSM1098240 | GSE45159 | 0.300427 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1599 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249139 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978067 |
|
1 | age: 60,tissue: adipose tissue,log10 body mass index: 1.375963588,log10 basal metabolic rate (kcal): 1791,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.291799537,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.502500249,plasma free fatty acids under the curve ogtt (mmol/l * min): 17.4,fat mass (%): 19.6,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.796850795,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 181.5,log10 homair (insulin resistance index based on homa): 0.108865574,log10 homais (insulin secretion index based on homa): 1.611014834,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.432375938,insgenin (insulinogenic index): 1.899573413,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.371714203,log10 matsuda insulin sensitivity index: 0.860605238,muscle mass (%): 47,lg10 serum c-reactive protein (mg/l): 0.116939647,lg10 plasma adiponectin (mg/l): 0.963787827,ogtt fasting plasma free fatty acid (mmol/l): 0.38,ogtt 30 min plasma free fatty acid (mmol/l): 0.18,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.9,ogtt 30 min plasma glucose (mmol/l): 9,ogtt 120 min plasma glucose (mmol/l): 5.8,log10 il1 receptor antagonist (pg/ml): 2.498834149,log10 il1 beta (pg/ml): -0.397940009,log10 ogtt fasting plasma insulin (mu/l): 0.69019608,ogtt 30 min plasma insulin (mu/l): 1.661812686,ogtt 120 min plasma insulin (mu/l): 1.572871602,log10 ogtt fasting plasma proinsulin (pm/l): 1.033423755,ogtt 30 min plasma proinsulin (pm/l): 1.376576957,ogtt 120 min plasma proinsulin (pm/l): 1.655138435,log10 bioimpedance: Resistance: 2.717670503,log10 bioimpedance (reactance): 1.770852012,waist to hip ratio: 0.912621359,log10 serum bilirubin (umol/l): 1.591064607,log10 serum alanine aminotransfrase (u/l): 1.322219295,log10 creatinine (umol/l): 1.959041392,log10 total cholesterol (mmol/l): 0.692846919,log10 ldl cholesterol (mmol/l): 0.411619706,log10 hdl cholesterol (mmol/l): 0.209515015,log10 total triglycerides (mmol/l): 0.096910013,log10 serum apoa1 (g/l): 0.161368002,log10 serum apob (g/l): -0.086186148,log10 urinary albumin excretion rate (ug/min): 0.61196828 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098241 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249140,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978068 | GSM1098241 | GSE45159 | 0.16865 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1619 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249140 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978068 |
|
1 | age: 56,tissue: adipose tissue,log10 body mass index: 1.467642944,log10 basal metabolic rate (kcal): 1592,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.526495272,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.905597511,plasma free fatty acids under the curve ogtt (mmol/l * min): 26.85,fat mass (%): 23.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.31458324,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 493.5,log10 homair (insulin resistance index based on homa): 0.159700843,log10 homais (insulin secretion index based on homa): 1.522878745,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.267054336,insgenin (insulinogenic index): 1.365147495,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.173040508,log10 matsuda insulin sensitivity index: 0.829928213,muscle mass (%): 41.7,lg10 serum c-reactive protein (mg/l): 0.815112658,lg10 plasma adiponectin (mg/l): 0.838849091,ogtt fasting plasma free fatty acid (mmol/l): 0.46,ogtt 30 min plasma free fatty acid (mmol/l): 0.31,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 6.5,ogtt 30 min plasma glucose (mmol/l): 10.9,ogtt 120 min plasma glucose (mmol/l): 11.6,log10 il1 receptor antagonist (pg/ml): 2.649305645,log10 il1 beta (pg/ml): -0.602059991,log10 ogtt fasting plasma insulin (mu/l): 0.698970004,ogtt 30 min plasma insulin (mu/l): 1.342422681,ogtt 120 min plasma insulin (mu/l): 1.574031268,log10 ogtt fasting plasma proinsulin (pm/l): 1.037426498,ogtt 30 min plasma proinsulin (pm/l): 1.176091259,ogtt 120 min plasma proinsulin (pm/l): 1.511883361,log10 bioimpedance: Resistance: 2.654176542,log10 bioimpedance (reactance): 1.612783857,waist to hip ratio: 0.944444444,log10 serum bilirubin (umol/l): 1.322219295,log10 serum alanine aminotransfrase (u/l): 1.785329835,log10 creatinine (umol/l): 1.903089987,log10 total cholesterol (mmol/l): 0.656098202,log10 ldl cholesterol (mmol/l): 0.376576957,log10 hdl cholesterol (mmol/l): 0.318063335,log10 total triglycerides (mmol/l): -0.167491087,log10 serum apoa1 (g/l): 0.139879086,log10 serum apob (g/l): -0.187086643,log10 urinary albumin excretion rate (ug/min): 0.919731658 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098242 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249141,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978069 | GSM1098242 | GSE45159 | 0.060876 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1653 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249141 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978069 |
|
1 | age: 54,tissue: adipose tissue,log10 body mass index: 1.449085526,log10 basal metabolic rate (kcal): 1501,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.537146159,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.676510436,plasma free fatty acids under the curve ogtt (mmol/l * min): 19.95,fat mass (%): 21.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.909143047,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 253.5,log10 homair (insulin resistance index based on homa): 0.281992354,log10 homais (insulin secretion index based on homa): 1.784141614,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.513310843,insgenin (insulinogenic index): 1.959810464,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.43697321,log10 matsuda insulin sensitivity index: 0.71490465,muscle mass (%): 44.7,lg10 serum c-reactive protein (mg/l): -0.351639989,lg10 plasma adiponectin (mg/l): 0.633468456,ogtt fasting plasma free fatty acid (mmol/l): 0.34,ogtt 30 min plasma free fatty acid (mmol/l): 0.21,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5.9,ogtt 30 min plasma glucose (mmol/l): 9,ogtt 120 min plasma glucose (mmol/l): 7.4,log10 il1 receptor antagonist (pg/ml): 2.380807986,log10 il1 beta (pg/ml): -0.585026652,log10 ogtt fasting plasma insulin (mu/l): 0.86332286,ogtt 30 min plasma insulin (mu/l): 1.7355989,ogtt 120 min plasma insulin (mu/l): 1.660865478,log10 ogtt fasting plasma proinsulin (pm/l): 1.240549248,ogtt 30 min plasma proinsulin (pm/l): 1.671172843,ogtt 120 min plasma proinsulin (pm/l): 1.826074803,log10 bioimpedance: Resistance: 2.675778342,log10 bioimpedance (reactance): 1.73239376,waist to hip ratio: 0.92,log10 serum bilirubin (umol/l): 1.041392685,log10 serum alanine aminotransfrase (u/l): 1.491361694,log10 creatinine (umol/l): 1.903089987,log10 total cholesterol (mmol/l): 0.688419822,log10 ldl cholesterol (mmol/l): 0.45484486,log10 hdl cholesterol (mmol/l): 0.193124598,log10 total triglycerides (mmol/l): 0.167317335,log10 serum apoa1 (g/l): 0.176091259,log10 serum apob (g/l): -0.004364805,log10 urinary albumin excretion rate (ug/min): 1.032184683 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098243 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249142,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978070 | GSM1098243 | GSE45159 | 0.187188 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1666 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249142 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978070 |
|
1 | age: 52,tissue: adipose tissue,log10 body mass index: 1.307654584,log10 basal metabolic rate (kcal): 1606,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.22740466,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.013549143,plasma free fatty acids under the curve ogtt (mmol/l * min): 12.9,fat mass (%): 13.9,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.346513733,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 39,log10 homair (insulin resistance index based on homa): -0.167491087,log10 homais (insulin secretion index based on homa): 1.574031268,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.332276832,insgenin (insulinogenic index): 2.242307528,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.286276786,log10 matsuda insulin sensitivity index: 1.12951172,muscle mass (%): 69.9,lg10 serum c-reactive protein (mg/l): -0.853871964,lg10 plasma adiponectin (mg/l): 0.681241237,ogtt fasting plasma free fatty acid (mmol/l): 0.21,ogtt 30 min plasma free fatty acid (mmol/l): 0.14,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.1,ogtt 30 min plasma glucose (mmol/l): 6.8,ogtt 120 min plasma glucose (mmol/l): 3.7,log10 il1 receptor antagonist (pg/ml): 2.313360951,log10 il1 beta (pg/ml): 0,log10 ogtt fasting plasma insulin (mu/l): 0.477121255,ogtt 30 min plasma insulin (mu/l): 1.720159303,ogtt 120 min plasma insulin (mu/l): 0.934498451,log10 ogtt fasting plasma proinsulin (pm/l): 1.012837225,ogtt 30 min plasma proinsulin (pm/l): 1.383815366,ogtt 120 min plasma proinsulin (pm/l): 1.356025857,log10 bioimpedance: Resistance: 2.668385917,log10 bioimpedance (reactance): 1.763427994,waist to hip ratio: 0.844444444,log10 serum bilirubin (umol/l): 1,log10 serum alanine aminotransfrase (u/l): 1.380211242,log10 creatinine (umol/l): 1.986771734,log10 total cholesterol (mmol/l): 0.764176132,log10 ldl cholesterol (mmol/l): 0.564666064,log10 hdl cholesterol (mmol/l): 0.23299611,log10 total triglycerides (mmol/l): -0.13667714,log10 serum apoa1 (g/l): 0.089905111,log10 serum apob (g/l): -0.091514981,log10 urinary albumin excretion rate (ug/min): 0.693567076 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098244 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249143,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978071 | GSM1098244 | GSE45159 | 0.17386 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1674 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249143 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978071 |
|
1 | age: 58,tissue: adipose tissue,log10 body mass index: 1.346038272,log10 basal metabolic rate (kcal): 1587,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.475108188,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.414990444,plasma free fatty acids under the curve ogtt (mmol/l * min): 10.2,fat mass (%): 13.5,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.900112063,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 175.5,log10 homair (insulin resistance index based on homa): 0.419772231,log10 homais (insulin secretion index based on homa): 1.782950133,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.505692507,insgenin (insulinogenic index): 1.938365747,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.406335758,log10 matsuda insulin sensitivity index: 0.657467551,muscle mass (%): 48.8,lg10 serum c-reactive protein (mg/l): -0.503070352,lg10 plasma adiponectin (mg/l): 0.832508913,ogtt fasting plasma free fatty acid (mmol/l): 0.23,ogtt 30 min plasma free fatty acid (mmol/l): 0.09,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 6.5,ogtt 30 min plasma glucose (mmol/l): 10.4,ogtt 120 min plasma glucose (mmol/l): 5.2,log10 il1 receptor antagonist (pg/ml): 2.158995377,log10 il1 beta (pg/ml): -0.537602002,log10 ogtt fasting plasma insulin (mu/l): 0.959041392,ogtt 30 min plasma insulin (mu/l): 1.8162413,ogtt 120 min plasma insulin (mu/l): 1.451786436,log10 ogtt fasting plasma proinsulin (pm/l): 1.451786436,ogtt 30 min plasma proinsulin (pm/l): 1.596597096,ogtt 120 min plasma proinsulin (pm/l): 1.638489257,log10 bioimpedance: Resistance: 2.679427897,log10 bioimpedance (reactance): 1.672097858,waist to hip ratio: 0.894736842,log10 serum bilirubin (umol/l): 0.84509804,log10 serum alanine aminotransfrase (u/l): 1.230448921,log10 creatinine (umol/l): 1.913813852,log10 total cholesterol (mmol/l): 0.835690571,log10 ldl cholesterol (mmol/l): 0.669316881,log10 hdl cholesterol (mmol/l): 0.198657087,log10 total triglycerides (mmol/l): 0.093421685,log10 serum apoa1 (g/l): 0.187520721,log10 serum apob (g/l): 0.10720997,log10 urinary albumin excretion rate (ug/min): 1.180890142 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098245 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249144,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978072 | GSM1098245 | GSE45159 | 0.13427 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1678 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249144 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978072 |
|
1 | age: 58,tissue: adipose tissue,log10 body mass index: 1.321147221,log10 basal metabolic rate (kcal): 1595,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.66866566,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.508170937,plasma free fatty acids under the curve ogtt (mmol/l * min): 21.75,fat mass (%): 16.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.512740463,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 58.5,log10 homair (insulin resistance index based on homa): -0.189021143,log10 homais (insulin secretion index based on homa): 1.393784049,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.068185862,insgenin (insulinogenic index): 1.892094603,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 3.992465148,log10 matsuda insulin sensitivity index: 1.229341053,muscle mass (%): 49.6,lg10 serum c-reactive protein (mg/l): -0.853871964,lg10 plasma adiponectin (mg/l): 1.133538908,ogtt fasting plasma free fatty acid (mmol/l): 0.52,ogtt 30 min plasma free fatty acid (mmol/l): 0.21,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 7.1,ogtt 120 min plasma glucose (mmol/l): 4.9,log10 il1 receptor antagonist (pg/ml): 2.056790548,log10 il1 beta (pg/ml): -0.013228266,log10 ogtt fasting plasma insulin (mu/l): 0.414973348,ogtt 30 min plasma insulin (mu/l): 1.344392274,ogtt 120 min plasma insulin (mu/l): 1.113943352,log10 ogtt fasting plasma proinsulin (pm/l): 0.69019608,ogtt 30 min plasma proinsulin (pm/l): 1.130333768,ogtt 120 min plasma proinsulin (pm/l): 1.414973348,log10 bioimpedance: Resistance: 2.779596491,log10 bioimpedance (reactance): 1.875061263,waist to hip ratio: 0.867346939,log10 serum bilirubin (umol/l): 1.146128036,log10 serum alanine aminotransfrase (u/l): 1.176091259,log10 creatinine (umol/l): 1.86332286,log10 total cholesterol (mmol/l): 0.762678564,log10 ldl cholesterol (mmol/l): 0.445604203,log10 hdl cholesterol (mmol/l): 0.369215857,log10 total triglycerides (mmol/l): -0.15490196,log10 serum apoa1 (g/l): 0.235528447,log10 serum apob (g/l): -0.096910013,log10 urinary albumin excretion rate (ug/min): 1.248323645 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098246 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249145,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978073 | GSM1098246 | GSE45159 | 0.176752 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1702 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249145 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978073 |
|
1 | age: 52,tissue: adipose tissue,log10 body mass index: 1.512530195,log10 basal metabolic rate (kcal): 1749,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.723610629,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.392910911,plasma free fatty acids under the curve ogtt (mmol/l * min): 23.7,fat mass (%): 27.1,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.719388821,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 171,log10 homair (insulin resistance index based on homa): 0.299095496,log10 homais (insulin secretion index based on homa): 1.881900688,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.556736578,insgenin (insulinogenic index): 2.096107498,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.481098497,log10 matsuda insulin sensitivity index: 0.734518713,muscle mass (%): 40.2,lg10 serum c-reactive protein (mg/l): 0.435685138,lg10 plasma adiponectin (mg/l): 0.531478917,ogtt fasting plasma free fatty acid (mmol/l): 0.39,ogtt 30 min plasma free fatty acid (mmol/l): 0.26,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 9.5,ogtt 120 min plasma glucose (mmol/l): 4.2,log10 il1 receptor antagonist (pg/ml): 2.627550188,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.903089987,ogtt 30 min plasma insulin (mu/l): 1.949877704,ogtt 120 min plasma insulin (mu/l): 1.079181246,log10 ogtt fasting plasma proinsulin (pm/l): 1.096910013,ogtt 30 min plasma proinsulin (pm/l): 1.606381365,ogtt 120 min plasma proinsulin (pm/l): 1.612783857,log10 bioimpedance: Resistance: 2.650307523,log10 bioimpedance (reactance): 1.633468456,waist to hip ratio: 1.018181818,log10 serum bilirubin (umol/l): 1.301029996,log10 serum alanine aminotransfrase (u/l): 1.681241237,log10 creatinine (umol/l): 1.857332496,log10 total cholesterol (mmol/l): 0.741939078,log10 ldl cholesterol (mmol/l): 0.51851394,log10 hdl cholesterol (mmol/l): 0.004321374,log10 total triglycerides (mmol/l): 0.338456494,log10 serum apoa1 (g/l): 0.096910013,log10 serum apob (g/l): 0.08278537,log10 urinary albumin excretion rate (ug/min): 0.857162551 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098247 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249146,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978074 | GSM1098247 | GSE45159 | 0.175511 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1722 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249146 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978074 |
|
1 | age: 59,tissue: adipose tissue,log10 body mass index: 1.428578921,log10 basal metabolic rate (kcal): 1734,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.260527536,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.5061315,plasma free fatty acids under the curve ogtt (mmol/l * min): 10.8,fat mass (%): 18.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.791976821,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 190.5,log10 homair (insulin resistance index based on homa): 0.230789411,log10 homais (insulin secretion index based on homa): 1.758846095,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.498186452,insgenin (insulinogenic index): 2.051308997,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.427145161,log10 matsuda insulin sensitivity index: 0.785091732,muscle mass (%): 47,lg10 serum c-reactive protein (mg/l): 0.380211242,lg10 plasma adiponectin (mg/l): 0.770852012,ogtt fasting plasma free fatty acid (mmol/l): 0.15,ogtt 30 min plasma free fatty acid (mmol/l): 0.12,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.8,ogtt 30 min plasma glucose (mmol/l): 9.5,ogtt 120 min plasma glucose (mmol/l): 5.1,log10 il1 receptor antagonist (pg/ml): 2.429929836,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.819543936,ogtt 30 min plasma insulin (mu/l): 1.880813592,ogtt 120 min plasma insulin (mu/l): 1.117271296,log10 ogtt fasting plasma proinsulin (pm/l): 0.857332496,ogtt 30 min plasma proinsulin (pm/l): 1.338456494,ogtt 120 min plasma proinsulin (pm/l): 1.260071388,log10 bioimpedance: Resistance: 2.617000341,log10 bioimpedance (reactance): 1.643452676,waist to hip ratio: 0.931372549,log10 serum bilirubin (umol/l): 1.146128036,log10 serum alanine aminotransfrase (u/l): 1.505149978,log10 creatinine (umol/l): 1.968482949,log10 total cholesterol (mmol/l): 0.758911892,log10 ldl cholesterol (mmol/l): 0.56937391,log10 hdl cholesterol (mmol/l): 0.217483944,log10 total triglycerides (mmol/l): 0.164352856,log10 serum apoa1 (g/l): 0.10720997,log10 serum apob (g/l): -0.026872146,log10 urinary albumin excretion rate (ug/min): 1.05270635 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098248 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249147,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978075 | GSM1098248 | GSE45159 | 0.204179 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1725 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249147 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978075 |
|
1 | age: 56,tissue: adipose tissue,log10 body mass index: 1.520671054,log10 basal metabolic rate (kcal): 1381,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 7.120312714,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.3156401,plasma free fatty acids under the curve ogtt (mmol/l * min): 24,fat mass (%): 26,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.25915477,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 397.5,log10 homair (insulin resistance index based on homa): 0.808885867,log10 homais (insulin secretion index based on homa): 2.091770373,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.988630293,insgenin (insulinogenic index): 1.875728895,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.915378727,log10 matsuda insulin sensitivity index: 0.149691359,muscle mass (%): 40,lg10 serum c-reactive protein (mg/l): -0.076238039,lg10 plasma adiponectin (mg/l): 0.77815125,ogtt fasting plasma free fatty acid (mmol/l): 0.49,ogtt 30 min plasma free fatty acid (mmol/l): 0.24,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 6.9,ogtt 30 min plasma glucose (mmol/l): 12.1,ogtt 120 min plasma glucose (mmol/l): 8.8,log10 il1 receptor antagonist (pg/ml): 2.501251022,log10 il1 beta (pg/ml): 0.697229343,log10 ogtt fasting plasma insulin (mu/l): 1.322219295,ogtt 30 min plasma insulin (mu/l): 1.935003151,ogtt 120 min plasma insulin (mu/l): 2.378397901,log10 ogtt fasting plasma proinsulin (pm/l): 1.503790683,ogtt 30 min plasma proinsulin (pm/l): 1.720159303,ogtt 120 min plasma proinsulin (pm/l): 1.984077034,log10 bioimpedance: Resistance: 2.668385917,log10 bioimpedance (reactance): 1.672097858,waist to hip ratio: 1.113861386,log10 serum bilirubin (umol/l): 1,log10 serum alanine aminotransfrase (u/l): 1.832508913,log10 creatinine (umol/l): 1.748188027,log10 total cholesterol (mmol/l): 0.906873535,log10 ldl cholesterol (mmol/l): 0.72916479,log10 hdl cholesterol (mmol/l): 0.204119983,log10 total triglycerides (mmol/l): 0.269512944,log10 serum apoa1 (g/l): 0.209515015,log10 serum apob (g/l): 0.193124598,log10 urinary albumin excretion rate (ug/min): 0.798521898 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098249 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249148,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978076 | GSM1098249 | GSE45159 | 0.098109 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1757 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249148 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978076 |
|
1 | age: 59,tissue: adipose tissue,log10 body mass index: 1.412912526,log10 basal metabolic rate (kcal): 1613,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.686623353,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.732760914,plasma free fatty acids under the curve ogtt (mmol/l * min): 11.85,fat mass (%): 16.7,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.677719642,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 75,log10 homair (insulin resistance index based on homa): 0.147779347,log10 homais (insulin secretion index based on homa): 1.577236408,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.312938609,insgenin (insulinogenic index): 1.894177554,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.227475343,log10 matsuda insulin sensitivity index: 0.927466773,muscle mass (%): 47.3,lg10 serum c-reactive protein (mg/l): -0.450996738,lg10 plasma adiponectin (mg/l): 0.740362689,ogtt fasting plasma free fatty acid (mmol/l): 0.22,ogtt 30 min plasma free fatty acid (mmol/l): 0.12,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 6.2,ogtt 30 min plasma glucose (mmol/l): 9.4,ogtt 120 min plasma glucose (mmol/l): 3.6,log10 il1 receptor antagonist (pg/ml): 2.17912073,log10 il1 beta (pg/ml): -0.795880017,log10 ogtt fasting plasma insulin (mu/l): 0.707570176,ogtt 30 min plasma insulin (mu/l): 1.671172843,ogtt 120 min plasma insulin (mu/l): 1.075546961,log10 ogtt fasting plasma proinsulin (pm/l): 1.103803721,ogtt 30 min plasma proinsulin (pm/l): 1.537819095,ogtt 120 min plasma proinsulin (pm/l): 1.574031268,log10 bioimpedance: Resistance: 2.62838893,log10 bioimpedance (reactance): 1.643452676,waist to hip ratio: 0.865,log10 serum bilirubin (umol/l): 1,log10 serum alanine aminotransfrase (u/l): 1.301029996,log10 creatinine (umol/l): 1.857332496,log10 total cholesterol (mmol/l): 0.564666064,log10 ldl cholesterol (mmol/l): 0.326335861,log10 hdl cholesterol (mmol/l): -0.004364805,log10 total triglycerides (mmol/l): 0.214843848,log10 serum apoa1 (g/l): 0.089905111,log10 serum apob (g/l): -0.065501549,log10 urinary albumin excretion rate (ug/min): 0.810180579 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098250 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249149,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978077 | GSM1098250 | GSE45159 | 0.218901 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1764 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249149 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978077 |
|
1 | age: 55,tissue: adipose tissue,log10 body mass index: 1.44406498,log10 basal metabolic rate (kcal): 1451,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.68421978,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.801017968,plasma free fatty acids under the curve ogtt (mmol/l * min): 42.15,fat mass (%): 22.1,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.868050854,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 262.5,log10 homair (insulin resistance index based on homa): 0.094975513,log10 homais (insulin secretion index based on homa): 1.677780705,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.189518386,insgenin (insulinogenic index): 1.596920352,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.074487305,log10 matsuda insulin sensitivity index: 0.976146889,muscle mass (%): 43.1,lg10 serum c-reactive protein (mg/l): -0.003488328,lg10 plasma adiponectin (mg/l): 0.826074803,ogtt fasting plasma free fatty acid (mmol/l): 0.57,ogtt 30 min plasma free fatty acid (mmol/l): 0.5,ogtt 120 min plasma free fatty acid (mmol/l): 0.08,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 9,ogtt 120 min plasma glucose (mmol/l): 6.9,log10 il1 receptor antagonist (pg/ml): 2.48207283,log10 il1 beta (pg/ml): -0.420216403,log10 ogtt fasting plasma insulin (mu/l): 0.698970004,ogtt 30 min plasma insulin (mu/l): 1.437750563,ogtt 120 min plasma insulin (mu/l): 1.281033367,log10 ogtt fasting plasma proinsulin (pm/l): 1.149219113,ogtt 30 min plasma proinsulin (pm/l): 1.440909082,ogtt 120 min plasma proinsulin (pm/l): 1.650307523,log10 bioimpedance: Resistance: 2.698100546,log10 bioimpedance (reactance): 1.716003344,waist to hip ratio: 0.95959596,log10 serum bilirubin (umol/l): 1.301029996,log10 serum alanine aminotransfrase (u/l): 1.579783597,log10 creatinine (umol/l): 1.86332286,log10 total cholesterol (mmol/l): 0.887054378,log10 ldl cholesterol (mmol/l): 0.7355989,log10 hdl cholesterol (mmol/l): 0.326335861,log10 total triglycerides (mmol/l): 0.064457989,log10 serum apoa1 (g/l): 0.285557309,log10 serum apob (g/l): 0.164352856,log10 urinary albumin excretion rate (ug/min): 1.313650938 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098251 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249150,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978078 | GSM1098251 | GSE45159 | 0.039329 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1768 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249150 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978078 |
|
1 | age: 54,tissue: adipose tissue,log10 body mass index: 1.388478806,log10 basal metabolic rate (kcal): 1431,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.600779512,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.521616776,plasma free fatty acids under the curve ogtt (mmol/l * min): 25.35,fat mass (%): 18.5,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.811374694,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 238.5,log10 homair (insulin resistance index based on homa): 0.112456041,log10 homais (insulin secretion index based on homa): 1.72427587,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.335898992,insgenin (insulinogenic index): 1.453755036,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.251784177,log10 matsuda insulin sensitivity index: 0.896028713,muscle mass (%): 46.3,lg10 serum c-reactive protein (mg/l): 0.602059991,lg10 plasma adiponectin (mg/l): 0.986771734,ogtt fasting plasma free fatty acid (mmol/l): 0.45,ogtt 30 min plasma free fatty acid (mmol/l): 0.28,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 5.5,ogtt 30 min plasma glucose (mmol/l): 9.7,ogtt 120 min plasma glucose (mmol/l): 5.2,log10 il1 receptor antagonist (pg/ml): 2.282576801,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.72427587,ogtt 30 min plasma insulin (mu/l): 1.401400541,ogtt 120 min plasma insulin (mu/l): 1.652246341,log10 ogtt fasting plasma proinsulin (pm/l): 1.127104798,ogtt 30 min plasma proinsulin (pm/l): 1.328379603,ogtt 120 min plasma proinsulin (pm/l): 1.789580712,log10 bioimpedance: Resistance: 2.728353782,log10 bioimpedance (reactance): 1.785329835,waist to hip ratio: 0.947368421,log10 serum bilirubin (umol/l): 1.176091259,log10 serum alanine aminotransfrase (u/l): 1.414973348,log10 creatinine (umol/l): 1.886490725,log10 total cholesterol (mmol/l): 0.728353782,log10 ldl cholesterol (mmol/l): 0.445604203,log10 hdl cholesterol (mmol/l): 0.359835482,log10 total triglycerides (mmol/l): -0.017728767,log10 serum apoa1 (g/l): 0.267171728,log10 serum apob (g/l): -0.075720714,log10 urinary albumin excretion rate (ug/min): 0.949694882 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098252 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249151,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978079 | GSM1098252 | GSE45159 | 0.276419 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1777 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249151 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978079 |
|
1 | age: 54,tissue: adipose tissue,log10 body mass index: 1.422408922,log10 basal metabolic rate (kcal): 1566,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.666941996,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.852710764,plasma free fatty acids under the curve ogtt (mmol/l * min): 21,fat mass (%): 22.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.73978061,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 147,log10 homair (insulin resistance index based on homa): 0.174544349,log10 homais (insulin secretion index based on homa): 1.67669361,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.627632088,insgenin (insulinogenic index): 1.882443217,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.583448167,log10 matsuda insulin sensitivity index: 0.730670091,muscle mass (%): 44.1,lg10 serum c-reactive protein (mg/l): -0.175223538,lg10 plasma adiponectin (mg/l): 0.633468456,ogtt fasting plasma free fatty acid (mmol/l): 0.3,ogtt 30 min plasma free fatty acid (mmol/l): 0.26,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.9,ogtt 30 min plasma glucose (mmol/l): 9.4,ogtt 120 min plasma glucose (mmol/l): 4.5,log10 il1 receptor antagonist (pg/ml): 2.199837422,log10 il1 beta (pg/ml): -0.408935393,log10 ogtt fasting plasma insulin (mu/l): 0.755874856,ogtt 30 min plasma insulin (mu/l): 1.700703717,ogtt 120 min plasma insulin (mu/l): 1.945960704,log10 ogtt fasting plasma proinsulin (pm/l): 1.1430148,ogtt 30 min plasma proinsulin (pm/l): 1.387389826,ogtt 120 min plasma proinsulin (pm/l): 1.790988475,log10 bioimpedance: Resistance: 2.720985744,log10 bioimpedance (reactance): 1.763427994,waist to hip ratio: 0.953846154,log10 serum bilirubin (umol/l): 1.113943352,log10 serum alanine aminotransfrase (u/l): 1.477121255,log10 creatinine (umol/l): 1.86923172,log10 total cholesterol (mmol/l): 0.802773725,log10 ldl cholesterol (mmol/l): 0.6599162,log10 hdl cholesterol (mmol/l): 0.139879086,log10 total triglycerides (mmol/l): 0.093421685,log10 serum apoa1 (g/l): 0.181843588,log10 serum apob (g/l): 0.120573931,log10 urinary albumin excretion rate (ug/min): 1.111365929 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098253 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249152,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978080 | GSM1098253 | GSE45159 | 0.294805 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1784 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249152 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978080 |
|
1 | age: 57,tissue: adipose tissue,log10 body mass index: 1.489355711,log10 basal metabolic rate (kcal): 1738,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.542253687,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.929550479,plasma free fatty acids under the curve ogtt (mmol/l * min): 36.9,fat mass (%): 22.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.737247343,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 157.5,log10 homair (insulin resistance index based on homa): 0.355728148,log10 homais (insulin secretion index based on homa): 1.883784832,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.835969445,insgenin (insulinogenic index): 2.507855872,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.793846239,log10 matsuda insulin sensitivity index: 0.557825389,muscle mass (%): 44.8,lg10 serum c-reactive protein (mg/l): 0.331427297,lg10 plasma adiponectin (mg/l): 0.69019608,ogtt fasting plasma free fatty acid (mmol/l): 0.65,ogtt 30 min plasma free fatty acid (mmol/l): 0.4,ogtt 120 min plasma free fatty acid (mmol/l): 0.07,ogtt fasting plasma glucose (mmol/l): 5.8,ogtt 30 min plasma glucose (mmol/l): 8.5,ogtt 120 min plasma glucose (mmol/l): 5.7,log10 il1 receptor antagonist (pg/ml): 2.421274791,log10 il1 beta (pg/ml): -0.602059991,log10 ogtt fasting plasma insulin (mu/l): 0.944482672,ogtt 30 min plasma insulin (mu/l): 2.186673867,ogtt 120 min plasma insulin (mu/l): 1.662757832,log10 ogtt fasting plasma proinsulin (pm/l): 1.361727836,ogtt 30 min plasma proinsulin (pm/l): 1.851258349,ogtt 120 min plasma proinsulin (pm/l): 1.973127854,log10 bioimpedance: Resistance: 2.597695186,log10 bioimpedance (reactance): 1.643452676,waist to hip ratio: 0.981308411,log10 serum bilirubin (umol/l): 1.602059991,log10 serum alanine aminotransfrase (u/l): 1.763427994,log10 creatinine (umol/l): 1.897627091,log10 total cholesterol (mmol/l): 0.686636269,log10 ldl cholesterol (mmol/l): 0.509202522,log10 hdl cholesterol (mmol/l): -0.036212173,log10 total triglycerides (mmol/l): 0.352182518,log10 serum apoa1 (g/l): 0.056904851,log10 serum apob (g/l): 0.071882007,log10 urinary albumin excretion rate (ug/min): 1.021189299 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098254 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249153,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978081 | GSM1098254 | GSE45159 | 0.121957 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1840 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249153 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978081 |
|
1 | age: 60,tissue: adipose tissue,log10 body mass index: 1.542755717,log10 basal metabolic rate (kcal): 1465,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.385885025,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.76156832,plasma free fatty acids under the curve ogtt (mmol/l * min): 55.05,fat mass (%): 24.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.44604941,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 531,log10 homair (insulin resistance index based on homa): 0.660486016,log10 homais (insulin secretion index based on homa): 1.888164309,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.60260252,insgenin (insulinogenic index): 1.646263654,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.473545359,log10 matsuda insulin sensitivity index: 0.398433097,muscle mass (%): 40.2,lg10 serum c-reactive protein (mg/l): 0.08350262,lg10 plasma adiponectin (mg/l): 1.041392685,ogtt fasting plasma free fatty acid (mmol/l): 0.89,ogtt 30 min plasma free fatty acid (mmol/l): 0.62,ogtt 120 min plasma free fatty acid (mmol/l): 0.1,ogtt fasting plasma glucose (mmol/l): 7.2,ogtt 30 min plasma glucose (mmol/l): 13.5,ogtt 120 min plasma glucose (mmol/l): 10.6,log10 il1 receptor antagonist (pg/ml): 2.280601132,log10 il1 beta (pg/ml): 0.322219295,log10 ogtt fasting plasma insulin (mu/l): 1.155336037,ogtt 30 min plasma insulin (mu/l): 1.783903579,ogtt 120 min plasma insulin (mu/l): 1.795880017,log10 ogtt fasting plasma proinsulin (pm/l): 1.409933123,ogtt 30 min plasma proinsulin (pm/l): 1.627365857,ogtt 120 min plasma proinsulin (pm/l): 1.879669206,log10 bioimpedance: Resistance: 2.571708832,log10 bioimpedance (reactance): 1.505149978,waist to hip ratio: 1.072727273,log10 serum bilirubin (umol/l): 1.230448921,log10 serum alanine aminotransfrase (u/l): 1.322219295,log10 creatinine (umol/l): 1.934498451,log10 total cholesterol (mmol/l): 0.853698212,log10 ldl cholesterol (mmol/l): 0.667452953,log10 hdl cholesterol (mmol/l): 0.100370545,log10 total triglycerides (mmol/l): 0.72916479,log10 serum apoa1 (g/l): 0.240549248,log10 serum apob (g/l): 0.301029996,log10 urinary albumin excretion rate (ug/min): 0.605614946 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098255 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249154,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978082 | GSM1098255 | GSE45159 | 0.054484 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1841 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249154 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978082 |
|
1 | age: 59,tissue: adipose tissue,log10 body mass index: 1.319337614,log10 basal metabolic rate (kcal): 1470,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.511211783,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.244708617,plasma free fatty acids under the curve ogtt (mmol/l * min): 10.2,fat mass (%): 12.1,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.579315938,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 57,log10 homair (insulin resistance index based on homa): -0.201119265,log10 homais (insulin secretion index based on homa): 1.301029996,log10 insulin area under the curve (ogtt) (pmol/l * min): 3.976670881,insgenin (insulinogenic index): 1.93815569,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 3.889245661,log10 matsuda insulin sensitivity index: 1.268699938,muscle mass (%): 49.5,lg10 serum c-reactive protein (mg/l): -0.410050399,lg10 plasma adiponectin (mg/l): 0.875061263,ogtt fasting plasma free fatty acid (mmol/l): 0.27,ogtt 30 min plasma free fatty acid (mmol/l): 0.08,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.9,ogtt 30 min plasma glucose (mmol/l): 7,ogtt 120 min plasma glucose (mmol/l): 5.7,log10 il1 receptor antagonist (pg/ml): 2.240748878,log10 il1 beta (pg/ml): -0.48148606,log10 ogtt fasting plasma insulin (mu/l): 0.380211242,ogtt 30 min plasma insulin (mu/l): 1.26245109,ogtt 120 min plasma insulin (mu/l): 0.995635195,log10 ogtt fasting plasma proinsulin (pm/l): 0.944482672,ogtt 30 min plasma proinsulin (pm/l): 1.206825876,ogtt 120 min plasma proinsulin (pm/l): 1.264817823,log10 bioimpedance: Resistance: 2.720159303,log10 bioimpedance (reactance): 1.73239376,waist to hip ratio: 0.827956989,log10 serum bilirubin (umol/l): 1.230448921,log10 serum alanine aminotransfrase (u/l): 1,log10 creatinine (umol/l): 1.903089987,log10 total cholesterol (mmol/l): 0.725911632,log10 ldl cholesterol (mmol/l): 0.481442629,log10 hdl cholesterol (mmol/l): 0.278753601,log10 total triglycerides (mmol/l): 0.004321374,log10 serum apoa1 (g/l): 0.252853031,log10 serum apob (g/l): -0.031517051,log10 urinary albumin excretion rate (ug/min): 0.801914447 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098256 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249155,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978083 | GSM1098256 | GSE45159 | 0.217262 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1885 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249155 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978083 |
|
1 | age: 57,tissue: adipose tissue,log10 body mass index: 1.409849348,log10 basal metabolic rate (kcal): 1657,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.521311649,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.680077586,plasma free fatty acids under the curve ogtt (mmol/l * min): 30.45,fat mass (%): 20.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.00281502,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 342,log10 homair (insulin resistance index based on homa): 0.29578694,log10 homais (insulin secretion index based on homa): 1.850701918,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.776410589,insgenin (insulinogenic index): 2.137451498,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.733550337,log10 matsuda insulin sensitivity index: 0.569131479,muscle mass (%): 46.3,lg10 serum c-reactive protein (mg/l): -0.244125144,lg10 plasma adiponectin (mg/l): 0.51851394,ogtt fasting plasma free fatty acid (mmol/l): 0.51,ogtt 30 min plasma free fatty acid (mmol/l): 0.32,ogtt 120 min plasma free fatty acid (mmol/l): 0.08,ogtt fasting plasma glucose (mmol/l): 5.7,ogtt 30 min plasma glucose (mmol/l): 9.6,ogtt 120 min plasma glucose (mmol/l): 8.1,log10 il1 receptor antagonist (pg/ml): 2.287465805,log10 il1 beta (pg/ml): 0.029383778,log10 ogtt fasting plasma insulin (mu/l): 0.892094603,ogtt 30 min plasma insulin (mu/l): 1.986771734,ogtt 120 min plasma insulin (mu/l): 1.951337519,log10 ogtt fasting plasma proinsulin (pm/l): 1.113943352,ogtt 30 min plasma proinsulin (pm/l): 1.739572344,ogtt 120 min plasma proinsulin (pm/l): 1.960946196,log10 bioimpedance: Resistance: 2.694605199,log10 bioimpedance (reactance): 1.755874856,waist to hip ratio: 0.95049505,log10 serum bilirubin (umol/l): 1.397940009,log10 serum alanine aminotransfrase (u/l): 1.51851394,log10 creatinine (umol/l): 1.903089987,log10 total cholesterol (mmol/l): 0.775974331,log10 ldl cholesterol (mmol/l): 0.562292864,log10 hdl cholesterol (mmol/l): 0.133538908,log10 total triglycerides (mmol/l): 0.586587305,log10 serum apoa1 (g/l): 0.240549248,log10 serum apob (g/l): 0.139879086,log10 urinary albumin excretion rate (ug/min): 0.615978253 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098257 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249156,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978084 | GSM1098257 | GSE45159 | 0.218739 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1891 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249156 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978084 |
|
1 | age: 52,tissue: adipose tissue,log10 body mass index: 1.566823019,log10 basal metabolic rate (kcal): 1768,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.548199059,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.358365399,plasma free fatty acids under the curve ogtt (mmol/l * min): 30.9,fat mass (%): 28.6,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.931476234,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 184.5,log10 homair (insulin resistance index based on homa): 0.480198642,log10 homais (insulin secretion index based on homa): 1.822505527,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.325495139,insgenin (insulinogenic index): 1.752048448,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.138081546,log10 matsuda insulin sensitivity index: 0.703550682,muscle mass (%): 39.4,lg10 serum c-reactive protein (mg/l): 0.849910558,lg10 plasma adiponectin (mg/l): 0.591064607,ogtt fasting plasma free fatty acid (mmol/l): 0.42,ogtt 30 min plasma free fatty acid (mmol/l): 0.38,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 6.6,ogtt 30 min plasma glucose (mmol/l): 10.2,ogtt 120 min plasma glucose (mmol/l): 5.9,log10 il1 receptor antagonist (pg/ml): 2.433609843,log10 il1 beta (pg/ml): -0.30980392,log10 ogtt fasting plasma insulin (mu/l): 1.012837225,ogtt 30 min plasma insulin (mu/l): 1.645422269,ogtt 120 min plasma insulin (mu/l): 1.204119983,log10 ogtt fasting plasma proinsulin (pm/l): 1,ogtt 30 min plasma proinsulin (pm/l): 1.33243846,ogtt 120 min plasma proinsulin (pm/l): 1.53529412,log10 bioimpedance: Resistance: 2.599883072,log10 bioimpedance (reactance): 1.591064607,waist to hip ratio: 1.043103448,log10 serum bilirubin (umol/l): 1.505149978,log10 serum alanine aminotransfrase (u/l): 1.531478917,log10 creatinine (umol/l): 1.903089987,log10 total cholesterol (mmol/l): 0.733999287,log10 ldl cholesterol (mmol/l): 0.597695186,log10 hdl cholesterol (mmol/l): -0.050609993,log10 total triglycerides (mmol/l): 0.28780173,log10 serum apoa1 (g/l): 0.079181246,log10 serum apob (g/l): 0.10720997,log10 urinary albumin excretion rate (ug/min): 1.168082612 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098258 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249157,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978085 | GSM1098258 | GSE45159 | 0.156619 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1892 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249157 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978085 |
|
1 | age: 56,tissue: adipose tissue,log10 body mass index: 1.406315415,log10 basal metabolic rate (kcal): 1643,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.425563154,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.573596607,plasma free fatty acids under the curve ogtt (mmol/l * min): 18,fat mass (%): 18.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.957827561,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 322.5,log10 homair (insulin resistance index based on homa): 0.492915522,log10 homais (insulin secretion index based on homa): 2.075720714,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.628184508,insgenin (insulinogenic index): 2.004216484,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.524785449,log10 matsuda insulin sensitivity index: 0.551520623,muscle mass (%): 47,lg10 serum c-reactive protein (mg/l): -0.467245621,lg10 plasma adiponectin (mg/l): 0.146128036,ogtt fasting plasma free fatty acid (mmol/l): 0.32,ogtt 30 min plasma free fatty acid (mmol/l): 0.19,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 9.7,ogtt 120 min plasma glucose (mmol/l): 7.3,log10 il1 receptor antagonist (pg/ml): 2.205204364,log10 il1 beta (pg/ml): -0.244125144,log10 ogtt fasting plasma insulin (mu/l): 1.096910013,ogtt 30 min plasma insulin (mu/l): 1.911157609,ogtt 120 min plasma insulin (mu/l): 1.648360011,log10 ogtt fasting plasma proinsulin (pm/l): 0.919078092,ogtt 30 min plasma proinsulin (pm/l): 1.133538908,ogtt 120 min plasma proinsulin (pm/l): 1.392696953,log10 bioimpedance: Resistance: 2.662757832,log10 bioimpedance (reactance): 1.698970004,waist to hip ratio: 0.927835052,log10 serum bilirubin (umol/l): 1.113943352,log10 serum alanine aminotransfrase (u/l): 1.322219295,log10 creatinine (umol/l): 1.929418926,log10 total cholesterol (mmol/l): 0.654176542,log10 ldl cholesterol (mmol/l): 0.409933123,log10 hdl cholesterol (mmol/l): 0.056904851,log10 total triglycerides (mmol/l): 0.198657087,log10 serum apoa1 (g/l): 0.100370545,log10 serum apob (g/l): -0.050609993,log10 urinary albumin excretion rate (ug/min): 0.931691785 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098259 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249158,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978086 | GSM1098259 | GSE45159 | 0.641122 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1896 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249158 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978086 |
|
1 | age: 56,tissue: adipose tissue,log10 body mass index: 1.43964122,log10 basal metabolic rate (kcal): 1592,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.46520479,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.635255458,plasma free fatty acids under the curve ogtt (mmol/l * min): 16.5,fat mass (%): 18.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.09671515,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 207,log10 homair (insulin resistance index based on homa): 0.336593137,log10 homais (insulin secretion index based on homa): 1.529509324,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.119783586,insgenin (insulinogenic index): 1.017911589,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 3.925518358,log10 matsuda insulin sensitivity index: 0.840102059,muscle mass (%): 46.1,lg10 serum c-reactive protein (mg/l): 0.079904468,lg10 plasma adiponectin (mg/l): 1.012837225,ogtt fasting plasma free fatty acid (mmol/l): 0.29,ogtt 30 min plasma free fatty acid (mmol/l): 0.18,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 7.4,ogtt 30 min plasma glucose (mmol/l): 13.1,ogtt 120 min plasma glucose (mmol/l): 4.4,log10 il1 receptor antagonist (pg/ml): 2.210425542,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.819543936,ogtt 30 min plasma insulin (mu/l): 1.217483944,ogtt 120 min plasma insulin (mu/l): 1.390935107,log10 ogtt fasting plasma proinsulin (pm/l): 1.245512668,ogtt 30 min plasma proinsulin (pm/l): 1.397940009,ogtt 120 min plasma proinsulin (pm/l): 1.813580989,log10 bioimpedance: Resistance: 2.613841822,log10 bioimpedance (reactance): 1.62324929,waist to hip ratio: 0.96,log10 serum bilirubin (umol/l): 1.176091259,log10 serum alanine aminotransfrase (u/l): 1.230448921,log10 creatinine (umol/l): 1.919078092,log10 total cholesterol (mmol/l): 0.762678564,log10 ldl cholesterol (mmol/l): 0.557507202,log10 hdl cholesterol (mmol/l): 0.176091259,log10 total triglycerides (mmol/l): 0.301029996,log10 serum apoa1 (g/l): 0.217483944,log10 serum apob (g/l): 0.086359831,log10 urinary albumin excretion rate (ug/min): 0.800105826 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098260 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249159,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978087 | GSM1098260 | GSE45159 | 0.268976 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1915 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249159 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978087 |
|
1 | age: 55,tissue: adipose tissue,log10 body mass index: 1.350977817,log10 basal metabolic rate (kcal): 1753,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.75408472,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.916007293,plasma free fatty acids under the curve ogtt (mmol/l * min): 17.4,fat mass (%): 17.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.927037169,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 205.5,log10 homair (insulin resistance index based on homa): -0.027488604,log10 homais (insulin secretion index based on homa): 1.357145938,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.010002974,insgenin (insulinogenic index): 1.474997561,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 3.895256753,log10 matsuda insulin sensitivity index: 1.130449848,muscle mass (%): 47,lg10 serum c-reactive protein (mg/l): -0.077793723,lg10 plasma adiponectin (mg/l): 1.056904851,ogtt fasting plasma free fatty acid (mmol/l): 0.29,ogtt 30 min plasma free fatty acid (mmol/l): 0.18,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 6.4,ogtt 30 min plasma glucose (mmol/l): 10.5,ogtt 120 min plasma glucose (mmol/l): 5.5,log10 il1 receptor antagonist (pg/ml): 1.932270776,log10 il1 beta (pg/ml): -0.853871964,log10 ogtt fasting plasma insulin (mu/l): 0.51851394,ogtt 30 min plasma insulin (mu/l): 1.374748346,ogtt 120 min plasma insulin (mu/l): 0.716003344,log10 ogtt fasting plasma proinsulin (pm/l): 0.826074803,ogtt 30 min plasma proinsulin (pm/l): 1.017033339,ogtt 120 min plasma proinsulin (pm/l): 1.021189299,log10 bioimpedance: Resistance: 2.715167358,log10 bioimpedance (reactance): 1.716003344,waist to hip ratio: 0.94,log10 serum bilirubin (umol/l): 1.113943352,log10 serum alanine aminotransfrase (u/l): 1.602059991,log10 creatinine (umol/l): 1.84509804,log10 total cholesterol (mmol/l): 0.688419822,log10 ldl cholesterol (mmol/l): 0.392696953,log10 hdl cholesterol (mmol/l): 0.367355921,log10 total triglycerides (mmol/l): -0.26760624,log10 serum apoa1 (g/l): 0.252853031,log10 serum apob (g/l): -0.13667714,log10 urinary albumin excretion rate (ug/min): 1.187385025 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098261 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249160,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978088 | GSM1098261 | GSE45159 | 0.177057 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1921 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249160 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978088 |
|
1 | age: 61,tissue: adipose tissue,log10 body mass index: 1.408707506,log10 basal metabolic rate (kcal): 1411,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.74771644,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.710474183,plasma free fatty acids under the curve ogtt (mmol/l * min): 29.55,fat mass (%): 32.6,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.00702727,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 369,log10 homair (insulin resistance index based on homa): 0.452638161,log10 homais (insulin secretion index based on homa): 2.064457989,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.781353197,insgenin (insulinogenic index): 1.945140196,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.716771032,log10 matsuda insulin sensitivity index: 0.480077272,muscle mass (%): 38,lg10 serum c-reactive protein (mg/l): 0.479719235,lg10 plasma adiponectin (mg/l): 0.939519253,ogtt fasting plasma free fatty acid (mmol/l): 0.62,ogtt 30 min plasma free fatty acid (mmol/l): 0.3,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5.5,ogtt 30 min plasma glucose (mmol/l): 10,ogtt 120 min plasma glucose (mmol/l): 7.7,log10 il1 receptor antagonist (pg/ml): 2.230448921,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 1.064457989,ogtt 30 min plasma insulin (mu/l): 1.890421019,ogtt 120 min plasma insulin (mu/l): 2.06595298,log10 ogtt fasting plasma proinsulin (pm/l): 1.245512668,ogtt 30 min plasma proinsulin (pm/l): 1.752048448,ogtt 120 min plasma proinsulin (pm/l): 1.990338855,log10 bioimpedance: Resistance: 2.729974286,log10 bioimpedance (reactance): 1.707570176,waist to hip ratio: 0.949494949,log10 serum bilirubin (umol/l): 1.204119983,log10 serum alanine aminotransfrase (u/l): 1.397940009,log10 creatinine (umol/l): 1.838849091,log10 total cholesterol (mmol/l): 0.872156273,log10 ldl cholesterol (mmol/l): 0.717670503,log10 hdl cholesterol (mmol/l): 0.164352856,log10 total triglycerides (mmol/l): 0.322219295,log10 serum apoa1 (g/l): 0.184691431,log10 serum apob (g/l): 0.195899652,log10 urinary albumin excretion rate (ug/min): 1.061017763 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098262 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249161,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978089 | GSM1098262 | GSE45159 | 0.077092 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1924 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249161 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978089 |
|
1 | age: 59,tissue: adipose tissue,log10 body mass index: 1.437267632,log10 basal metabolic rate (kcal): 1532,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.553362644,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.681414034,plasma free fatty acids under the curve ogtt (mmol/l * min): 28.2,fat mass (%): 21.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.21249639,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 478.5,log10 homair (insulin resistance index based on homa): 0.529259204,log10 homais (insulin secretion index based on homa): 2.031408464,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.914427786,insgenin (insulinogenic index): 2.115438343,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.862298384,log10 matsuda insulin sensitivity index: 0.357558815,muscle mass (%): 44,lg10 serum c-reactive protein (mg/l): -0.107348966,lg10 plasma adiponectin (mg/l): 0.740362689,ogtt fasting plasma free fatty acid (mmol/l): 0.44,ogtt 30 min plasma free fatty acid (mmol/l): 0.33,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 5.9,ogtt 30 min plasma glucose (mmol/l): 11.7,ogtt 120 min plasma glucose (mmol/l): 8.8,log10 il1 receptor antagonist (pg/ml): 2.205826659,log10 il1 beta (pg/ml): -0.769551079,log10 ogtt fasting plasma insulin (mu/l): 1.11058971,ogtt 30 min plasma insulin (mu/l): 2.1430148,ogtt 120 min plasma insulin (mu/l): 2.058805487,log10 ogtt fasting plasma proinsulin (pm/l): 1.382017043,ogtt 30 min plasma proinsulin (pm/l): 1.809559715,ogtt 120 min plasma proinsulin (pm/l): 2.174931594,log10 bioimpedance: Resistance: 2.681241237,log10 bioimpedance (reactance): 1.698970004,waist to hip ratio: 1.005208333,log10 serum bilirubin (umol/l): 1.204119983,log10 serum alanine aminotransfrase (u/l): 1.414973348,log10 creatinine (umol/l): 1.892094603,log10 total cholesterol (mmol/l): 0.840733235,log10 ldl cholesterol (mmol/l): 0.679427897,log10 hdl cholesterol (mmol/l): 0.120573931,log10 total triglycerides (mmol/l): 0.480006943,log10 serum apoa1 (g/l): 0.173186268,log10 serum apob (g/l): 0.195899652,log10 urinary albumin excretion rate (ug/min): 0.600721641 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098263 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249162,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978090 | GSM1098263 | GSE45159 | 0.287799 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1932 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249162 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978090 |
|
1 | age: 58,tissue: adipose tissue,log10 body mass index: 1.424048892,log10 basal metabolic rate (kcal): 1620,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.51621818,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.63545403,plasma free fatty acids under the curve ogtt (mmol/l * min): 5.25,fat mass (%): 19.5,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.292321633,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): -21,log10 homair (insulin resistance index based on homa): 0.128399269,log10 homais (insulin secretion index based on homa): 1.770464422,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.417239121,insgenin (insulinogenic index): 2.864511081,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.344470872,log10 matsuda insulin sensitivity index: 0.927031951,muscle mass (%): 46.5,lg10 serum c-reactive protein (mg/l): 0.216957207,lg10 plasma adiponectin (mg/l): 0.934498451,ogtt fasting plasma free fatty acid (mmol/l): 0.13,ogtt 30 min plasma free fatty acid (mmol/l): 0.04,ogtt 120 min plasma free fatty acid (mmol/l): 0.02,ogtt fasting plasma glucose (mmol/l): 5.4,ogtt 30 min plasma glucose (mmol/l): 5.8,ogtt 120 min plasma glucose (mmol/l): 4.4,log10 il1 receptor antagonist (pg/ml): 2.138618434,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.748188027,ogtt 30 min plasma insulin (mu/l): 1.7355989,ogtt 120 min plasma insulin (mu/l): 1.350248018,log10 ogtt fasting plasma proinsulin (pm/l): 1.086359831,ogtt 30 min plasma proinsulin (pm/l): 1.418301291,ogtt 120 min plasma proinsulin (pm/l): 1.5774918,log10 bioimpedance: Resistance: 2.665580991,log10 bioimpedance (reactance): 1.72427587,waist to hip ratio: 0.92,log10 serum bilirubin (umol/l): 1.230448921,log10 serum alanine aminotransfrase (u/l): 1.041392685,log10 creatinine (umol/l): 1.903089987,log10 total cholesterol (mmol/l): 0.790988475,log10 ldl cholesterol (mmol/l): 0.580924976,log10 hdl cholesterol (mmol/l): 0.303196057,log10 total triglycerides (mmol/l): -0.180456064,log10 serum apoa1 (g/l): 0.198657087,log10 serum apob (g/l): -0.008773924,log10 urinary albumin excretion rate (ug/min): 0.655218496 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098264 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249163,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978091 | GSM1098264 | GSE45159 | 0.387732 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1937 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249163 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978091 |
|
1 | age: 53,tissue: adipose tissue,log10 body mass index: 1.457369054,log10 basal metabolic rate (kcal): 1843,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.328130476,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.816160727,plasma free fatty acids under the curve ogtt (mmol/l * min): 22.65,fat mass (%): 20.5,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.476746204,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 112.5,log10 homair (insulin resistance index based on homa): 0.139179176,log10 homais (insulin secretion index based on homa): 1.917330426,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.678108474,insgenin (insulinogenic index): 2.55590019,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.635393259,log10 matsuda insulin sensitivity index: 0.785164788,muscle mass (%): 45.8,lg10 serum c-reactive protein (mg/l): -0.024568191,lg10 plasma adiponectin (mg/l): 0.908485019,ogtt fasting plasma free fatty acid (mmol/l): 0.32,ogtt 30 min plasma free fatty acid (mmol/l): 0.26,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 5,ogtt 30 min plasma glucose (mmol/l): 6.8,ogtt 120 min plasma glucose (mmol/l): 5.1,log10 il1 receptor antagonist (pg/ml): 2.191730393,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.792391689,ogtt 30 min plasma insulin (mu/l): 2.057285644,ogtt 120 min plasma insulin (mu/l): 1.348304863,log10 ogtt fasting plasma proinsulin (pm/l): 1.146128036,ogtt 30 min plasma proinsulin (pm/l): 1.657055853,ogtt 120 min plasma proinsulin (pm/l): 1.657055853,log10 bioimpedance: Resistance: 2.598790507,log10 bioimpedance (reactance): 1.62324929,waist to hip ratio: 0.961538462,log10 serum bilirubin (umol/l): 1.477121255,log10 serum alanine aminotransfrase (u/l): 1.462397998,log10 creatinine (umol/l): 1.959041392,log10 total cholesterol (mmol/l): 0.835056102,log10 ldl cholesterol (mmol/l): 0.695481676,log10 hdl cholesterol (mmol/l): 0.029383778,log10 total triglycerides (mmol/l): 0.394451681,log10 serum apoa1 (g/l): 0.158362492,log10 serum apob (g/l): 0.184691431,log10 urinary albumin excretion rate (ug/min): 0.839703008 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098265 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249164,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978092 | GSM1098265 | GSE45159 | 0.245199 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1942 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249164 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978092 |
|
1 | age: 57,tissue: adipose tissue,log10 body mass index: 1.415417138,log10 basal metabolic rate (kcal): 1674,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.673759129,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.838816248,plasma free fatty acids under the curve ogtt (mmol/l * min): 27.75,fat mass (%): 20,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.8587581,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 232.5,log10 homair (insulin resistance index based on homa): -0.057275608,log10 homais (insulin secretion index based on homa): 1.470781077,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.004235366,insgenin (insulinogenic index): 1.198367654,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 3.883661435,log10 matsuda insulin sensitivity index: 1.136934161,muscle mass (%): 46.3,lg10 serum c-reactive protein (mg/l): -0.441291429,lg10 plasma adiponectin (mg/l): 0.770852012,ogtt fasting plasma free fatty acid (mmol/l): 0.41,ogtt 30 min plasma free fatty acid (mmol/l): 0.33,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 5.8,ogtt 30 min plasma glucose (mmol/l): 9.6,ogtt 120 min plasma glucose (mmol/l): 5.9,log10 il1 receptor antagonist (pg/ml): 2.232614983,log10 il1 beta (pg/ml): -0.744727495,log10 ogtt fasting plasma insulin (mu/l): 0.531478917,ogtt 30 min plasma insulin (mu/l): 1.127104798,ogtt 120 min plasma insulin (mu/l): 1.264817823,log10 ogtt fasting plasma proinsulin (pm/l): 1.012837225,ogtt 30 min plasma proinsulin (pm/l): 1.294466226,ogtt 120 min plasma proinsulin (pm/l): 1.635483747,log10 bioimpedance: Resistance: 2.679427897,log10 bioimpedance (reactance): 1.73239376,waist to hip ratio: 0.954773869,log10 serum bilirubin (umol/l): 1.230448921,log10 serum alanine aminotransfrase (u/l): 1.146128036,log10 creatinine (umol/l): 1.86332286,log10 total cholesterol (mmol/l): 0.728353782,log10 ldl cholesterol (mmol/l): 0.498310554,log10 hdl cholesterol (mmol/l): 0.303196057,log10 total triglycerides (mmol/l): -0.259637311,log10 serum apoa1 (g/l): 0.238046103,log10 serum apob (g/l): -0.055517328,log10 urinary albumin excretion rate (ug/min): 0.62324929 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098266 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249165,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978093 | GSM1098266 | GSE45159 | 0.200733 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM1984 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249165 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978093 |
|
1 | age: 66,tissue: adipose tissue,log10 body mass index: 1.460261511,log10 basal metabolic rate (kcal): 1512,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.397147031,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.435113409,plasma free fatty acids under the curve ogtt (mmol/l * min): 27,fat mass (%): 31.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.19229281,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 390,log10 homair (insulin resistance index based on homa): 0.246060674,log10 homais (insulin secretion index based on homa): 1.609238576,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.514268758,insgenin (insulinogenic index): 1.671257016,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.45158689,log10 matsuda insulin sensitivity index: 0.685639426,muscle mass (%): 46.8,lg10 serum c-reactive protein (mg/l): 0.533772058,lg10 plasma adiponectin (mg/l): 0.819543936,ogtt fasting plasma free fatty acid (mmol/l): 0.41,ogtt 30 min plasma free fatty acid (mmol/l): 0.31,ogtt 120 min plasma free fatty acid (mmol/l): 0.05,ogtt fasting plasma glucose (mmol/l): 6.5,ogtt 30 min plasma glucose (mmol/l): 10.9,ogtt 120 min plasma glucose (mmol/l): 9.3,log10 il1 receptor antagonist (pg/ml): 2.157093949,log10 il1 beta (pg/ml): -0.698970004,log10 ogtt fasting plasma insulin (mu/l): 0.785329835,ogtt 30 min plasma insulin (mu/l): 1.607455023,ogtt 120 min plasma insulin (mu/l): 1.812913357,log10 ogtt fasting plasma proinsulin (pm/l): 1.025305865,ogtt 30 min plasma proinsulin (pm/l): 1.348304863,ogtt 120 min plasma proinsulin (pm/l): 1.701567985,log10 bioimpedance: Resistance: 2.666517981,log10 bioimpedance (reactance): 1.716003344,waist to hip ratio: 0.99047619,log10 serum bilirubin (umol/l): 1.176091259,log10 serum alanine aminotransfrase (u/l): 1.342422681,log10 creatinine (umol/l): 1.924279286,log10 total cholesterol (mmol/l): 0.805500858,log10 ldl cholesterol (mmol/l): 0.633468456,log10 hdl cholesterol (mmol/l): 0.120573931,log10 total triglycerides (mmol/l): 0.209515015,log10 serum apoa1 (g/l): 0.170261715,log10 serum apob (g/l): 0.120573931,log10 urinary albumin excretion rate (ug/min): 0.542262243 | 675 Charles E. Young Dr. S. MRL 3220 | Los Angeles | USA | University of California Los Angeles | Mete,,Civelek | Illumina Casava1.7 software used for basecalling.,Sequencing files were converted to FASTQ format using a custom Perl script. In order to assign the indexed reads to each METSIM subject, a Python script was used to partition the FASTQ file for each lane into multiple FASTQ files, each of which corresponded to one individual. To be included in the partitioned file, a read had to have an exact match to one of the 48 possible index sequences, unambiguously identifying the individual from whom the read originated. Reads which did not exactly match an index sequence were discarded.,The reads were then aligned to the hg19 version of the genome using the Novoalign tool with the following settings: -l16 -t30 -h90 -rA -R 1 -m -g 200 âk. Novoalign software trims the adapter sequences while aligning.,We used the Bioconductor package GenomicRanges for R (v.2.14.0) to count the number of reads with alignment coordinates that overlap the coordinates of known mature miRNAs. Whenever a read mapped to 'x' genomic loci, the read would contribute a count of 1/x to those regions. The genomic coordinates for known mature miRNAs were downloaded from miRBase version 18.,To enable comparison of counts between samples, we normalized the expression values by dividing the counts for a given mature miRNA by the sum of all the miRNA counts for the corresponding individual. For subsequent analysis, we considered the expression levels of 356 miRNAs that had at least 5 reads in half of the study participants.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include unnormalized weighted counts for each miRNA | Abdominal subcutaneous adipose tissue was obtained with needle biopsies. Total RNA was isolated from the adipose tissue using Qiagen miRNeasy kit according to manufacturerâs instructions. RNA Integrity Number (RIN) values were assessed with the Agilent Bioanalyzer 2100 instrument. Samples with RIN values greater than 7.0 were used for transcriptional profiling.,Small RNA libraries were prepared using the Illumina TruSeq Small RNA protocol utilizing up to 48 unique index sequences (Illumina Catalog Number FC-102-1009). For two samples (METSIM490 and METSIM6589) we also prepared small RNA libraries using Illumina Small RNA v1.5 sample preparation protocol (Catalog # FC-930-1501) | GSM1098267 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249166,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978094 | GSM1098267 | GSE45159 | 0.208397 | adipose tissue | Public on Apr 01 2013 | Mar 14 2013 | 9606 | METSIM2019 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX249166 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01978094 |