Datasets:

gabrielaltay

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archs4-human-gene-v2.5-meta-sample

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age: 61,tissue: adipose tissue,log10 body mass index: 1.338948892,log10 basal metabolic rate (kcal): 1548,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.381044137,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.333436702,plasma free fatty acids under the curve ogtt (mmol/l * min): 24.3,fat mass (%): 27.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.87958325,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 270,log10 homair (insulin resistance index based on homa): 0.188397198,log10 homais (insulin secretion index based on homa): 1.77120239,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.498186452,insgenin (insulinogenic index): 1.871572936,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.431797842,log10 matsuda insulin sensitivity index: 0.769064012,muscle mass (%): 38.7,lg10 serum c-reactive protein (mg/l): 0.212187604,lg10 plasma adiponectin (mg/l): 0.939519253,ogtt fasting plasma free fatty acid (mmol/l): 0.35,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): 5.6,ogtt 30 min plasma glucose (mmol/l): 8.6,ogtt 120 min plasma glucose (mmol/l): 7.6,log10 il1 receptor antagonist (pg/ml): 2.595628474,log10 il1 beta (pg/ml): -0.721246399,log10 ogtt fasting plasma insulin (mu/l): 0.792391689,ogtt 30 min plasma insulin (mu/l): 1.63748973,ogtt 120 min plasma insulin (mu/l): 1.753583059,log10 ogtt fasting plasma proinsulin (pm/l): 1.238046103,ogtt 30 min plasma proinsulin (pm/l): 1.596597096,ogtt 120 min plasma proinsulin (pm/l): 1.911690159,log10 bioimpedance: Resistance: 2.748188027,log10 bioimpedance (reactance): 1.73239376,waist to hip ratio: 0.890625,log10 serum bilirubin (umol/l): 1.255272505,log10 serum alanine aminotransfrase (u/l): 2.071882007,log10 creatinine (umol/l): 1.934498451,log10 total cholesterol (mmol/l): 0.800717078,log10 ldl cholesterol (mmol/l): 0.612783857,log10 hdl cholesterol (mmol/l): 0.204119983,log10 total triglycerides (mmol/l): 0.23299611,log10 serum apoa1 (g/l): 0.245512668,log10 serum apob (g/l): 0.136720567,log10 urinary albumin excretion rate (ug/min): 0.755487266

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 –k. 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 manufacturer’s 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)

GSM1098368

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=SRX249267,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978195

GSM1098368

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM7436

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249267

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978195

age: 57,tissue: adipose tissue,log10 body mass index: 1.440479134,log10 basal metabolic rate (kcal): 1472,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.767579447,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.937603777,plasma free fatty acids under the curve ogtt (mmol/l * min): 22.2,fat mass (%): 24.8,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): 228,log10 homair (insulin resistance index based on homa): 0.505451467,log10 homais (insulin secretion index based on homa): 2.117271296,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.910314846,insgenin (insulinogenic index): 2.339503744,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.856789289,log10 matsuda insulin sensitivity index: 0.432215057,muscle mass (%): 41.4,lg10 serum c-reactive protein (mg/l): 0.662757832,lg10 plasma adiponectin (mg/l): 0.544068044,ogtt fasting plasma free fatty acid (mmol/l): 0.35,ogtt 30 min plasma free fatty acid (mmol/l): 0.23,ogtt 120 min plasma free fatty acid (mmol/l): 0.07,ogtt fasting plasma glucose (mmol/l): 5.5,ogtt 30 min plasma glucose (mmol/l): 9.3,ogtt 120 min plasma glucose (mmol/l): 5.5,log10 il1 receptor antagonist (pg/ml): 2.678982471,log10 il1 beta (pg/ml): NA,log10 ogtt fasting plasma insulin (mu/l): 1.117271296,ogtt 30 min plasma insulin (mu/l): 2.180412633,ogtt 120 min plasma insulin (mu/l): 1.977266212,log10 ogtt fasting plasma proinsulin (pm/l): 1.424881637,ogtt 30 min plasma proinsulin (pm/l): 1.868056362,ogtt 120 min plasma proinsulin (pm/l): 1.91750551,log10 bioimpedance: Resistance: 2.753583059,log10 bioimpedance (reactance): 1.770852012,waist to hip ratio: 1.06185567,log10 serum bilirubin (umol/l): 1.176091259,log10 serum alanine aminotransfrase (u/l): 1.380211242,log10 creatinine (umol/l): 1.838849091,log10 total cholesterol (mmol/l): 0.832508913,log10 ldl cholesterol (mmol/l): 0.701567985,log10 hdl cholesterol (mmol/l): -0.075720714,log10 total triglycerides (mmol/l): 0.383815366,log10 serum apoa1 (g/l): 0.093421685,log10 serum apob (g/l): 0.230448921,log10 urinary albumin excretion rate (ug/min): 0.790759615

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 –k. 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 manufacturer’s 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)

GSM1098369

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=SRX249268,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978196

GSM1098369

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM7482

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249268

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978196

age: 50,tissue: adipose tissue,log10 body mass index: 1.498615312,log10 basal metabolic rate (kcal): 1704,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.601836376,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.160711732,plasma free fatty acids under the curve ogtt (mmol/l * min): 16.35,fat mass (%): 24.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.801708359,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 172.5,log10 homair (insulin resistance index based on homa): 0.196820744,log10 homais (insulin secretion index based on homa): 1.673941999,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.434393235,insgenin (insulinogenic index): 1.938019097,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.360612345,log10 matsuda insulin sensitivity index: 0.830887163,muscle mass (%): 42.1,lg10 serum c-reactive protein (mg/l): -0.494850022,lg10 plasma adiponectin (mg/l): 1.28780173,ogtt fasting plasma free fatty acid (mmol/l): 0.37,ogtt 30 min plasma free fatty acid (mmol/l): 0.15,ogtt 120 min plasma free fatty acid (mmol/l): 0.04,ogtt fasting plasma glucose (mmol/l): 6,ogtt 30 min plasma glucose (mmol/l): 10,ogtt 120 min plasma glucose (mmol/l): 4.5,log10 il1 receptor antagonist (pg/ml): 2.230295614,log10 il1 beta (pg/ml): NA,log10 ogtt fasting plasma insulin (mu/l): 0.770852012,ogtt 30 min plasma insulin (mu/l): 1.804139432,ogtt 120 min plasma insulin (mu/l): 1.139879086,log10 ogtt fasting plasma proinsulin (pm/l): 0.77815125,ogtt 30 min plasma proinsulin (pm/l): 1.230448921,ogtt 120 min plasma proinsulin (pm/l): 1.240549248,log10 bioimpedance: Resistance: 2.633468456,log10 bioimpedance (reactance): 1.643452676,waist to hip ratio: 0.972727273,log10 serum bilirubin (umol/l): 1.230448921,log10 serum alanine aminotransfrase (u/l): 1.491361694,log10 creatinine (umol/l): 1.892094603,log10 total cholesterol (mmol/l): 0.704150517,log10 ldl cholesterol (mmol/l): 0.505149978,log10 hdl cholesterol (mmol/l): 0.103803721,log10 total triglycerides (mmol/l): 0.056904851,log10 serum apoa1 (g/l): 0.089905111,log10 serum apob (g/l): -0.045757491,log10 urinary albumin excretion rate (ug/min): 1.121145747

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 –k. 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 manufacturer’s 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)

GSM1098370

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=SRX249269,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978197

GSM1098370

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM7530

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249269

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978197

age: 49,tissue: adipose tissue,log10 body mass index: 1.382269942,log10 basal metabolic rate (kcal): 1731,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.524492232,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.750072755,plasma free fatty acids under the curve ogtt (mmol/l * min): 16.5,fat mass (%): 15.5,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.497851837,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 15,log10 homair (insulin resistance index based on homa): 0.020729485,log10 homais (insulin secretion index based on homa): 1.522878745,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.168821463,insgenin (insulinogenic index): 2.040898888,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.074487305,log10 matsuda insulin sensitivity index: 1.081552736,muscle mass (%): 48.6,lg10 serum c-reactive protein (mg/l): -0.37675071,lg10 plasma adiponectin (mg/l): 0.602059991,ogtt fasting plasma free fatty acid (mmol/l): 0.27,ogtt 30 min plasma free fatty acid (mmol/l): 0.17,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): 7.5,ogtt 120 min plasma glucose (mmol/l): 4.1,log10 il1 receptor antagonist (pg/ml): 2.296423849,log10 il1 beta (pg/ml): NA,log10 ogtt fasting plasma insulin (mu/l): 0.602059991,ogtt 30 min plasma insulin (mu/l): 1.522444234,ogtt 120 min plasma insulin (mu/l): 0.949390007,log10 ogtt fasting plasma proinsulin (pm/l): 1.340444115,ogtt 30 min plasma proinsulin (pm/l): 1.418301291,ogtt 120 min plasma proinsulin (pm/l): 1.44870632,log10 bioimpedance: Resistance: 2.640481437,log10 bioimpedance (reactance): 1.653212514,waist to hip ratio: 0.895,log10 serum bilirubin (umol/l): 1.176091259,log10 serum alanine aminotransfrase (u/l): 1.255272505,log10 creatinine (umol/l): 1.913813852,log10 total cholesterol (mmol/l): 0.615950052,log10 ldl cholesterol (mmol/l): 0.418301291,log10 hdl cholesterol (mmol/l): 0.127104798,log10 total triglycerides (mmol/l): -0.161150909,log10 serum apoa1 (g/l): 0.064457989,log10 serum apob (g/l): -0.200659451,log10 urinary albumin excretion rate (ug/min): 0.552574628

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 –k. 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 manufacturer’s 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)

GSM1098371

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=SRX249270,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978198

GSM1098371

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM7611

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249270

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978198

age: 47,tissue: adipose tissue,log10 body mass index: 1.517447814,log10 basal metabolic rate (kcal): 1895,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.239936646,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.059702127,plasma free fatty acids under the curve ogtt (mmol/l * min): 32.1,fat mass (%): 26.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.818582177,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 135,log10 homair (insulin resistance index based on homa): 0.547419141,log10 homais (insulin secretion index based on homa): 1.932053683,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.533225352,insgenin (insulinogenic index): 2.109056724,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.401555618,log10 matsuda insulin sensitivity index: 0.595214804,muscle mass (%): 42.1,lg10 serum c-reactive protein (mg/l): 0.681241237,lg10 plasma adiponectin (mg/l): 0.908485019,ogtt fasting plasma free fatty acid (mmol/l): 0.45,ogtt 30 min plasma free fatty acid (mmol/l): 0.31,ogtt 120 min plasma free fatty acid (mmol/l): 0.15,ogtt fasting plasma glucose (mmol/l): 6.4,ogtt 30 min plasma glucose (mmol/l): 9.7,ogtt 120 min plasma glucose (mmol/l): 5,log10 il1 receptor antagonist (pg/ml): 2.980898323,log10 il1 beta (pg/ml): NA,log10 ogtt fasting plasma insulin (mu/l): 1.093421685,ogtt 30 min plasma insulin (mu/l): 1.919601024,ogtt 120 min plasma insulin (mu/l): 1.06069784,log10 ogtt fasting plasma proinsulin (pm/l): 1.315970345,ogtt 30 min plasma proinsulin (pm/l): 1.603144373,ogtt 120 min plasma proinsulin (pm/l): 1.588831726,log10 bioimpedance: Resistance: 2.630427875,log10 bioimpedance (reactance): 1.681241237,waist to hip ratio: 1.009009009,log10 serum bilirubin (umol/l): 1.342422681,log10 serum alanine aminotransfrase (u/l): 1.662757832,log10 creatinine (umol/l): 1.991226076,log10 total cholesterol (mmol/l): 0.781755375,log10 ldl cholesterol (mmol/l): 0.612783857,log10 hdl cholesterol (mmol/l): -0.026872146,log10 total triglycerides (mmol/l): 0.440909082,log10 serum apoa1 (g/l): 0.004321374,log10 serum apob (g/l): 0.008600172,log10 urinary albumin excretion rate (ug/min): NA

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 –k. 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 manufacturer’s 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)

GSM1098372

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=SRX249271,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978199

GSM1098372

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM7693

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249271

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978199

age: 61,tissue: adipose tissue,log10 body mass index: 1.398532633,log10 basal metabolic rate (kcal): 1581,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.501448642,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.437773362,plasma free fatty acids under the curve ogtt (mmol/l * min): 22.35,fat mass (%): 21.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.02375435,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 321,log10 homair (insulin resistance index based on homa): 0.323595824,log10 homais (insulin secretion index based on homa): 1.800717078,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.489029868,insgenin (insulinogenic index): 1.712055185,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.400468911,log10 matsuda insulin sensitivity index: 0.678959223,muscle mass (%): 55.8,lg10 serum c-reactive protein (mg/l): 0.071882007,lg10 plasma adiponectin (mg/l): 1.029383778,ogtt fasting plasma free fatty acid (mmol/l): 0.34,ogtt 30 min plasma free fatty acid (mmol/l): 0.22,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): 9.4,ogtt 120 min plasma glucose (mmol/l): 8.6,log10 il1 receptor antagonist (pg/ml): 2.435716988,log10 il1 beta (pg/ml): NA,log10 ogtt fasting plasma insulin (mu/l): 0.897627091,ogtt 30 min plasma insulin (mu/l): 1.56937391,ogtt 120 min plasma insulin (mu/l): 1.7930916,log10 ogtt fasting plasma proinsulin (pm/l): 1.146128036,ogtt 30 min plasma proinsulin (pm/l): 1.456366033,ogtt 120 min plasma proinsulin (pm/l): 1.910624405,log10 bioimpedance: Resistance: 2.63447727,log10 bioimpedance (reactance): 1.681241237,waist to hip ratio: 0.927835052,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): 0.7355989,log10 ldl cholesterol (mmol/l): 0.509202522,log10 hdl cholesterol (mmol/l): 0.170261715,log10 total triglycerides (mmol/l): 0.113943352,log10 serum apoa1 (g/l): 0.133538908,log10 serum apob (g/l): -0.070581074,log10 urinary albumin excretion rate (ug/min): 0.764787289

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 –k. 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 manufacturer’s 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)

GSM1098373

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=SRX249272,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978200

GSM1098373

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM7717

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249272

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978200

age: 57,tissue: adipose tissue,log10 body mass index: 1.39498930656603,log10 basal metabolic rate (kcal): 1645,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.50062976688509,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.47079015248221,plasma free fatty acids under the curve ogtt (mmol/l * min): 10.2,fat mass (%): 12.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.74483383749955,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 222,log10 homair (insulin resistance index based on homa): -0.500898235252165,log10 homais (insulin secretion index based on homa): 1.52287874523691,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.5520085915843,insgenin (insulinogenic index): 1.8866726285976,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.4160717760782,log10 matsuda insulin sensitivity index: 0.534404469414011,muscle mass (%): 51.4,lg10 serum c-reactive protein (mg/l): NA,lg10 plasma adiponectin (mg/l): 0.944482672150169,ogtt fasting plasma free fatty acid (mmol/l): 0.42,ogtt 30 min plasma free fatty acid (mmol/l): 0.05,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): 6.1,ogtt 120 min plasma glucose (mmol/l): 8.4,log10 il1 receptor antagonist (pg/ml): NA,log10 il1 beta (pg/ml): NA,log10 ogtt fasting plasma insulin (mu/l): 0.477121254719662,ogtt 30 min plasma insulin (mu/l): 1.63144376901317,ogtt 120 min plasma insulin (mu/l): 1.48995847942483,log10 ogtt fasting plasma proinsulin (pm/l): NA,ogtt 30 min plasma proinsulin (pm/l): NA,ogtt 120 min plasma proinsulin (pm/l): NA,log10 bioimpedance: Resistance: 2.58658730467175,log10 bioimpedance (reactance): 1.63346845557959,waist to hip ratio: 0.885416667,log10 serum bilirubin (umol/l): 1.04139268515822,log10 serum alanine aminotransfrase (u/l): 1.43136376415899,log10 creatinine (umol/l): 1.90848501887865,log10 total cholesterol (mmol/l): 0.751279103983342,log10 ldl cholesterol (mmol/l): 0.301029995663981,log10 hdl cholesterol (mmol/l): 0.444044795918076,log10 total triglycerides (mmol/l): -0.0132282657337552,log10 serum apoa1 (g/l): 0.257678574869184,log10 serum apob (g/l): -0.0604807473813815,log10 urinary albumin excretion rate (ug/min): 0.949742008220188

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 –k. 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 manufacturer’s 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)

GSM1098374

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=SRX249273,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978201

GSM1098374

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM7897

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249273

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978201

age: 66,tissue: adipose tissue,log10 body mass index: 1.305339969,log10 basal metabolic rate (kcal): 1547,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.263886322,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 5.997708097,plasma free fatty acids under the curve ogtt (mmol/l * min): 13.8,fat mass (%): 21.9,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): 142.5,log10 homair (insulin resistance index based on homa): -0.045114567,log10 homais (insulin secretion index based on homa): 1.661645681,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.232538718,insgenin (insulinogenic index): 1.705696868,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.154545692,log10 matsuda insulin sensitivity index: 1.085902215,muscle mass (%): 46.1,lg10 serum c-reactive protein (mg/l): -0.102372909,lg10 plasma adiponectin (mg/l): 1.037426498,ogtt fasting plasma free fatty acid (mmol/l): 0.28,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): 5.2,ogtt 30 min plasma glucose (mmol/l): 9.3,ogtt 120 min plasma glucose (mmol/l): 2.9,log10 il1 receptor antagonist (pg/ml): 2.080193419,log10 il1 beta (pg/ml): NA,log10 ogtt fasting plasma insulin (mu/l): 0.591064607,ogtt 30 min plasma insulin (mu/l): 1.586587305,ogtt 120 min plasma insulin (mu/l): 1.021189299,log10 ogtt fasting plasma proinsulin (pm/l): 1.071882007,ogtt 30 min plasma proinsulin (pm/l): 1.503790683,ogtt 120 min plasma proinsulin (pm/l): 1.613841822,log10 bioimpedance: Resistance: 2.73479983,log10 bioimpedance (reactance): 1.740362689,waist to hip ratio: 0.880434783,log10 serum bilirubin (umol/l): 1.113943352,log10 serum alanine aminotransfrase (u/l): 1.278753601,log10 creatinine (umol/l): 1.959041392,log10 total cholesterol (mmol/l): 0.777426822,log10 ldl cholesterol (mmol/l): 0.571708832,log10 hdl cholesterol (mmol/l): 0.222716471,log10 total triglycerides (mmol/l): 0.146128036,log10 serum apoa1 (g/l): 0.170261715,log10 serum apob (g/l): 0.033423755,log10 urinary albumin excretion rate (ug/min): 1.329163104

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 –k. 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 manufacturer’s 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)

GSM1098375

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=SRX249274,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978202

GSM1098375

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM7927

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249274

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978202

age: 55,tissue: adipose tissue,log10 body mass index: 1.39614807,log10 basal metabolic rate (kcal): 1556,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.661568137,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.781389161,plasma free fatty acids under the curve ogtt (mmol/l * min): 7.8,fat mass (%): 18.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.784634846,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 186,log10 homair (insulin resistance index based on homa): 0.127248819,log10 homais (insulin secretion index based on homa): 1.655305503,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.502263204,insgenin (insulinogenic index): 1.95568775,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.447839958,log10 matsuda insulin sensitivity index: 0.830764204,muscle mass (%): 44.9,lg10 serum c-reactive protein (mg/l): 0.133538908,lg10 plasma adiponectin (mg/l): 1.225309282,ogtt fasting plasma free fatty acid (mmol/l): 0.11,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): 5.8,ogtt 30 min plasma glucose (mmol/l): 9.8,ogtt 120 min plasma glucose (mmol/l): 4.6,log10 il1 receptor antagonist (pg/ml): 2.209515015,log10 il1 beta (pg/ml): NA,log10 ogtt fasting plasma insulin (mu/l): 0.716003344,ogtt 30 min plasma insulin (mu/l): 1.815577748,ogtt 120 min plasma insulin (mu/l): 1.459392488,log10 ogtt fasting plasma proinsulin (pm/l): 0.913813852,ogtt 30 min plasma proinsulin (pm/l): 1.285557309,ogtt 120 min plasma proinsulin (pm/l): 1.457881897,log10 bioimpedance: Resistance: 2.682145076,log10 bioimpedance (reactance): 1.653212514,waist to hip ratio: 1.086956522,log10 serum bilirubin (umol/l): 0.84509804,log10 serum alanine aminotransfrase (u/l): 1.51851394,log10 creatinine (umol/l): 1.86923172,log10 total cholesterol (mmol/l): 0.643452676,log10 ldl cholesterol (mmol/l): 0.372912003,log10 hdl cholesterol (mmol/l): 0.181843588,log10 total triglycerides (mmol/l): -0.026872146,log10 serum apoa1 (g/l): 0.158362492,log10 serum apob (g/l): -0.13076828,log10 urinary albumin excretion rate (ug/min): 0.943331206

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 –k. 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 manufacturer’s 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)

GSM1098376

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=SRX249275,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978203

GSM1098376

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM7948

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249275

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978203

age: 52,tissue: adipose tissue,log10 body mass index: 1.321147221,log10 basal metabolic rate (kcal): 1552,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.408547286,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.356931614,plasma free fatty acids under the curve ogtt (mmol/l * min): 16.5,fat mass (%): 11.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.911391988,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 291,log10 homair (insulin resistance index based on homa): -0.141596493,log10 homais (insulin secretion index based on homa): 1.441208699,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.218115186,insgenin (insulinogenic index): 1.329720249,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.159446873,log10 matsuda insulin sensitivity index: 1.067256369,muscle mass (%): 49.7,lg10 serum c-reactive protein (mg/l): -0.468521083,lg10 plasma adiponectin (mg/l): 0.886490725,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): 0.02,ogtt fasting plasma glucose (mmol/l): 5.6,ogtt 30 min plasma glucose (mmol/l): 9.7,ogtt 120 min plasma glucose (mmol/l): 6.6,log10 il1 receptor antagonist (pg/ml): 2.112806017,log10 il1 beta (pg/ml): NA,log10 ogtt fasting plasma insulin (mu/l): 0.462397998,ogtt 30 min plasma insulin (mu/l): 1.243038049,ogtt 120 min plasma insulin (mu/l): 1.567026366,log10 ogtt fasting plasma proinsulin (pm/l): 0.944482672,ogtt 30 min plasma proinsulin (pm/l): 1.089905111,ogtt 120 min plasma proinsulin (pm/l): 1.767897616,log10 bioimpedance: Resistance: 2.667452953,log10 bioimpedance (reactance): 1.662757832,waist to hip ratio: 0.873684211,log10 serum bilirubin (umol/l): 1.176091259,log10 serum alanine aminotransfrase (u/l): 1.278753601,log10 creatinine (umol/l): 1.939519253,log10 total cholesterol (mmol/l): 0.79518459,log10 ldl cholesterol (mmol/l): 0.600972896,log10 hdl cholesterol (mmol/l): 0.271841607,log10 total triglycerides (mmol/l): -0.142667504,log10 serum apoa1 (g/l): 0.214843848,log10 serum apob (g/l): 0.025305865,log10 urinary albumin excretion rate (ug/min): 1.000876478

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 –k. 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 manufacturer’s 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)

GSM1098377

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=SRX249276,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978204

GSM1098377

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM7954

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249276

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978204

age: 47,tissue: adipose tissue,log10 body mass index: 1.378849373,log10 basal metabolic rate (kcal): 1910,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.824074583,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.066533729,plasma free fatty acids under the curve ogtt (mmol/l * min): 17.25,fat mass (%): 14.5,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.813781191,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 192,log10 homair (insulin resistance index based on homa): -0.00154691,log10 homais (insulin secretion index based on homa): 1.500602351,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.125090713,insgenin (insulinogenic index): 1.7307266,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.0253878,log10 matsuda insulin sensitivity index: 1.073796653,muscle mass (%): 51.8,lg10 serum c-reactive protein (mg/l): -0.48148606,lg10 plasma adiponectin (mg/l): 1.136720567,ogtt fasting plasma free fatty acid (mmol/l): 0.38,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): 5.9,ogtt 30 min plasma glucose (mmol/l): 8.8,ogtt 120 min plasma glucose (mmol/l): 6.3,log10 il1 receptor antagonist (pg/ml): 2.201096565,log10 il1 beta (pg/ml): NA,log10 ogtt fasting plasma insulin (mu/l): 0.579783597,ogtt 30 min plasma insulin (mu/l): 1.474216264,ogtt 120 min plasma insulin (mu/l): 0.924279286,log10 ogtt fasting plasma proinsulin (pm/l): 1.167317335,ogtt 30 min plasma proinsulin (pm/l): 1.605305046,ogtt 120 min plasma proinsulin (pm/l): 1.596597096,log10 bioimpedance: Resistance: 2.620136055,log10 bioimpedance (reactance): 1.698970004,waist to hip ratio: 0.878787879,log10 serum bilirubin (umol/l): 1.301029996,log10 serum alanine aminotransfrase (u/l): 1.322219295,log10 creatinine (umol/l): 1.838849091,log10 total cholesterol (mmol/l): 0.72916479,log10 ldl cholesterol (mmol/l): 0.45331834,log10 hdl cholesterol (mmol/l): 0.326335861,log10 total triglycerides (mmol/l): 0.10720997,log10 serum apoa1 (g/l): 0.290034611,log10 serum apob (g/l): -0.080921908,log10 urinary albumin excretion rate (ug/min): 1.124938736

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 –k. 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 manufacturer’s 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)

GSM1098378

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=SRX249277,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978205

GSM1098378

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM7988

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249277

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978205

age: 61,tissue: adipose tissue,log10 body mass index: 1.458333616,log10 basal metabolic rate (kcal): 1736,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.361796869,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.640702401,plasma free fatty acids under the curve ogtt (mmol/l * min): 16.95,fat mass (%): 27.6,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): 151.5,log10 homair (insulin resistance index based on homa): 0.3680595,log10 homais (insulin secretion index based on homa): 1.870208761,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.603772075,insgenin (insulinogenic index): 2.349106039,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.528273777,log10 matsuda insulin sensitivity index: 0.647879221,muscle mass (%): 46.7,lg10 serum c-reactive protein (mg/l): -0.031517051,lg10 plasma adiponectin (mg/l): 1.173186268,ogtt fasting plasma free fatty acid (mmol/l): 0.3,ogtt 30 min plasma free fatty acid (mmol/l): 0.17,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): 7.6,ogtt 120 min plasma glucose (mmol/l): 7,log10 il1 receptor antagonist (pg/ml): 2.273695588,log10 il1 beta (pg/ml): NA,log10 ogtt fasting plasma insulin (mu/l): 0.949390007,ogtt 30 min plasma insulin (mu/l): 1.858537198,ogtt 120 min plasma insulin (mu/l): 1.694605199,log10 ogtt fasting plasma proinsulin (pm/l): 1.173186268,ogtt 30 min plasma proinsulin (pm/l): 1.565847819,ogtt 120 min plasma proinsulin (pm/l): 1.745074792,log10 bioimpedance: Resistance: 2.617000341,log10 bioimpedance (reactance): 1.662757832,waist to hip ratio: 0.990196078,log10 serum bilirubin (umol/l): 1.079181246,log10 serum alanine aminotransfrase (u/l): 1.755874856,log10 creatinine (umol/l): 1.939519253,log10 total cholesterol (mmol/l): 0.874481818,log10 ldl cholesterol (mmol/l): 0.716003344,log10 hdl cholesterol (mmol/l): 0.064457989,log10 total triglycerides (mmol/l): 0.387389826,log10 serum apoa1 (g/l): 0.139879086,log10 serum apob (g/l): 0.190331698,log10 urinary albumin excretion rate (ug/min): 1.167136416

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 –k. 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 manufacturer’s 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)

GSM1098379

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=SRX249278,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978206

GSM1098379

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM8054

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249278

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978206

age: 58,tissue: adipose tissue,log10 body mass index: 1.407569229,log10 basal metabolic rate (kcal): 1683,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.69162975,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.741064217,plasma free fatty acids under the curve ogtt (mmol/l * min): 9.15,fat mass (%): 16.5,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.46454575,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): -1.5,log10 homair (insulin resistance index based on homa): 0.117639498,log10 homais (insulin secretion index based on homa): 1.619788758,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.2974541,insgenin (insulinogenic index): 2.171099313,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.210479043,log10 matsuda insulin sensitivity index: 0.96744496,muscle mass (%): 49.1,lg10 serum c-reactive protein (mg/l): -0.124938737,lg10 plasma adiponectin (mg/l): 0.86332286,ogtt fasting plasma free fatty acid (mmol/l): 0.16,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): 5.9,ogtt 30 min plasma glucose (mmol/l): 7.3,ogtt 120 min plasma glucose (mmol/l): 4,log10 il1 receptor antagonist (pg/ml): 2.145600358,log10 il1 beta (pg/ml): NA,log10 ogtt fasting plasma insulin (mu/l): 0.698970004,ogtt 30 min plasma insulin (mu/l): 1.597695186,ogtt 120 min plasma insulin (mu/l): 1.278753601,log10 ogtt fasting plasma proinsulin (pm/l): 1.021189299,ogtt 30 min plasma proinsulin (pm/l): 1.413299764,ogtt 120 min plasma proinsulin (pm/l): 1.523746467,log10 bioimpedance: Resistance: 2.632457292,log10 bioimpedance (reactance): 1.698970004,waist to hip ratio: 0.940594059,log10 serum bilirubin (umol/l): 1.176091259,log10 serum alanine aminotransfrase (u/l): 1.380211242,log10 creatinine (umol/l): 1.857332496,log10 total cholesterol (mmol/l): 0.769377326,log10 ldl cholesterol (mmol/l): 0.505149978,log10 hdl cholesterol (mmol/l): 0.324282455,log10 total triglycerides (mmol/l): 0.064457989,log10 serum apoa1 (g/l): 0.285557309,log10 serum apob (g/l): -0.026872146,log10 urinary albumin excretion rate (ug/min): 0.920818754

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 –k. 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 manufacturer’s 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)

GSM1098380

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=SRX249279,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978207

GSM1098380

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM8067

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249279

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978207

age: 67,tissue: adipose tissue,log10 body mass index: 1.411121148,log10 basal metabolic rate (kcal): 1667,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.92540635,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 7.124992201,plasma free fatty acids under the curve ogtt (mmol/l * min): 46.65,fat mass (%): 32.9,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.04644195,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 421.5,log10 homair (insulin resistance index based on homa): 0.178273325,log10 homais (insulin secretion index based on homa): 1.851937465,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.364344586,insgenin (insulinogenic index): 1.699364638,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.267898856,log10 matsuda insulin sensitivity index: 0.829071452,muscle mass (%): 28.3,lg10 serum c-reactive protein (mg/l): 0.033423755,lg10 plasma adiponectin (mg/l): 1.012837225,ogtt fasting plasma free fatty acid (mmol/l): 0.76,ogtt 30 min plasma free fatty acid (mmol/l): 0.49,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): 9.7,ogtt 120 min plasma glucose (mmol/l): 8.8,log10 il1 receptor antagonist (pg/ml): 2.465888243,log10 il1 beta (pg/ml): NA,log10 ogtt fasting plasma insulin (mu/l): 0.806179974,ogtt 30 min plasma insulin (mu/l): 1.63447727,ogtt 120 min plasma insulin (mu/l): 1.416640507,log10 ogtt fasting plasma proinsulin (pm/l): 0.903089987,ogtt 30 min plasma proinsulin (pm/l): 1.369215857,ogtt 120 min plasma proinsulin (pm/l): 1.713490543,log10 bioimpedance: Resistance: 2.716003344,log10 bioimpedance (reactance): 1.633468456,waist to hip ratio: 1.018691589,log10 serum bilirubin (umol/l): 1.602059991,log10 serum alanine aminotransfrase (u/l): 1.748188027,log10 creatinine (umol/l): 1.785329835,log10 total cholesterol (mmol/l): 0.804139432,log10 ldl cholesterol (mmol/l): 0.552668216,log10 hdl cholesterol (mmol/l): 0.387389826,log10 total triglycerides (mmol/l): -0.207608311,log10 serum apoa1 (g/l): 0.318063335,log10 serum apob (g/l): -0.022276395,log10 urinary albumin excretion rate (ug/min): 1.412536907

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 –k. 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 manufacturer’s 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)

GSM1098381

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=SRX249280,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978208

GSM1098381

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM8135

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249280

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978208

age: 66,tissue: adipose tissue,log10 body mass index: 1.488375019,log10 basal metabolic rate (kcal): 1607,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.090305286,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.447204097,plasma free fatty acids under the curve ogtt (mmol/l * min): 30.3,fat mass (%): 31.5,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.830515207,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 178.5,log10 homair (insulin resistance index based on homa): 0.26565623,log10 homais (insulin secretion index based on homa): 1.71856556,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.647177512,insgenin (insulinogenic index): 2.344306825,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.596410144,log10 matsuda insulin sensitivity index: 0.676142101,muscle mass (%): 35.2,lg10 serum c-reactive protein (mg/l): 0.687528961,lg10 plasma adiponectin (mg/l): 0.857332496,ogtt fasting plasma free fatty acid (mmol/l): 0.34,ogtt 30 min plasma free fatty acid (mmol/l): 0.33,ogtt 120 min plasma free fatty acid (mmol/l): 0.12,ogtt fasting plasma glucose (mmol/l): 6.1,ogtt 30 min plasma glucose (mmol/l): 8.4,ogtt 120 min plasma glucose (mmol/l): 7,log10 il1 receptor antagonist (pg/ml): 2.415891078,log10 il1 beta (pg/ml): NA,log10 ogtt fasting plasma insulin (mu/l): 0.832508913,ogtt 30 min plasma insulin (mu/l): 1.961421094,ogtt 120 min plasma insulin (mu/l): 1.603144373,log10 ogtt fasting plasma proinsulin (pm/l): 1.260071388,ogtt 30 min plasma proinsulin (pm/l): 1.640481437,ogtt 120 min plasma proinsulin (pm/l): 1.92992956,log10 bioimpedance: Resistance: 2.62324929,log10 bioimpedance (reactance): 1.568201724,waist to hip ratio: 1,log10 serum bilirubin (umol/l): 1.255272505,log10 serum alanine aminotransfrase (u/l): 1.51851394,log10 creatinine (umol/l): 2.004321374,log10 total cholesterol (mmol/l): 0.687528961,log10 ldl cholesterol (mmol/l): 0.471291711,log10 hdl cholesterol (mmol/l): 0.139879086,log10 total triglycerides (mmol/l): 0.103803721,log10 serum apoa1 (g/l): 0.149219113,log10 serum apob (g/l): -0.017728767,log10 urinary albumin excretion rate (ug/min): 0.913979329

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 –k. 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 manufacturer’s 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)

GSM1098382

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=SRX249281,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978209

GSM1098382

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM8305

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249281

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978209

age: 64,tissue: adipose tissue,log10 body mass index: 1.346110948,log10 basal metabolic rate (kcal): 1511,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.29129487,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.063351044,plasma free fatty acids under the curve ogtt (mmol/l * min): 16.05,fat mass (%): 23,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.47370575,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): -57,log10 homair (insulin resistance index based on homa): 0.087465911,log10 homais (insulin secretion index based on homa): 1.472100453,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.317666442,insgenin (insulinogenic index): 2.698535493,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.247605064,log10 matsuda insulin sensitivity index: 0.962807002,muscle mass (%): 51.8,lg10 serum c-reactive protein (mg/l): -0.468521083,lg10 plasma adiponectin (mg/l): 0.770852012,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): 0.03,ogtt fasting plasma glucose (mmol/l): 6.4,ogtt 30 min plasma glucose (mmol/l): 6.8,ogtt 120 min plasma glucose (mmol/l): 4.6,log10 il1 receptor antagonist (pg/ml): 1.920018916,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.633468456,ogtt 30 min plasma insulin (mu/l): 1.575187845,ogtt 120 min plasma insulin (mu/l): 1.404833717,log10 ogtt fasting plasma proinsulin (pm/l): 0.919078092,ogtt 30 min plasma proinsulin (pm/l): 1.298853076,ogtt 120 min plasma proinsulin (pm/l): 1.558708571,log10 bioimpedance: Resistance: 2.704150517,log10 bioimpedance (reactance): 1.740362689,waist to hip ratio: 0.835164835,log10 serum bilirubin (umol/l): 1.51851394,log10 serum alanine aminotransfrase (u/l): 1.278753601,log10 creatinine (umol/l): 1.954242509,log10 total cholesterol (mmol/l): 0.673941999,log10 ldl cholesterol (mmol/l): 0.485721426,log10 hdl cholesterol (mmol/l): 0.068185862,log10 total triglycerides (mmol/l): 0.113943352,log10 serum apoa1 (g/l): 0.049218023,log10 serum apob (g/l): -0.060480747,log10 urinary albumin excretion rate (ug/min): 0.717519207

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 –k. 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 manufacturer’s 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)

GSM1098383

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=SRX249282,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978210

GSM1098383

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM10062

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249282

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978210

age: 63,tissue: adipose tissue,log10 body mass index: 1.471049685,log10 basal metabolic rate (kcal): 1575,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.352348725,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.546157171,plasma free fatty acids under the curve ogtt (mmol/l * min): 16.35,fat mass (%): 34.7,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.640244936,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 126,log10 homair (insulin resistance index based on homa): -0.04769199,log10 homais (insulin secretion index based on homa): 1.535113202,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.459663837,insgenin (insulinogenic index): 2.052651199,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.418732057,log10 matsuda insulin sensitivity index: 0.954161986,muscle mass (%): 43.6,lg10 serum c-reactive protein (mg/l): 1.671635597,lg10 plasma adiponectin (mg/l): 1.037426498,ogtt fasting plasma free fatty acid (mmol/l): 0.31,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): 5.6,ogtt 30 min plasma glucose (mmol/l): 8.3,ogtt 120 min plasma glucose (mmol/l): 4.8,log10 il1 receptor antagonist (pg/ml): 2.253434935,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.556302501,ogtt 30 min plasma insulin (mu/l): 1.7355989,ogtt 120 min plasma insulin (mu/l): 1.51851394,log10 ogtt fasting plasma proinsulin (pm/l): 0.995635195,ogtt 30 min plasma proinsulin (pm/l): 1.416640507,ogtt 120 min plasma proinsulin (pm/l): 1.81756537,log10 bioimpedance: Resistance: 2.682145076,log10 bioimpedance (reactance): 1.748188027,waist to hip ratio: 0.96713615,log10 serum bilirubin (umol/l): 1.255272505,log10 serum alanine aminotransfrase (u/l): 1.643452676,log10 creatinine (umol/l): 1.939519253,log10 total cholesterol (mmol/l): 0.831229694,log10 ldl cholesterol (mmol/l): 0.668385917,log10 hdl cholesterol (mmol/l): 0.247973266,log10 total triglycerides (mmol/l): -0.031517051,log10 serum apoa1 (g/l): 0.152288344,log10 serum apob (g/l): 0.103803721,log10 urinary albumin excretion rate (ug/min): 0.794598101

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 –k. 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 manufacturer’s 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)

GSM1098384

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=SRX249283,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978211

GSM1098384

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM10252

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249283

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978211

age: 64,tissue: adipose tissue,log10 body mass index: 1.390135575,log10 basal metabolic rate (kcal): 1652,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.50833036,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.562124232,plasma free fatty acids under the curve ogtt (mmol/l * min): 15.75,fat mass (%): 26,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.656424863,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 159,log10 homair (insulin resistance index based on homa): 0.165541077,log10 homais (insulin secretion index based on homa): 1.80760623,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.452139252,insgenin (insulinogenic index): 2.005291245,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.378960847,log10 matsuda insulin sensitivity index: 0.851154631,muscle mass (%): 41.7,lg10 serum c-reactive protein (mg/l): -0.853871964,lg10 plasma adiponectin (mg/l): 1.184691431,ogtt fasting plasma free fatty acid (mmol/l): 0.26,ogtt 30 min plasma free fatty acid (mmol/l): 0.16,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): 8.5,ogtt 120 min plasma glucose (mmol/l): 4.8,log10 il1 receptor antagonist (pg/ml): 1.988380565,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.785329835,ogtt 30 min plasma insulin (mu/l): 1.766412847,ogtt 120 min plasma insulin (mu/l): 1.397940009,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): 1.401400541,log10 bioimpedance: Resistance: 2.675778342,log10 bioimpedance (reactance): 1.672097858,waist to hip ratio: 0.892156863,log10 serum bilirubin (umol/l): 1.414973348,log10 serum alanine aminotransfrase (u/l): 1.113943352,log10 creatinine (umol/l): 1.897627091,log10 total cholesterol (mmol/l): 0.757396029,log10 ldl cholesterol (mmol/l): 0.456366033,log10 hdl cholesterol (mmol/l): 0.436162647,log10 total triglycerides (mmol/l): -0.096910013,log10 serum apoa1 (g/l): 0.26245109,log10 serum apob (g/l): -0.142667504,log10 urinary albumin excretion rate (ug/min): 0.688658402

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 –k. 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 manufacturer’s 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)

GSM1098385

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=SRX249284,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978212

GSM1098385

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM10271

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249284

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978212

age: 54,tissue: adipose tissue,log10 body mass index: 1.523322968,log10 basal metabolic rate (kcal): 1590,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.516464277,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.982376966,plasma free fatty acids under the curve ogtt (mmol/l * min): 19.2,fat mass (%): 26.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.987974524,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 91.5,log10 homair (insulin resistance index based on homa): 0.965671971,log10 homais (insulin secretion index based on homa): 2.109144469,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.792398694,insgenin (insulinogenic index): 2.221972816,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.629011823,log10 matsuda insulin sensitivity index: 0.207130077,muscle mass (%): 41.3,lg10 serum c-reactive protein (mg/l): 0.305351369,lg10 plasma adiponectin (mg/l): 0.792391689,ogtt fasting plasma free fatty acid (mmol/l): 0.27,ogtt 30 min plasma free fatty acid (mmol/l): 0.2,ogtt 120 min plasma free fatty acid (mmol/l): 0.07,ogtt fasting plasma glucose (mmol/l): 7.7,ogtt 30 min plasma glucose (mmol/l): 10.5,ogtt 120 min plasma glucose (mmol/l): 6,log10 il1 receptor antagonist (pg/ml): 2.514786748,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 1.431363764,ogtt 30 min plasma insulin (mu/l): 2.020361283,ogtt 120 min plasma insulin (mu/l): 1.907948522,log10 ogtt fasting plasma proinsulin (pm/l): 1.465382851,ogtt 30 min plasma proinsulin (pm/l): 1.671172843,ogtt 120 min plasma proinsulin (pm/l): 1.790285164,log10 bioimpedance: Resistance: 2.643452676,log10 bioimpedance (reactance): 1.681241237,waist to hip ratio: 1.037383178,log10 serum bilirubin (umol/l): 0.903089987,log10 serum alanine aminotransfrase (u/l): 1.792391689,log10 creatinine (umol/l): 1.908485019,log10 total cholesterol (mmol/l): 0.757396029,log10 ldl cholesterol (mmol/l): 0.613841822,log10 hdl cholesterol (mmol/l): -0.013228266,log10 total triglycerides (mmol/l): 0.204119983,log10 serum apoa1 (g/l): 0.049218023,log10 serum apob (g/l): 0.11058971,log10 urinary albumin excretion rate (ug/min): 1.402718583

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 –k. 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 manufacturer’s 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)

GSM1098386

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=SRX249285,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978213

GSM1098386

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM10277

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249285

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978213

age: 65,tissue: adipose tissue,log10 body mass index: 1.35868671,log10 basal metabolic rate (kcal): 1640,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.729115454,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.625796971,plasma free fatty acids under the curve ogtt (mmol/l * min): 22.2,fat mass (%): 31.8,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): 226.5,log10 homair (insulin resistance index based on homa): 0.058763341,log10 homais (insulin secretion index based on homa): 1.641568533,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.406335758,insgenin (insulinogenic index): 2.024560295,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.345883213,log10 matsuda insulin sensitivity index: 0.894695546,muscle mass (%): 43.7,lg10 serum c-reactive protein (mg/l): -0.537602002,lg10 plasma adiponectin (mg/l): 0.785329835,ogtt fasting plasma free fatty acid (mmol/l): 0.28,ogtt 30 min plasma free fatty acid (mmol/l): 0.24,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): 7.8,ogtt 120 min plasma glucose (mmol/l): 7.7,log10 il1 receptor antagonist (pg/ml): 2.244722323,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 0.662757832,ogtt 30 min plasma insulin (mu/l): 1.63748973,ogtt 120 min plasma insulin (mu/l): 1.544068044,log10 ogtt fasting plasma proinsulin (pm/l): 1.086359831,ogtt 30 min plasma proinsulin (pm/l): 1.397940009,ogtt 120 min plasma proinsulin (pm/l): 1.743509765,log10 bioimpedance: Resistance: 2.771587481,log10 bioimpedance (reactance): 1.86332286,waist to hip ratio: 0.908163265,log10 serum bilirubin (umol/l): 1.146128036,log10 serum alanine aminotransfrase (u/l): 1.544068044,log10 creatinine (umol/l): 1.838849091,log10 total cholesterol (mmol/l): 0.618048097,log10 ldl cholesterol (mmol/l): 0.460897843,log10 hdl cholesterol (mmol/l): 0.06069784,log10 total triglycerides (mmol/l): 0.008600172,log10 serum apoa1 (g/l): 0.056904851,log10 serum apob (g/l): -0.070581074,log10 urinary albumin excretion rate (ug/min): 1.068715812

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 –k. 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 manufacturer’s 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)

GSM1098387

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=SRX249286,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978214

GSM1098387

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM10346

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249286

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978214

age: 66,tissue: adipose tissue,log10 body mass index: 1.39073176,log10 basal metabolic rate (kcal): 1706,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.457694434,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.505502737,plasma free fatty acids under the curve ogtt (mmol/l * min): 30.45,fat mass (%): 22.1,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): 108,log10 homair (insulin resistance index based on homa): -0.061702705,log10 homais (insulin secretion index based on homa): 1.391206626,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.20588073,insgenin (insulinogenic index): 1.539076099,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.138649995,log10 matsuda insulin sensitivity index: 1.059985451,muscle mass (%): 44,lg10 serum c-reactive protein (mg/l): -0.086186148,lg10 plasma adiponectin (mg/l): 1.089905111,ogtt fasting plasma free fatty acid (mmol/l): 0.46,ogtt 30 min plasma free fatty acid (mmol/l): 0.37,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 6.1,ogtt 30 min plasma glucose (mmol/l): 9.1,ogtt 120 min plasma glucose (mmol/l): 4.5,log10 il1 receptor antagonist (pg/ml): 2.03762567,log10 il1 beta (pg/ml): -0.537602002,log10 ogtt fasting plasma insulin (mu/l): 0.505149978,ogtt 30 min plasma insulin (mu/l): 1.311753861,ogtt 120 min plasma insulin (mu/l): 1.492760389,log10 ogtt fasting plasma proinsulin (pm/l): 1.029383778,ogtt 30 min plasma proinsulin (pm/l): 1.209515015,ogtt 120 min plasma proinsulin (pm/l): 1.725094521,log10 bioimpedance: Resistance: 2.63748973,log10 bioimpedance (reactance): 1.62324929,waist to hip ratio: 0.891089109,log10 serum bilirubin (umol/l): 1.447158031,log10 serum alanine aminotransfrase (u/l): 1.361727836,log10 creatinine (umol/l): 1.908485019,log10 total cholesterol (mmol/l): 0.820201459,log10 ldl cholesterol (mmol/l): 0.558708571,log10 hdl cholesterol (mmol/l): 0.411619706,log10 total triglycerides (mmol/l): -0.050609993,log10 serum apoa1 (g/l): 0.290034611,log10 serum apob (g/l): -0.004364805,log10 urinary albumin excretion rate (ug/min): 0.854484654

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 –k. 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 manufacturer’s 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)

GSM1098388

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=SRX249287,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978215

GSM1098388

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM10381

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249287

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978215

age: 61,tissue: adipose tissue,log10 body mass index: 1.446085957,log10 basal metabolic rate (kcal): 1642,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.197906938,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.474299238,plasma free fatty acids under the curve ogtt (mmol/l * min): 11.4,fat mass (%): 30.6,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): 217.5,log10 homair (insulin resistance index based on homa): 0.260071388,log10 homais (insulin secretion index based on homa): 1.666785321,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.331548761,insgenin (insulinogenic index): 1.635899539,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.224688417,log10 matsuda insulin sensitivity index: 0.831199215,muscle mass (%): 40.2,lg10 serum c-reactive protein (mg/l): 0.376576957,lg10 plasma adiponectin (mg/l): 0.716003344,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): 0.02,ogtt fasting plasma glucose (mmol/l): 6.3,ogtt 30 min plasma glucose (mmol/l): 12.1,ogtt 120 min plasma glucose (mmol/l): 3.4,log10 il1 receptor antagonist (pg/ml): 2.190835748,log10 il1 beta (pg/ml): -0.744727495,log10 ogtt fasting plasma insulin (mu/l): 0.812913357,ogtt 30 min plasma insulin (mu/l): 1.683947131,ogtt 120 min plasma insulin (mu/l): 1.11058971,log10 ogtt fasting plasma proinsulin (pm/l): 1.243038049,ogtt 30 min plasma proinsulin (pm/l): 1.463892989,ogtt 120 min plasma proinsulin (pm/l): 1.633468456,log10 bioimpedance: Resistance: 2.661812686,log10 bioimpedance (reactance): 1.672097858,waist to hip ratio: 0.979166667,log10 serum bilirubin (umol/l): 0.84509804,log10 serum alanine aminotransfrase (u/l): 1.397940009,log10 creatinine (umol/l): 1.982271233,log10 total cholesterol (mmol/l): 0.733999287,log10 ldl cholesterol (mmol/l): 0.517195898,log10 hdl cholesterol (mmol/l): 0.201397124,log10 total triglycerides (mmol/l): -0.031517051,log10 serum apoa1 (g/l): 0.193124598,log10 serum apob (g/l): -0.036212173,log10 urinary albumin excretion rate (ug/min): 0.707570176

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 –k. 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 manufacturer’s 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)

GSM1098389

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=SRX249288,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978216

GSM1098389

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM10389

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249288

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978216

age: 60,tissue: adipose tissue,log10 body mass index: 1.458797192,log10 basal metabolic rate (kcal): 1612,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.506289531,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.932673993,plasma free fatty acids under the curve ogtt (mmol/l * min): 37.95,fat mass (%): 24.5,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 10.33315535,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 534,log10 homair (insulin resistance index based on homa): 0.669874502,log10 homais (insulin secretion index based on homa): 2.076588435,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.854882693,insgenin (insulinogenic index): 1.981810931,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.775034891,log10 matsuda insulin sensitivity index: 0.291652646,muscle mass (%): 40,lg10 serum c-reactive protein (mg/l): 0.77524626,lg10 plasma adiponectin (mg/l): 0.591064607,ogtt fasting plasma free fatty acid (mmol/l): 0.55,ogtt 30 min plasma free fatty acid (mmol/l): 0.42,ogtt 120 min plasma free fatty acid (mmol/l): 0.1,ogtt fasting plasma glucose (mmol/l): 6.3,ogtt 30 min plasma glucose (mmol/l): 12.2,ogtt 120 min plasma glucose (mmol/l): 10.3,log10 il1 receptor antagonist (pg/ml): 2.48248769,log10 il1 beta (pg/ml): -1.045757491,log10 ogtt fasting plasma insulin (mu/l): 1.222716471,ogtt 30 min plasma insulin (mu/l): 2.045322979,ogtt 120 min plasma insulin (mu/l): 2.047664195,log10 ogtt fasting plasma proinsulin (pm/l): 1.571708832,ogtt 30 min plasma proinsulin (pm/l): 1.996949248,ogtt 120 min plasma proinsulin (pm/l): 2.253338005,log10 bioimpedance: Resistance: 2.682145076,log10 bioimpedance (reactance): 1.591064607,waist to hip ratio: 1.018867925,log10 serum bilirubin (umol/l): 0.84509804,log10 serum alanine aminotransfrase (u/l): 1.505149978,log10 creatinine (umol/l): 1.903089987,log10 total cholesterol (mmol/l): 0.852479994,log10 ldl cholesterol (mmol/l): 0.59439255,log10 hdl cholesterol (mmol/l): -0.045757491,log10 total triglycerides (mmol/l): 0.781036939,log10 serum apoa1 (g/l): 0.161368002,log10 serum apob (g/l): 0.255272505,log10 urinary albumin excretion rate (ug/min): NA

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 –k. 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 manufacturer’s 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)

GSM1098390

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=SRX249289,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978217

GSM1098390

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM10419

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249289

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978217

age: 50,tissue: adipose tissue,log10 body mass index: 1.408203206,log10 basal metabolic rate (kcal): 1528,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.345195522,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.556232233,plasma free fatty acids under the curve ogtt (mmol/l * min): 27.3,fat mass (%): 19.8,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.789533645,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 249,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): 4.384640101,insgenin (insulinogenic index): 1.803457116,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.346939463,log10 matsuda insulin sensitivity index: 1.042419386,muscle mass (%): 44.5,lg10 serum c-reactive protein (mg/l): -0.494850022,lg10 plasma adiponectin (mg/l): 0.838849091,ogtt fasting plasma free fatty acid (mmol/l): 0.57,ogtt 30 min plasma free fatty acid (mmol/l): 0.29,ogtt 120 min plasma free fatty acid (mmol/l): 0.03,ogtt fasting plasma glucose (mmol/l): 5.3,ogtt 30 min plasma glucose (mmol/l): 9.3,ogtt 120 min plasma glucose (mmol/l): 5.5,log10 il1 receptor antagonist (pg/ml): 2.29307514,log10 il1 beta (pg/ml): NA,log10 ogtt fasting plasma insulin (mu/l): 0.447158031,ogtt 30 min plasma insulin (mu/l): 1.655138435,ogtt 120 min plasma insulin (mu/l): 1.456366033,log10 ogtt fasting plasma proinsulin (pm/l): 0.897627091,ogtt 30 min plasma proinsulin (pm/l): 1.320146286,ogtt 120 min plasma proinsulin (pm/l): 1.593286067,log10 bioimpedance: Resistance: 2.698100546,log10 bioimpedance (reactance): 1.698970004,waist to hip ratio: 0.979166667,log10 serum bilirubin (umol/l): 1.278753601,log10 serum alanine aminotransfrase (u/l): 1.278753601,log10 creatinine (umol/l): 1.959041392,log10 total cholesterol (mmol/l): 0.791690649,log10 ldl cholesterol (mmol/l): 0.655138435,log10 hdl cholesterol (mmol/l): 0.164352856,log10 total triglycerides (mmol/l): -0.036212173,log10 serum apoa1 (g/l): 0.173186268,log10 serum apob (g/l): 0.079181246,log10 urinary albumin excretion rate (ug/min): 0.745699227

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 –k. 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 manufacturer’s 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)

GSM1098391

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=SRX249290,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978218

GSM1098391

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM10691

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249290

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978218

age: 56,tissue: adipose tissue,log10 body mass index: 1.365955279,log10 basal metabolic rate (kcal): 1618,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.611891944,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.649892647,plasma free fatty acids under the curve ogtt (mmol/l * min): 12,fat mass (%): 13.3,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.938109326,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 225,log10 homair (insulin resistance index based on homa): 0.179551791,log10 homais (insulin secretion index based on homa): 1.586265724,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.455986239,insgenin (insulinogenic index): 1.943494516,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.392468317,log10 matsuda insulin sensitivity index: 0.79182238,muscle mass (%): 48,lg10 serum c-reactive protein (mg/l): -0.142667504,lg10 plasma adiponectin (mg/l): 0.86923172,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): 0.04,ogtt fasting plasma glucose (mmol/l): 6.3,ogtt 30 min plasma glucose (mmol/l): 9.3,ogtt 120 min plasma glucose (mmol/l): 7.3,log10 il1 receptor antagonist (pg/ml): 2.272445019,log10 il1 beta (pg/ml): NA,log10 ogtt fasting plasma insulin (mu/l): 0.73239376,ogtt 30 min plasma insulin (mu/l): 1.692846919,ogtt 120 min plasma insulin (mu/l): 1.583198774,log10 ogtt fasting plasma proinsulin (pm/l): 0.73239376,ogtt 30 min plasma proinsulin (pm/l): 1.227886705,ogtt 120 min plasma proinsulin (pm/l): 1.568201724,log10 bioimpedance: Resistance: 2.636487896,log10 bioimpedance (reactance): 1.591064607,waist to hip ratio: 0.87,log10 serum bilirubin (umol/l): 1.041392685,log10 serum alanine aminotransfrase (u/l): 1.146128036,log10 creatinine (umol/l): 1.880813592,log10 total cholesterol (mmol/l): 0.667452953,log10 ldl cholesterol (mmol/l): 0.437750563,log10 hdl cholesterol (mmol/l): 0.184691431,log10 total triglycerides (mmol/l): -0.045757491,log10 serum apoa1 (g/l): 0.1430148,log10 serum apob (g/l): -0.102372909,log10 urinary albumin excretion rate (ug/min): 1.166331422

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 –k. 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 manufacturer’s 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)

GSM1098392

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=SRX249291,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978219

GSM1098392

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM10830

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249291

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978219

age: 52,tissue: adipose tissue,log10 body mass index: 1.41615038,log10 basal metabolic rate (kcal): 1711,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.466969775,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.75548099,plasma free fatty acids under the curve ogtt (mmol/l * min): 18.75,fat mass (%): 20.6,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.82336724,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 222,log10 homair (insulin resistance index based on homa): -0.005243055,log10 homais (insulin secretion index based on homa): 1.549671922,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.155912689,insgenin (insulinogenic index): 1.562984086,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.061113054,log10 matsuda insulin sensitivity index: 1.061962987,muscle mass (%): 46.2,lg10 serum c-reactive protein (mg/l): -0.522878745,lg10 plasma adiponectin (mg/l): 0.977723605,ogtt fasting plasma free fatty acid (mmol/l): 0.33,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): 5.7,ogtt 30 min plasma glucose (mmol/l): 10,ogtt 120 min plasma glucose (mmol/l): 4.9,log10 il1 receptor antagonist (pg/ml): 2.124699809,log10 il1 beta (pg/ml): NA,log10 ogtt fasting plasma insulin (mu/l): 0.591064607,ogtt 30 min plasma insulin (mu/l): 1.478566496,ogtt 120 min plasma insulin (mu/l): 1.064457989,log10 ogtt fasting plasma proinsulin (pm/l): 1.212187604,ogtt 30 min plasma proinsulin (pm/l): 1.480006943,ogtt 120 min plasma proinsulin (pm/l): 1.617000341,log10 bioimpedance: Resistance: 2.685741739,log10 bioimpedance (reactance): 1.748188027,waist to hip ratio: 0.94,log10 serum bilirubin (umol/l): 1.531478917,log10 serum alanine aminotransfrase (u/l): 1.255272505,log10 creatinine (umol/l): 1.924279286,log10 total cholesterol (mmol/l): 0.737192643,log10 ldl cholesterol (mmol/l): 0.499687083,log10 hdl cholesterol (mmol/l): 0.330413773,log10 total triglycerides (mmol/l): -0.26760624,log10 serum apoa1 (g/l): 0.222716471,log10 serum apob (g/l): -0.065501549,log10 urinary albumin excretion rate (ug/min): 0.62291013

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 –k. 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 manufacturer’s 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)

GSM1098393

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=SRX249292,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978220

GSM1098393

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM11138

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249292

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978220

age: 53,tissue: adipose tissue,log10 body mass index: 1.367376327,log10 basal metabolic rate (kcal): 1589,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.187847951,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.299460806,plasma free fatty acids under the curve ogtt (mmol/l * min): 30,fat mass (%): 16.2,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.73470962,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 216,log10 homair (insulin resistance index based on homa): -0.305687354,log10 homais (insulin secretion index based on homa): 1.367976785,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.352529815,insgenin (insulinogenic index): 1.783546282,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.322343361,log10 matsuda insulin sensitivity index: 1.108767833,muscle mass (%): 47.3,lg10 serum c-reactive protein (mg/l): 0.045322979,lg10 plasma adiponectin (mg/l): 0.929418926,ogtt fasting plasma free fatty acid (mmol/l): 0.52,ogtt 30 min plasma free fatty acid (mmol/l): 0.34,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): 7.7,ogtt 120 min plasma glucose (mmol/l): 6.9,log10 il1 receptor antagonist (pg/ml): 2.402089351,log10 il1 beta (pg/ml): NA,log10 ogtt fasting plasma insulin (mu/l): 0.322219295,ogtt 30 min plasma insulin (mu/l): 1.421603927,ogtt 120 min plasma insulin (mu/l): 1.67669361,log10 ogtt fasting plasma proinsulin (pm/l): 0.949390007,ogtt 30 min plasma proinsulin (pm/l): 1.316180099,ogtt 120 min plasma proinsulin (pm/l): 1.981818607,log10 bioimpedance: Resistance: 2.691965103,log10 bioimpedance (reactance): 1.698970004,waist to hip ratio: 0.989130435,log10 serum bilirubin (umol/l): 1.041392685,log10 serum alanine aminotransfrase (u/l): 1.230448921,log10 creatinine (umol/l): 1.995635195,log10 total cholesterol (mmol/l): 0.86569606,log10 ldl cholesterol (mmol/l): 0.689308859,log10 hdl cholesterol (mmol/l): 0.26245109,log10 total triglycerides (mmol/l): 0.071882007,log10 serum apoa1 (g/l): 0.257678575,log10 serum apob (g/l): 0.127104798,log10 urinary albumin excretion rate (ug/min): 0.749187554

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 –k. 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 manufacturer’s 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)

GSM1098394

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=SRX249293,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978221

GSM1098394

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM11295

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249293

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978221

age: 47,tissue: adipose tissue,log10 body mass index: 1.37285687,log10 basal metabolic rate (kcal): 1498,log2 estimated glomerular filtration rate using modification of diet in renal disease (egfr_mdrd): 6.239936646,log10 estimated creatinine clearance rate using cockfcrot-gault formulaa (egcr): 6.329022795,plasma free fatty acids under the curve ogtt (mmol/l * min): 28.5,fat mass (%): 20.4,log10 plasma glucose area under the curve (ogtt) (mmol/l * min): 9.787086325,plasma glucose area under the curve above basal (ogtt) (mmol/l * min): 235.5,log10 homair (insulin resistance index based on homa): 0.165541077,log10 homais (insulin secretion index based on homa): 1.80760623,log10 insulin area under the curve (ogtt) (pmol/l * min): 4.882330969,insgenin (insulinogenic index): 2.319528073,log10 insulin area under the curve above basal (ogtt) (pmol/l * min): 4.856571815,log10 matsuda insulin sensitivity index: 0.618762803,muscle mass (%): 46.4,lg10 serum c-reactive protein (mg/l): 0.049218023,lg10 plasma adiponectin (mg/l): 1,ogtt fasting plasma free fatty acid (mmol/l): 0.53,ogtt 30 min plasma free fatty acid (mmol/l): 0.29,ogtt 120 min plasma free fatty acid (mmol/l): 0.07,ogtt fasting plasma glucose (mmol/l): 5.4,ogtt 30 min plasma glucose (mmol/l): 9.1,ogtt 120 min plasma glucose (mmol/l): 5.7,log10 il1 receptor antagonist (pg/ml): 2.297235102,log10 il1 beta (pg/ml): NA,log10 ogtt fasting plasma insulin (mu/l): 0.785329835,ogtt 30 min plasma insulin (mu/l): 2.129689892,ogtt 120 min plasma insulin (mu/l): 2.003029471,log10 ogtt fasting plasma proinsulin (pm/l): 1.224014811,ogtt 30 min plasma proinsulin (pm/l): 1.83305782,ogtt 120 min plasma proinsulin (pm/l): 1.923244019,log10 bioimpedance: Resistance: 2.781755375,log10 bioimpedance (reactance): 1.880813592,waist to hip ratio: 0.956989247,log10 serum bilirubin (umol/l): 0.954242509,log10 serum alanine aminotransfrase (u/l): 1.653212514,log10 creatinine (umol/l): 1.991226076,log10 total cholesterol (mmol/l): 0.784617293,log10 ldl cholesterol (mmol/l): 0.541579244,log10 hdl cholesterol (mmol/l): 0.26245109,log10 total triglycerides (mmol/l): 0.255272505,log10 serum apoa1 (g/l): 0.276461804,log10 serum apob (g/l): 0.041392685,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 –k. 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 manufacturer’s 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)

GSM1098395

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=SRX249294,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978222

GSM1098395

GSE45159

adipose tissue

Public on Apr 01 2013

Mar 14 2013

9606

METSIM11401

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249294

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978222

cell type: Induced endothelial cells from cultured foreskin fibroblast cells (Stegment)

3333 Burnet Ave

Cincinnati

USA

Cincinnati Children's Hospital Medical Center

Rebekah,,Karns

Trimmed sequences were generated as fastq outputs and analyzed based on the TopHat/Cufflinks pipeline based on reference annotations produced by the Ensembl Gencode project. Differential and significant gene expression analysis was carried out using gene-level FPKM (fragments per kilobase of gene locus summarized mRNA per million reads) expression levels.,Gene-level expression was normalized and baselined to the 80th percentile of that sample's overall expression in GeneSpring v7.,Genome_build: GRCh37/hg19,Supplementary_files_format_and_content: Each sample has a corresponding .txt file with normalized FPKM

Using RNeasy Mini Kit (Qiagen), total RNA was extracted and quantitative polymerase chain reaction was performed using Taqman gene expression assays (Applied Biosystems),RNA-Seq–based expression analysis was carried out using RNA samples converted into individual cDNA libraries using Illumina (San Diego, CA). TruSeq methods employed single reads of 50 base-lengths sequenced at 20-30 million read depths using the Illumina HiSeq 2500 instrument.

GSM1098572

Illumina HiSeq 2500

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL16791

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249507,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978505

GSM1098572

GSE45176

Induced endothelial cell

Public on Apr 14 2013

Mar 14 2013

9606

iEC: Rep1

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249507

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978505

cell type: Induced endothelial cells from cultured foreskin fibroblast cells (Stegment)

3333 Burnet Ave

Cincinnati

USA

Cincinnati Children's Hospital Medical Center

Rebekah,,Karns

Trimmed sequences were generated as fastq outputs and analyzed based on the TopHat/Cufflinks pipeline based on reference annotations produced by the Ensembl Gencode project. Differential and significant gene expression analysis was carried out using gene-level FPKM (fragments per kilobase of gene locus summarized mRNA per million reads) expression levels.,Gene-level expression was normalized and baselined to the 80th percentile of that sample's overall expression in GeneSpring v7.,Genome_build: GRCh37/hg19,Supplementary_files_format_and_content: Each sample has a corresponding .txt file with normalized FPKM

Using RNeasy Mini Kit (Qiagen), total RNA was extracted and quantitative polymerase chain reaction was performed using Taqman gene expression assays (Applied Biosystems),RNA-Seq–based expression analysis was carried out using RNA samples converted into individual cDNA libraries using Illumina (San Diego, CA). TruSeq methods employed single reads of 50 base-lengths sequenced at 20-30 million read depths using the Illumina HiSeq 2500 instrument.

GSM1098573

Illumina HiSeq 2500

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL16791

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249508,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978506

GSM1098573

GSE45176

Induced endothelial cell

Public on Apr 14 2013

Mar 14 2013

9606

iEC: Rep2

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249508

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978506

cell type: Human Dermal Microvascular Endothelial Cells (Lonza)

3333 Burnet Ave

Cincinnati

USA

Cincinnati Children's Hospital Medical Center

Rebekah,,Karns

Trimmed sequences were generated as fastq outputs and analyzed based on the TopHat/Cufflinks pipeline based on reference annotations produced by the Ensembl Gencode project. Differential and significant gene expression analysis was carried out using gene-level FPKM (fragments per kilobase of gene locus summarized mRNA per million reads) expression levels.,Gene-level expression was normalized and baselined to the 80th percentile of that sample's overall expression in GeneSpring v7.,Genome_build: GRCh37/hg19,Supplementary_files_format_and_content: Each sample has a corresponding .txt file with normalized FPKM

Using RNeasy Mini Kit (Qiagen), total RNA was extracted and quantitative polymerase chain reaction was performed using Taqman gene expression assays (Applied Biosystems),RNA-Seq–based expression analysis was carried out using RNA samples converted into individual cDNA libraries using Illumina (San Diego, CA). TruSeq methods employed single reads of 50 base-lengths sequenced at 20-30 million read depths using the Illumina HiSeq 2500 instrument.

GSM1098574

Illumina HiSeq 2500

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL16791

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249509,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978507

GSM1098574

GSE45176

Human microvascular endothilial cell

Public on Apr 14 2013

Mar 14 2013

9606

Human microvascular endothelial cell

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249509

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978507

cell type: Cultured foreskin fibroblast cells (Stegment)

3333 Burnet Ave

Cincinnati

USA

Cincinnati Children's Hospital Medical Center

Rebekah,,Karns

Trimmed sequences were generated as fastq outputs and analyzed based on the TopHat/Cufflinks pipeline based on reference annotations produced by the Ensembl Gencode project. Differential and significant gene expression analysis was carried out using gene-level FPKM (fragments per kilobase of gene locus summarized mRNA per million reads) expression levels.,Gene-level expression was normalized and baselined to the 80th percentile of that sample's overall expression in GeneSpring v7.,Genome_build: GRCh37/hg19,Supplementary_files_format_and_content: Each sample has a corresponding .txt file with normalized FPKM

Using RNeasy Mini Kit (Qiagen), total RNA was extracted and quantitative polymerase chain reaction was performed using Taqman gene expression assays (Applied Biosystems),RNA-Seq–based expression analysis was carried out using RNA samples converted into individual cDNA libraries using Illumina (San Diego, CA). TruSeq methods employed single reads of 50 base-lengths sequenced at 20-30 million read depths using the Illumina HiSeq 2500 instrument.

GSM1098575

Illumina HiSeq 2500

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL16791

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX249510,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978508

GSM1098575

GSE45176

Fibroblast

Public on Apr 14 2013

Mar 14 2013

9606

Fibroblast

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX249510

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978508

cell line: MDA-MB-453,cell type: breast cancer

1400 Pressler Street

Houston

USA

University of Texas MD Anderson Cancer Center

Yiwen,,Chen

Basecalls performed using CASAVA version 1.9,RNA-seq reads were aligned to hg19 using TopHat v2.0.4,Differential expression was characterized using Cuffdiff (version 0.0.5).,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each condition

Total RNA was prepared using RNeasy Mini Kit (Qiagen) according to the manufacturer's instruction. The polyadenylated mRNA was purified using oligo d(T)25 beads (NEB).,1 ng of mRNA was used for library preparation using Encore Complete RNA-seq kit (NuGEN) according to the manufacturer's instruction.

GSM1099035

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

polyA RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX250097,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978926

GSM1099035

GSE45202,GSE45203

MDA-MB-453 cells transfected with control siRNA followed by vehicle treatment

Public on Mar 16 2013

Mar 15 2013

9606

MDA-MB-453 siCtrl-veh

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX250097

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978926

cell line: MDA-MB-453,cell type: breast cancer

1400 Pressler Street

Houston

USA

University of Texas MD Anderson Cancer Center

Yiwen,,Chen

Basecalls performed using CASAVA version 1.9,RNA-seq reads were aligned to hg19 using TopHat v2.0.4,Differential expression was characterized using Cuffdiff (version 0.0.5).,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each condition

Total RNA was prepared using RNeasy Mini Kit (Qiagen) according to the manufacturer's instruction. The polyadenylated mRNA was purified using oligo d(T)25 beads (NEB).,1 ng of mRNA was used for library preparation using Encore Complete RNA-seq kit (NuGEN) according to the manufacturer's instruction.

GSM1099036

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

polyA RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX250098,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978927

GSM1099036

GSE45202,GSE45203

MDA-MB-453 cells transfected with control siRNA followed by DHT treatment

Public on Mar 16 2013

Mar 15 2013

9606

MDA-MB-453 siCtrl-DHT

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX250098

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978927

cell line: MDA-MB-453,cell type: breast cancer

1400 Pressler Street

Houston

USA

University of Texas MD Anderson Cancer Center

Yiwen,,Chen

Basecalls performed using CASAVA version 1.9,RNA-seq reads were aligned to hg19 using TopHat v2.0.4,Differential expression was characterized using Cuffdiff (version 0.0.5).,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each condition

Total RNA was prepared using RNeasy Mini Kit (Qiagen) according to the manufacturer's instruction. The polyadenylated mRNA was purified using oligo d(T)25 beads (NEB).,1 ng of mRNA was used for library preparation using Encore Complete RNA-seq kit (NuGEN) according to the manufacturer's instruction.

GSM1099037

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

polyA RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX250099,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01978928

GSM1099037

GSE45202,GSE45203

MDA-MB-453 cells transfected with MYC siRNA followed by DHT treatment

Public on Mar 16 2013

Mar 15 2013

9606

MDA-MB-453 siMYC-DHT

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX250099

https://www.ncbi.nlm.nih.gov/biosample/SAMN01978928

origen of cultured cells: RPE isolated from 16 weeks gestation human fetus,transepithelial electrical resistance: 730 ± 10 ohm*cm^2,peak transepitheilal electrical resistance (ksr only): N/A

10 Amistad Street

New Haven

USA

Yale University

Mei,,Zhong

Basecalls performed using CASAVA version 1.7.0 and 1.8.1,Sequenced reads from the sequencing run were imported into the public Galaxy platform, a free online bioinformatics interface available at http://main.g2.bx.psu.edu. The sequences were aligned against the hg19 reference genome using the Tophat for Illumina (version 1.5.0) with default parameters.,Transcripts were assembled using Cufflinks (version 0.0.5) with quartile normalization and bias correction.,Fold change in transcript expression were analyzed using Cuffdiff (version 0.0.5) with false discovery rate of 0.05, minimum alignment count of 100, quartile normalization, and bias correction.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files for RPKM values of each sample and tab-delimited text files for fold changes between two compared cell types

Libraries were prepared according to Illumina’s mRNA Sequencing Sample Preparation Guide for mRNA-Seq 8 Sample Prep Kit (Cat# RS-100-0801) for illumina Genome Analyzer II and TruSeq RNA Sample Preparation Guide for TruSeq RNA Sample Prep Kit v2 (Cat RS-122-2001) for HiSeq 2000. Briefly, poly-A containing mRNA molecules were purified from 10ug of total RNA using poly-T oligo-attached magnetic beads then fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. These cDNA fragments then go through an end repair process using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. These products are then purified and enriched with 15 cycles of PCR to create the final cDNA library. Library fragments of 150 to 350 bp (insert plus adaptor and PCR primer sequences) were isolated from 2% E-Gel EX Gel (Invirotgen #G4020-02). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

GSM1099813

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX251952,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983922

GSM1099813

GSE36695

Retinal Pigment Epithelium

Public on Mar 20 2013

Mar 18 2013

9606

hfRPESeq072611

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX251952

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983922

origen of cultured cells: hESC H1 line - derived RPE,transepithelial electrical resistance: 41±1 ohm*cm^2,peak transepitheilal electrical resistance (ksr only): 150±10 ohm*cm^2

10 Amistad Street

New Haven

USA

Yale University

Mei,,Zhong

Basecalls performed using CASAVA version 1.7.0 and 1.8.1,Sequenced reads from the sequencing run were imported into the public Galaxy platform, a free online bioinformatics interface available at http://main.g2.bx.psu.edu. The sequences were aligned against the hg19 reference genome using the Tophat for Illumina (version 1.5.0) with default parameters.,Transcripts were assembled using Cufflinks (version 0.0.5) with quartile normalization and bias correction.,Fold change in transcript expression were analyzed using Cuffdiff (version 0.0.5) with false discovery rate of 0.05, minimum alignment count of 100, quartile normalization, and bias correction.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files for RPKM values of each sample and tab-delimited text files for fold changes between two compared cell types

Libraries were prepared according to Illumina’s mRNA Sequencing Sample Preparation Guide for mRNA-Seq 8 Sample Prep Kit (Cat# RS-100-0801) for illumina Genome Analyzer II and TruSeq RNA Sample Preparation Guide for TruSeq RNA Sample Prep Kit v2 (Cat RS-122-2001) for HiSeq 2000. Briefly, poly-A containing mRNA molecules were purified from 10ug of total RNA using poly-T oligo-attached magnetic beads then fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. These cDNA fragments then go through an end repair process using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. These products are then purified and enriched with 15 cycles of PCR to create the final cDNA library. Library fragments of 150 to 350 bp (insert plus adaptor and PCR primer sequences) were isolated from 2% E-Gel EX Gel (Invirotgen #G4020-02). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

GSM1099814

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX251953,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983923

GSM1099814

GSE36695

Retinal Pigment Epithelium

Public on Mar 20 2013

Mar 18 2013

9606

H1RPE.ksr.061511

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX251953

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983923

origen of cultured cells: hESC H9 line - derived RPE,transepithelial electrical resistance: 37± 4 ohm*cm^2,peak transepitheilal electrical resistance (ksr only): 110±10 ohm*cm^2

10 Amistad Street

New Haven

USA

Yale University

Mei,,Zhong

Basecalls performed using CASAVA version 1.7.0 and 1.8.1,Sequenced reads from the sequencing run were imported into the public Galaxy platform, a free online bioinformatics interface available at http://main.g2.bx.psu.edu. The sequences were aligned against the hg19 reference genome using the Tophat for Illumina (version 1.5.0) with default parameters.,Transcripts were assembled using Cufflinks (version 0.0.5) with quartile normalization and bias correction.,Fold change in transcript expression were analyzed using Cuffdiff (version 0.0.5) with false discovery rate of 0.05, minimum alignment count of 100, quartile normalization, and bias correction.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files for RPKM values of each sample and tab-delimited text files for fold changes between two compared cell types

Libraries were prepared according to Illumina’s mRNA Sequencing Sample Preparation Guide for mRNA-Seq 8 Sample Prep Kit (Cat# RS-100-0801) for illumina Genome Analyzer II and TruSeq RNA Sample Preparation Guide for TruSeq RNA Sample Prep Kit v2 (Cat RS-122-2001) for HiSeq 2000. Briefly, poly-A containing mRNA molecules were purified from 10ug of total RNA using poly-T oligo-attached magnetic beads then fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. These cDNA fragments then go through an end repair process using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. These products are then purified and enriched with 15 cycles of PCR to create the final cDNA library. Library fragments of 150 to 350 bp (insert plus adaptor and PCR primer sequences) were isolated from 2% E-Gel EX Gel (Invirotgen #G4020-02). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

GSM1099815

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX251954,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983924

GSM1099815

GSE36695

Retinal Pigment Epithelium

Public on Mar 20 2013

Mar 18 2013

9606

H9RPE.ksr.041511

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX251954

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983924

origen of cultured cells: hESC H9 line - derived RPE,transepithelial electrical resistance: 49± 4 ohm*cm^2,peak transepitheilal electrical resistance (ksr only): 55±4 ohm*cm^2

10 Amistad Street

New Haven

USA

Yale University

Mei,,Zhong

Basecalls performed using CASAVA version 1.7.0 and 1.8.1,Sequenced reads from the sequencing run were imported into the public Galaxy platform, a free online bioinformatics interface available at http://main.g2.bx.psu.edu. The sequences were aligned against the hg19 reference genome using the Tophat for Illumina (version 1.5.0) with default parameters.,Transcripts were assembled using Cufflinks (version 0.0.5) with quartile normalization and bias correction.,Fold change in transcript expression were analyzed using Cuffdiff (version 0.0.5) with false discovery rate of 0.05, minimum alignment count of 100, quartile normalization, and bias correction.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files for RPKM values of each sample and tab-delimited text files for fold changes between two compared cell types

Libraries were prepared according to Illumina’s mRNA Sequencing Sample Preparation Guide for mRNA-Seq 8 Sample Prep Kit (Cat# RS-100-0801) for illumina Genome Analyzer II and TruSeq RNA Sample Preparation Guide for TruSeq RNA Sample Prep Kit v2 (Cat RS-122-2001) for HiSeq 2000. Briefly, poly-A containing mRNA molecules were purified from 10ug of total RNA using poly-T oligo-attached magnetic beads then fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. These cDNA fragments then go through an end repair process using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. These products are then purified and enriched with 15 cycles of PCR to create the final cDNA library. Library fragments of 150 to 350 bp (insert plus adaptor and PCR primer sequences) were isolated from 2% E-Gel EX Gel (Invirotgen #G4020-02). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

GSM1099816

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX251955,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983925

GSM1099816

GSE36695

Retinal Pigment Epithelium

Public on Mar 20 2013

Mar 18 2013

9606

H9RPE.ksr.060311

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX251955

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983925

cell type: mammary epithelial,cell line: MCF10A,sample type: 25 M reads

415 Lane Road, MR5-Rm. 2225

Charlottesville

USA

University of Virginia

Byong,Ha,Kang

RNA-seq reads were chastity filtered and assessed for overall quality with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).,Sequenced reads were mapped using STAR 2.2.0 against the human genome build hg19.,Reads that map to each gene were counted with HTSeq (http://www-huber.embl.de/users/anders/HTSeq/) under the union set, whereby reads that do not completely overlap a gene are still counted. The counts were normalized by the library size (read depth).,RPKM calculations were performed by normalizing to the median transcript length for each gene and the total library size of each sample.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include normalized count in the first column and RPKM value in the second column for each sample

Total RNA was isolated with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocols.,Each cDNA library was prepared with the NEBNext first-strand synthesis, second-strand synthesis, end repair, dA tailing, and quick ligation modules (New England Biolabs). Libraries were indexed with standard Illumina-type adapters and sequenced on an Illumina HiSeq 2000 using version 3 reagents that generate 180–200M reads per lane. Samples were 50-bp paired-end sequenced in duplicate at 25M and 50M or 100M reads per sample.

GSM1100205

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX251969,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983939

GSM1100205

GSE45258

breast

Public on Aug 06 2013

Mar 18 2013

9606

MCF10A cells run at 25M reads

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX251969

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983939

cell type: mammary epithelial,cell line: MCF10A,sample type: 50 M reads

415 Lane Road, MR5-Rm. 2225

Charlottesville

USA

University of Virginia

Byong,Ha,Kang

RNA-seq reads were chastity filtered and assessed for overall quality with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).,Sequenced reads were mapped using STAR 2.2.0 against the human genome build hg19.,Reads that map to each gene were counted with HTSeq (http://www-huber.embl.de/users/anders/HTSeq/) under the union set, whereby reads that do not completely overlap a gene are still counted. The counts were normalized by the library size (read depth).,RPKM calculations were performed by normalizing to the median transcript length for each gene and the total library size of each sample.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include normalized count in the first column and RPKM value in the second column for each sample

Total RNA was isolated with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocols.,Each cDNA library was prepared with the NEBNext first-strand synthesis, second-strand synthesis, end repair, dA tailing, and quick ligation modules (New England Biolabs). Libraries were indexed with standard Illumina-type adapters and sequenced on an Illumina HiSeq 2000 using version 3 reagents that generate 180–200M reads per lane. Samples were 50-bp paired-end sequenced in duplicate at 25M and 50M or 100M reads per sample.

GSM1100206

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX251970,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983940

GSM1100206

GSE45258

breast

Public on Aug 06 2013

Mar 18 2013

9606

MCF10A cells run at 100M reads

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX251970

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983940

cell type: colon adenocarcinoma,cell line: HT-29,treatment: IFN-g,sample type: 25 M reads

415 Lane Road, MR5-Rm. 2225

Charlottesville

USA

University of Virginia

Byong,Ha,Kang

RNA-seq reads were chastity filtered and assessed for overall quality with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).,Sequenced reads were mapped using STAR 2.2.0 against the human genome build hg19.,Reads that map to each gene were counted with HTSeq (http://www-huber.embl.de/users/anders/HTSeq/) under the union set, whereby reads that do not completely overlap a gene are still counted. The counts were normalized by the library size (read depth).,RPKM calculations were performed by normalizing to the median transcript length for each gene and the total library size of each sample.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include normalized count in the first column and RPKM value in the second column for each sample

Total RNA was isolated with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocols.,Each cDNA library was prepared with the NEBNext first-strand synthesis, second-strand synthesis, end repair, dA tailing, and quick ligation modules (New England Biolabs). Libraries were indexed with standard Illumina-type adapters and sequenced on an Illumina HiSeq 2000 using version 3 reagents that generate 180–200M reads per lane. Samples were 50-bp paired-end sequenced in duplicate at 25M and 50M or 100M reads per sample.

GSM1100207

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX251971,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983941

GSM1100207

GSE45258

colon

Public on Aug 06 2013

Mar 18 2013

9606

IFN-g stimulated HT-29 cells run at 25M reads

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX251971

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983941

cell type: colon adenocarcinoma,cell line: HT-29,treatment: IFN-g,sample type: 50 M reads

415 Lane Road, MR5-Rm. 2225

Charlottesville

USA

University of Virginia

Byong,Ha,Kang

RNA-seq reads were chastity filtered and assessed for overall quality with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).,Sequenced reads were mapped using STAR 2.2.0 against the human genome build hg19.,Reads that map to each gene were counted with HTSeq (http://www-huber.embl.de/users/anders/HTSeq/) under the union set, whereby reads that do not completely overlap a gene are still counted. The counts were normalized by the library size (read depth).,RPKM calculations were performed by normalizing to the median transcript length for each gene and the total library size of each sample.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include normalized count in the first column and RPKM value in the second column for each sample

Total RNA was isolated with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocols.,Each cDNA library was prepared with the NEBNext first-strand synthesis, second-strand synthesis, end repair, dA tailing, and quick ligation modules (New England Biolabs). Libraries were indexed with standard Illumina-type adapters and sequenced on an Illumina HiSeq 2000 using version 3 reagents that generate 180–200M reads per lane. Samples were 50-bp paired-end sequenced in duplicate at 25M and 50M or 100M reads per sample.

GSM1100208

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX251972,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983942

GSM1100208

GSE45258

colon

Public on Aug 06 2013

Mar 18 2013

9606

IFN-g stimulated HT-29 cells run at 50M reads

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX251972

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983942

cell type: breast adenocarcinoma,cell line: MDA-MB-436,sample type: 25 M reads

415 Lane Road, MR5-Rm. 2225

Charlottesville

USA

University of Virginia

Byong,Ha,Kang

RNA-seq reads were chastity filtered and assessed for overall quality with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).,Sequenced reads were mapped using STAR 2.2.0 against the human genome build hg19.,Reads that map to each gene were counted with HTSeq (http://www-huber.embl.de/users/anders/HTSeq/) under the union set, whereby reads that do not completely overlap a gene are still counted. The counts were normalized by the library size (read depth).,RPKM calculations were performed by normalizing to the median transcript length for each gene and the total library size of each sample.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include normalized count in the first column and RPKM value in the second column for each sample

Total RNA was isolated with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocols.,Each cDNA library was prepared with the NEBNext first-strand synthesis, second-strand synthesis, end repair, dA tailing, and quick ligation modules (New England Biolabs). Libraries were indexed with standard Illumina-type adapters and sequenced on an Illumina HiSeq 2000 using version 3 reagents that generate 180–200M reads per lane. Samples were 50-bp paired-end sequenced in duplicate at 25M and 50M or 100M reads per sample.

GSM1100209

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX251973,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983943

GSM1100209

GSE45258

breast

Public on Aug 06 2013

Mar 18 2013

9606

MDA-MB-436 cells run at 25M reads

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX251973

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983943

cell type: breast adenocarcinoma,cell line: MDA-MB-436,sample type: 50 M reads

415 Lane Road, MR5-Rm. 2225

Charlottesville

USA

University of Virginia

Byong,Ha,Kang

RNA-seq reads were chastity filtered and assessed for overall quality with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).,Sequenced reads were mapped using STAR 2.2.0 against the human genome build hg19.,Reads that map to each gene were counted with HTSeq (http://www-huber.embl.de/users/anders/HTSeq/) under the union set, whereby reads that do not completely overlap a gene are still counted. The counts were normalized by the library size (read depth).,RPKM calculations were performed by normalizing to the median transcript length for each gene and the total library size of each sample.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include normalized count in the first column and RPKM value in the second column for each sample

Total RNA was isolated with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocols.,Each cDNA library was prepared with the NEBNext first-strand synthesis, second-strand synthesis, end repair, dA tailing, and quick ligation modules (New England Biolabs). Libraries were indexed with standard Illumina-type adapters and sequenced on an Illumina HiSeq 2000 using version 3 reagents that generate 180–200M reads per lane. Samples were 50-bp paired-end sequenced in duplicate at 25M and 50M or 100M reads per sample.

GSM1100210

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX251974,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983944

GSM1100210

GSE45258

breast

Public on Aug 06 2013

Mar 18 2013

9606

MDA-MB-436 cells run at 50M reads

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX251974

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983944

tissue: Prefrontal Cortex,organism: human

320 Yue Yang Road

Shanghai

China

PICB

Liu,,He

Illumina Casava1.7 software used for basecalling, and only the ones passing illumina quality controls were retained.,Reads were mapped onto correponding reference genomes (hg19, panTro3) by Tophat-1.4.1, with parameters: -a 8 -m 2 no-coverage-search microexon-search segment-mismatches 3 segment-length 25.,We made a reciprocal lift-over between chimpanzee and human (Ensembl annotation v. 69, coding exons only), and used only exons that could be lift-overed to calculate RPKMs for each gene.,Then quantile normalization was applied, and each gene was z-transformed.,Genome_build: hg19, panTro3,Supplementary_files_format_and_content: tab-delimited text files including expression measurements for each gene from each sample.

Total RNA was isolated using Trizol reagent (Cat. No. 15596-026, Invitrogen). The libraries were constructed from the isolated total RNA according to the "TruSeq RNA Sample Preparation Kit" protocol (www.illumina.com) without modification. As the protocol includes the procedure of enrichment for the mRNA, an additional polyA selection was not necessary.,RNA libraries were prepared for sequencing using Illumina TruSeq protocols

GSM1100295

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252083,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983956

GSM1100295

GSE45263

Prefrontal Cortex

Public on Mar 31 2014

Mar 18 2013

9606

Human_EU_1

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252083

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983956

tissue: Prefrontal Cortex,organism: human

320 Yue Yang Road

Shanghai

China

PICB

Liu,,He

Illumina Casava1.7 software used for basecalling, and only the ones passing illumina quality controls were retained.,Reads were mapped onto correponding reference genomes (hg19, panTro3) by Tophat-1.4.1, with parameters: -a 8 -m 2 no-coverage-search microexon-search segment-mismatches 3 segment-length 25.,We made a reciprocal lift-over between chimpanzee and human (Ensembl annotation v. 69, coding exons only), and used only exons that could be lift-overed to calculate RPKMs for each gene.,Then quantile normalization was applied, and each gene was z-transformed.,Genome_build: hg19, panTro3,Supplementary_files_format_and_content: tab-delimited text files including expression measurements for each gene from each sample.

Total RNA was isolated using Trizol reagent (Cat. No. 15596-026, Invitrogen). The libraries were constructed from the isolated total RNA according to the "TruSeq RNA Sample Preparation Kit" protocol (www.illumina.com) without modification. As the protocol includes the procedure of enrichment for the mRNA, an additional polyA selection was not necessary.,RNA libraries were prepared for sequencing using Illumina TruSeq protocols

GSM1100296

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252084,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983957

GSM1100296

GSE45263

Prefrontal Cortex

Public on Mar 31 2014

Mar 18 2013

9606

Human_AF_2

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252084

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983957

tissue: Prefrontal Cortex,organism: human

320 Yue Yang Road

Shanghai

China

PICB

Liu,,He

Illumina Casava1.7 software used for basecalling, and only the ones passing illumina quality controls were retained.,Reads were mapped onto correponding reference genomes (hg19, panTro3) by Tophat-1.4.1, with parameters: -a 8 -m 2 no-coverage-search microexon-search segment-mismatches 3 segment-length 25.,We made a reciprocal lift-over between chimpanzee and human (Ensembl annotation v. 69, coding exons only), and used only exons that could be lift-overed to calculate RPKMs for each gene.,Then quantile normalization was applied, and each gene was z-transformed.,Genome_build: hg19, panTro3,Supplementary_files_format_and_content: tab-delimited text files including expression measurements for each gene from each sample.

Total RNA was isolated using Trizol reagent (Cat. No. 15596-026, Invitrogen). The libraries were constructed from the isolated total RNA according to the "TruSeq RNA Sample Preparation Kit" protocol (www.illumina.com) without modification. As the protocol includes the procedure of enrichment for the mRNA, an additional polyA selection was not necessary.,RNA libraries were prepared for sequencing using Illumina TruSeq protocols

GSM1100297

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252085,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983958

GSM1100297

GSE45263

Prefrontal Cortex

Public on Mar 31 2014

Mar 18 2013

9606

Human_EU_3

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252085

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983958

tissue: Prefrontal Cortex,organism: human

320 Yue Yang Road

Shanghai

China

PICB

Liu,,He

Illumina Casava1.7 software used for basecalling, and only the ones passing illumina quality controls were retained.,Reads were mapped onto correponding reference genomes (hg19, panTro3) by Tophat-1.4.1, with parameters: -a 8 -m 2 no-coverage-search microexon-search segment-mismatches 3 segment-length 25.,We made a reciprocal lift-over between chimpanzee and human (Ensembl annotation v. 69, coding exons only), and used only exons that could be lift-overed to calculate RPKMs for each gene.,Then quantile normalization was applied, and each gene was z-transformed.,Genome_build: hg19, panTro3,Supplementary_files_format_and_content: tab-delimited text files including expression measurements for each gene from each sample.

Total RNA was isolated using Trizol reagent (Cat. No. 15596-026, Invitrogen). The libraries were constructed from the isolated total RNA according to the "TruSeq RNA Sample Preparation Kit" protocol (www.illumina.com) without modification. As the protocol includes the procedure of enrichment for the mRNA, an additional polyA selection was not necessary.,RNA libraries were prepared for sequencing using Illumina TruSeq protocols

GSM1100298

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252086,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983959

GSM1100298

GSE45263

Prefrontal Cortex

Public on Mar 31 2014

Mar 18 2013

9606

Human_EU_4

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252086

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983959

tissue: Prefrontal Cortex,organism: human

320 Yue Yang Road

Shanghai

China

PICB

Liu,,He

Illumina Casava1.7 software used for basecalling, and only the ones passing illumina quality controls were retained.,Reads were mapped onto correponding reference genomes (hg19, panTro3) by Tophat-1.4.1, with parameters: -a 8 -m 2 no-coverage-search microexon-search segment-mismatches 3 segment-length 25.,We made a reciprocal lift-over between chimpanzee and human (Ensembl annotation v. 69, coding exons only), and used only exons that could be lift-overed to calculate RPKMs for each gene.,Then quantile normalization was applied, and each gene was z-transformed.,Genome_build: hg19, panTro3,Supplementary_files_format_and_content: tab-delimited text files including expression measurements for each gene from each sample.

Total RNA was isolated using Trizol reagent (Cat. No. 15596-026, Invitrogen). The libraries were constructed from the isolated total RNA according to the "TruSeq RNA Sample Preparation Kit" protocol (www.illumina.com) without modification. As the protocol includes the procedure of enrichment for the mRNA, an additional polyA selection was not necessary.,RNA libraries were prepared for sequencing using Illumina TruSeq protocols

GSM1100299

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252087,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983960

GSM1100299

GSE45263

Prefrontal Cortex

Public on Mar 31 2014

Mar 18 2013

9606

Human_AS_5

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252087

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983960

tissue: Prefrontal Cortex,organism: human

320 Yue Yang Road

Shanghai

China

PICB

Liu,,He

Illumina Casava1.7 software used for basecalling, and only the ones passing illumina quality controls were retained.,Reads were mapped onto correponding reference genomes (hg19, panTro3) by Tophat-1.4.1, with parameters: -a 8 -m 2 no-coverage-search microexon-search segment-mismatches 3 segment-length 25.,We made a reciprocal lift-over between chimpanzee and human (Ensembl annotation v. 69, coding exons only), and used only exons that could be lift-overed to calculate RPKMs for each gene.,Then quantile normalization was applied, and each gene was z-transformed.,Genome_build: hg19, panTro3,Supplementary_files_format_and_content: tab-delimited text files including expression measurements for each gene from each sample.

Total RNA was isolated using Trizol reagent (Cat. No. 15596-026, Invitrogen). The libraries were constructed from the isolated total RNA according to the "TruSeq RNA Sample Preparation Kit" protocol (www.illumina.com) without modification. As the protocol includes the procedure of enrichment for the mRNA, an additional polyA selection was not necessary.,RNA libraries were prepared for sequencing using Illumina TruSeq protocols

GSM1100300

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252088,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983961

GSM1100300

GSE45263

Prefrontal Cortex

Public on Mar 31 2014

Mar 18 2013

9606

Human_AF_6

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252088

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983961

tissue: Prefrontal Cortex,organism: human

320 Yue Yang Road

Shanghai

China

PICB

Liu,,He

Illumina Casava1.7 software used for basecalling, and only the ones passing illumina quality controls were retained.,Reads were mapped onto correponding reference genomes (hg19, panTro3) by Tophat-1.4.1, with parameters: -a 8 -m 2 no-coverage-search microexon-search segment-mismatches 3 segment-length 25.,We made a reciprocal lift-over between chimpanzee and human (Ensembl annotation v. 69, coding exons only), and used only exons that could be lift-overed to calculate RPKMs for each gene.,Then quantile normalization was applied, and each gene was z-transformed.,Genome_build: hg19, panTro3,Supplementary_files_format_and_content: tab-delimited text files including expression measurements for each gene from each sample.

Total RNA was isolated using Trizol reagent (Cat. No. 15596-026, Invitrogen). The libraries were constructed from the isolated total RNA according to the "TruSeq RNA Sample Preparation Kit" protocol (www.illumina.com) without modification. As the protocol includes the procedure of enrichment for the mRNA, an additional polyA selection was not necessary.,RNA libraries were prepared for sequencing using Illumina TruSeq protocols

GSM1100301

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252089,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983962

GSM1100301

GSE45263

Prefrontal Cortex

Public on Mar 31 2014

Mar 18 2013

9606

Human_AS_7

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252089

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983962

tissue: Prefrontal Cortex,organism: human

320 Yue Yang Road

Shanghai

China

PICB

Liu,,He

Illumina Casava1.7 software used for basecalling, and only the ones passing illumina quality controls were retained.,Reads were mapped onto correponding reference genomes (hg19, panTro3) by Tophat-1.4.1, with parameters: -a 8 -m 2 no-coverage-search microexon-search segment-mismatches 3 segment-length 25.,We made a reciprocal lift-over between chimpanzee and human (Ensembl annotation v. 69, coding exons only), and used only exons that could be lift-overed to calculate RPKMs for each gene.,Then quantile normalization was applied, and each gene was z-transformed.,Genome_build: hg19, panTro3,Supplementary_files_format_and_content: tab-delimited text files including expression measurements for each gene from each sample.

Total RNA was isolated using Trizol reagent (Cat. No. 15596-026, Invitrogen). The libraries were constructed from the isolated total RNA according to the "TruSeq RNA Sample Preparation Kit" protocol (www.illumina.com) without modification. As the protocol includes the procedure of enrichment for the mRNA, an additional polyA selection was not necessary.,RNA libraries were prepared for sequencing using Illumina TruSeq protocols

GSM1100302

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252090,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983963

GSM1100302

GSE45263

Prefrontal Cortex

Public on Mar 31 2014

Mar 18 2013

9606

Human_AF_8

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252090

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983963

tissue: Prefrontal Cortex,organism: human

320 Yue Yang Road

Shanghai

China

PICB

Liu,,He

Illumina Casava1.7 software used for basecalling, and only the ones passing illumina quality controls were retained.,Reads were mapped onto correponding reference genomes (hg19, panTro3) by Tophat-1.4.1, with parameters: -a 8 -m 2 no-coverage-search microexon-search segment-mismatches 3 segment-length 25.,We made a reciprocal lift-over between chimpanzee and human (Ensembl annotation v. 69, coding exons only), and used only exons that could be lift-overed to calculate RPKMs for each gene.,Then quantile normalization was applied, and each gene was z-transformed.,Genome_build: hg19, panTro3,Supplementary_files_format_and_content: tab-delimited text files including expression measurements for each gene from each sample.

Total RNA was isolated using Trizol reagent (Cat. No. 15596-026, Invitrogen). The libraries were constructed from the isolated total RNA according to the "TruSeq RNA Sample Preparation Kit" protocol (www.illumina.com) without modification. As the protocol includes the procedure of enrichment for the mRNA, an additional polyA selection was not necessary.,RNA libraries were prepared for sequencing using Illumina TruSeq protocols

GSM1100303

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252091,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983964

GSM1100303

GSE45263

Prefrontal Cortex

Public on Mar 31 2014

Mar 18 2013

9606

Human_AS_9

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252091

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983964

tissue: Prefrontal Cortex,organism: human

320 Yue Yang Road

Shanghai

China

PICB

Liu,,He

Illumina Casava1.7 software used for basecalling, and only the ones passing illumina quality controls were retained.,Reads were mapped onto correponding reference genomes (hg19, panTro3) by Tophat-1.4.1, with parameters: -a 8 -m 2 no-coverage-search microexon-search segment-mismatches 3 segment-length 25.,We made a reciprocal lift-over between chimpanzee and human (Ensembl annotation v. 69, coding exons only), and used only exons that could be lift-overed to calculate RPKMs for each gene.,Then quantile normalization was applied, and each gene was z-transformed.,Genome_build: hg19, panTro3,Supplementary_files_format_and_content: tab-delimited text files including expression measurements for each gene from each sample.

Total RNA was isolated using Trizol reagent (Cat. No. 15596-026, Invitrogen). The libraries were constructed from the isolated total RNA according to the "TruSeq RNA Sample Preparation Kit" protocol (www.illumina.com) without modification. As the protocol includes the procedure of enrichment for the mRNA, an additional polyA selection was not necessary.,RNA libraries were prepared for sequencing using Illumina TruSeq protocols

GSM1100304

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252092,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983965

GSM1100304

GSE45263

Prefrontal Cortex

Public on Mar 31 2014

Mar 18 2013

9606

Human_AS_10

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252092

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983965

tissue: Prefrontal Cortex,organism: human

320 Yue Yang Road

Shanghai

China

PICB

Liu,,He

Illumina Casava1.7 software used for basecalling, and only the ones passing illumina quality controls were retained.,Reads were mapped onto correponding reference genomes (hg19, panTro3) by Tophat-1.4.1, with parameters: -a 8 -m 2 no-coverage-search microexon-search segment-mismatches 3 segment-length 25.,We made a reciprocal lift-over between chimpanzee and human (Ensembl annotation v. 69, coding exons only), and used only exons that could be lift-overed to calculate RPKMs for each gene.,Then quantile normalization was applied, and each gene was z-transformed.,Genome_build: hg19, panTro3,Supplementary_files_format_and_content: tab-delimited text files including expression measurements for each gene from each sample.

Total RNA was isolated using Trizol reagent (Cat. No. 15596-026, Invitrogen). The libraries were constructed from the isolated total RNA according to the "TruSeq RNA Sample Preparation Kit" protocol (www.illumina.com) without modification. As the protocol includes the procedure of enrichment for the mRNA, an additional polyA selection was not necessary.,RNA libraries were prepared for sequencing using Illumina TruSeq protocols

GSM1100305

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252093,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983966

GSM1100305

GSE45263

Prefrontal Cortex

Public on Mar 31 2014

Mar 18 2013

9606

Human_EU_11

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252093

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983966

tissue: Prefrontal Cortex,organism: human

320 Yue Yang Road

Shanghai

China

PICB

Liu,,He

Illumina Casava1.7 software used for basecalling, and only the ones passing illumina quality controls were retained.,Reads were mapped onto correponding reference genomes (hg19, panTro3) by Tophat-1.4.1, with parameters: -a 8 -m 2 no-coverage-search microexon-search segment-mismatches 3 segment-length 25.,We made a reciprocal lift-over between chimpanzee and human (Ensembl annotation v. 69, coding exons only), and used only exons that could be lift-overed to calculate RPKMs for each gene.,Then quantile normalization was applied, and each gene was z-transformed.,Genome_build: hg19, panTro3,Supplementary_files_format_and_content: tab-delimited text files including expression measurements for each gene from each sample.

Total RNA was isolated using Trizol reagent (Cat. No. 15596-026, Invitrogen). The libraries were constructed from the isolated total RNA according to the "TruSeq RNA Sample Preparation Kit" protocol (www.illumina.com) without modification. As the protocol includes the procedure of enrichment for the mRNA, an additional polyA selection was not necessary.,RNA libraries were prepared for sequencing using Illumina TruSeq protocols

GSM1100306

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252094,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983967

GSM1100306

GSE45263

Prefrontal Cortex

Public on Mar 31 2014

Mar 18 2013

9606

Human_AF_12

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252094

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983967

tissue: Prefrontal Cortex,organism: human

320 Yue Yang Road

Shanghai

China

PICB

Liu,,He

Illumina Casava1.7 software used for basecalling, and only the ones passing illumina quality controls were retained.,Reads were mapped onto correponding reference genomes (hg19, panTro3) by Tophat-1.4.1, with parameters: -a 8 -m 2 no-coverage-search microexon-search segment-mismatches 3 segment-length 25.,We made a reciprocal lift-over between chimpanzee and human (Ensembl annotation v. 69, coding exons only), and used only exons that could be lift-overed to calculate RPKMs for each gene.,Then quantile normalization was applied, and each gene was z-transformed.,Genome_build: hg19, panTro3,Supplementary_files_format_and_content: tab-delimited text files including expression measurements for each gene from each sample.

Total RNA was isolated using Trizol reagent (Cat. No. 15596-026, Invitrogen). The libraries were constructed from the isolated total RNA according to the "TruSeq RNA Sample Preparation Kit" protocol (www.illumina.com) without modification. As the protocol includes the procedure of enrichment for the mRNA, an additional polyA selection was not necessary.,RNA libraries were prepared for sequencing using Illumina TruSeq protocols

GSM1100307

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252095,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983968

GSM1100307

GSE45263

Prefrontal Cortex

Public on Mar 31 2014

Mar 18 2013

9606

Human_AS_13

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252095

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983968

tissue: Prefrontal Cortex,organism: human

320 Yue Yang Road

Shanghai

China

PICB

Liu,,He

Illumina Casava1.7 software used for basecalling, and only the ones passing illumina quality controls were retained.,Reads were mapped onto correponding reference genomes (hg19, panTro3) by Tophat-1.4.1, with parameters: -a 8 -m 2 no-coverage-search microexon-search segment-mismatches 3 segment-length 25.,We made a reciprocal lift-over between chimpanzee and human (Ensembl annotation v. 69, coding exons only), and used only exons that could be lift-overed to calculate RPKMs for each gene.,Then quantile normalization was applied, and each gene was z-transformed.,Genome_build: hg19, panTro3,Supplementary_files_format_and_content: tab-delimited text files including expression measurements for each gene from each sample.

Total RNA was isolated using Trizol reagent (Cat. No. 15596-026, Invitrogen). The libraries were constructed from the isolated total RNA according to the "TruSeq RNA Sample Preparation Kit" protocol (www.illumina.com) without modification. As the protocol includes the procedure of enrichment for the mRNA, an additional polyA selection was not necessary.,RNA libraries were prepared for sequencing using Illumina TruSeq protocols

GSM1100308

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252096,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01983969

GSM1100308

GSE45263

Prefrontal Cortex

Public on Mar 31 2014

Mar 18 2013

9606

Human_EU_14

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252096

https://www.ncbi.nlm.nih.gov/biosample/SAMN01983969

tissue: bladder

Palle Juul-Jensens Bouleward 99

Aarhus

Denmark

Aarhus University

Morten,Muhlig,Nielsen

Illumina Casava software used for basecalling, and Tophat and Cufflinks used for transcript FPKM estiamtes.,Genome_build: hg18,Supplementary_files_format_and_content: Total transcript FPKM values in the GTF file format

Normal tissue provided by Biochain. Total RNA was isolated by a modified guanidine thiocyanate technique according to BioCahin certificate of analysis F-753-1-6 revA.,Using 500 ng of total-RNA from each of the samples, RNA-Seq libraries were constructed by depletion of rRNA followed by synthesis of directional, paired-end and indexed RNA-Seq libraries. The rRNA depleted RNA was purified using the RNA Clean & Concentrator™-5 columns (Zymo Research). Speed-vac was used to reduce the remaining sample volume to 9.5μL followed by synthesis of directional, paired-end and indexed RNA-Seq libraries using the ScriptSeq kit (Epicentre). Briefly, rRNA depleted RNA was chemically fragmented and cDNA was synthesized from a tagged random hexamer. The cDNA was terminal tagged using a 3’-end blocked and tagged oligo followed by MiniElute (Qiagen) purification. The di-tagged cDNA was then used as template in a 10 cycle PCR reaction. Libraries were purified by agarose gel electrophoresis selecting elements of 200-600 bp in size. The RNA-Seq libraries were denaturated and diluted to 10 pM with pre-chilled Hybridization buffer (Illumina) and loaded into TruSeq PE v3 flowcells (Illumina) on an Illumina cBot followed by indexed paired-end sequencing (101+7+101 bp) on a Illumina HiSeq 2000 using TruSeq SBS Kit v3 chemistry.

GSM1101966

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252502,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01984805

GSM1101966

GSE45326

Biochain:R-1234010-P

Public on Sep 01 2013

Mar 19 2013

9606

Bladder

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252502

https://www.ncbi.nlm.nih.gov/biosample/SAMN01984805

tissue: brain

Palle Juul-Jensens Bouleward 99

Aarhus

Denmark

Aarhus University

Morten,Muhlig,Nielsen

Illumina Casava software used for basecalling, and Tophat and Cufflinks used for transcript FPKM estiamtes.,Genome_build: hg18,Supplementary_files_format_and_content: Total transcript FPKM values in the GTF file format

Normal tissue provided by Biochain. Total RNA was isolated by a modified guanidine thiocyanate technique according to BioCahin certificate of analysis F-753-1-6 revA.,Using 500 ng of total-RNA from each of the samples, RNA-Seq libraries were constructed by depletion of rRNA followed by synthesis of directional, paired-end and indexed RNA-Seq libraries. The rRNA depleted RNA was purified using the RNA Clean & Concentrator™-5 columns (Zymo Research). Speed-vac was used to reduce the remaining sample volume to 9.5μL followed by synthesis of directional, paired-end and indexed RNA-Seq libraries using the ScriptSeq kit (Epicentre). Briefly, rRNA depleted RNA was chemically fragmented and cDNA was synthesized from a tagged random hexamer. The cDNA was terminal tagged using a 3’-end blocked and tagged oligo followed by MiniElute (Qiagen) purification. The di-tagged cDNA was then used as template in a 10 cycle PCR reaction. Libraries were purified by agarose gel electrophoresis selecting elements of 200-600 bp in size. The RNA-Seq libraries were denaturated and diluted to 10 pM with pre-chilled Hybridization buffer (Illumina) and loaded into TruSeq PE v3 flowcells (Illumina) on an Illumina cBot followed by indexed paired-end sequencing (101+7+101 bp) on a Illumina HiSeq 2000 using TruSeq SBS Kit v3 chemistry.

GSM1101967

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252503,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01984806

GSM1101967

GSE45326

Biochain:R-1234035-P

Public on Sep 01 2013

Mar 19 2013

9606

Brain

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252503

https://www.ncbi.nlm.nih.gov/biosample/SAMN01984806

tissue: breast

Palle Juul-Jensens Bouleward 99

Aarhus

Denmark

Aarhus University

Morten,Muhlig,Nielsen

Illumina Casava software used for basecalling, and Tophat and Cufflinks used for transcript FPKM estiamtes.,Genome_build: hg18,Supplementary_files_format_and_content: Total transcript FPKM values in the GTF file format

Normal tissue provided by Biochain. Total RNA was isolated by a modified guanidine thiocyanate technique according to BioCahin certificate of analysis F-753-1-6 revA.,Using 500 ng of total-RNA from each of the samples, RNA-Seq libraries were constructed by depletion of rRNA followed by synthesis of directional, paired-end and indexed RNA-Seq libraries. The rRNA depleted RNA was purified using the RNA Clean & Concentrator™-5 columns (Zymo Research). Speed-vac was used to reduce the remaining sample volume to 9.5μL followed by synthesis of directional, paired-end and indexed RNA-Seq libraries using the ScriptSeq kit (Epicentre). Briefly, rRNA depleted RNA was chemically fragmented and cDNA was synthesized from a tagged random hexamer. The cDNA was terminal tagged using a 3’-end blocked and tagged oligo followed by MiniElute (Qiagen) purification. The di-tagged cDNA was then used as template in a 10 cycle PCR reaction. Libraries were purified by agarose gel electrophoresis selecting elements of 200-600 bp in size. The RNA-Seq libraries were denaturated and diluted to 10 pM with pre-chilled Hybridization buffer (Illumina) and loaded into TruSeq PE v3 flowcells (Illumina) on an Illumina cBot followed by indexed paired-end sequencing (101+7+101 bp) on a Illumina HiSeq 2000 using TruSeq SBS Kit v3 chemistry.

GSM1101968

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252504,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01984807

GSM1101968

GSE45326

Biochain:R-1234086-P

Public on Sep 01 2013

Mar 19 2013

9606

Breast

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252504

https://www.ncbi.nlm.nih.gov/biosample/SAMN01984807

tissue: colon

Palle Juul-Jensens Bouleward 99

Aarhus

Denmark

Aarhus University

Morten,Muhlig,Nielsen

Illumina Casava software used for basecalling, and Tophat and Cufflinks used for transcript FPKM estiamtes.,Genome_build: hg18,Supplementary_files_format_and_content: Total transcript FPKM values in the GTF file format

Normal tissue provided by Biochain. Total RNA was isolated by a modified guanidine thiocyanate technique according to BioCahin certificate of analysis F-753-1-6 revA.,Using 500 ng of total-RNA from each of the samples, RNA-Seq libraries were constructed by depletion of rRNA followed by synthesis of directional, paired-end and indexed RNA-Seq libraries. The rRNA depleted RNA was purified using the RNA Clean & Concentrator™-5 columns (Zymo Research). Speed-vac was used to reduce the remaining sample volume to 9.5μL followed by synthesis of directional, paired-end and indexed RNA-Seq libraries using the ScriptSeq kit (Epicentre). Briefly, rRNA depleted RNA was chemically fragmented and cDNA was synthesized from a tagged random hexamer. The cDNA was terminal tagged using a 3’-end blocked and tagged oligo followed by MiniElute (Qiagen) purification. The di-tagged cDNA was then used as template in a 10 cycle PCR reaction. Libraries were purified by agarose gel electrophoresis selecting elements of 200-600 bp in size. The RNA-Seq libraries were denaturated and diluted to 10 pM with pre-chilled Hybridization buffer (Illumina) and loaded into TruSeq PE v3 flowcells (Illumina) on an Illumina cBot followed by indexed paired-end sequencing (101+7+101 bp) on a Illumina HiSeq 2000 using TruSeq SBS Kit v3 chemistry.

GSM1101969

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252505,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01984808

GSM1101969

GSE45326

Biochain:R-1234090-P

Public on Sep 01 2013

Mar 19 2013

9606

Colon

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252505

https://www.ncbi.nlm.nih.gov/biosample/SAMN01984808

tissue: heart

Palle Juul-Jensens Bouleward 99

Aarhus

Denmark

Aarhus University

Morten,Muhlig,Nielsen

Illumina Casava software used for basecalling, and Tophat and Cufflinks used for transcript FPKM estiamtes.,Genome_build: hg18,Supplementary_files_format_and_content: Total transcript FPKM values in the GTF file format

Normal tissue provided by Biochain. Total RNA was isolated by a modified guanidine thiocyanate technique according to BioCahin certificate of analysis F-753-1-6 revA.,Using 500 ng of total-RNA from each of the samples, RNA-Seq libraries were constructed by depletion of rRNA followed by synthesis of directional, paired-end and indexed RNA-Seq libraries. The rRNA depleted RNA was purified using the RNA Clean & Concentrator™-5 columns (Zymo Research). Speed-vac was used to reduce the remaining sample volume to 9.5μL followed by synthesis of directional, paired-end and indexed RNA-Seq libraries using the ScriptSeq kit (Epicentre). Briefly, rRNA depleted RNA was chemically fragmented and cDNA was synthesized from a tagged random hexamer. The cDNA was terminal tagged using a 3’-end blocked and tagged oligo followed by MiniElute (Qiagen) purification. The di-tagged cDNA was then used as template in a 10 cycle PCR reaction. Libraries were purified by agarose gel electrophoresis selecting elements of 200-600 bp in size. The RNA-Seq libraries were denaturated and diluted to 10 pM with pre-chilled Hybridization buffer (Illumina) and loaded into TruSeq PE v3 flowcells (Illumina) on an Illumina cBot followed by indexed paired-end sequencing (101+7+101 bp) on a Illumina HiSeq 2000 using TruSeq SBS Kit v3 chemistry.

GSM1101970

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252506,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01984809

GSM1101970

GSE45326

Biochain:R-1234122-P

Public on Sep 01 2013

Mar 19 2013

9606

Heart

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252506

https://www.ncbi.nlm.nih.gov/biosample/SAMN01984809

tissue: kidney

Palle Juul-Jensens Bouleward 99

Aarhus

Denmark

Aarhus University

Morten,Muhlig,Nielsen

Illumina Casava software used for basecalling, and Tophat and Cufflinks used for transcript FPKM estiamtes.,Genome_build: hg18,Supplementary_files_format_and_content: Total transcript FPKM values in the GTF file format

Normal tissue provided by Biochain. Total RNA was isolated by a modified guanidine thiocyanate technique according to BioCahin certificate of analysis F-753-1-6 revA.,Using 500 ng of total-RNA from each of the samples, RNA-Seq libraries were constructed by depletion of rRNA followed by synthesis of directional, paired-end and indexed RNA-Seq libraries. The rRNA depleted RNA was purified using the RNA Clean & Concentrator™-5 columns (Zymo Research). Speed-vac was used to reduce the remaining sample volume to 9.5μL followed by synthesis of directional, paired-end and indexed RNA-Seq libraries using the ScriptSeq kit (Epicentre). Briefly, rRNA depleted RNA was chemically fragmented and cDNA was synthesized from a tagged random hexamer. The cDNA was terminal tagged using a 3’-end blocked and tagged oligo followed by MiniElute (Qiagen) purification. The di-tagged cDNA was then used as template in a 10 cycle PCR reaction. Libraries were purified by agarose gel electrophoresis selecting elements of 200-600 bp in size. The RNA-Seq libraries were denaturated and diluted to 10 pM with pre-chilled Hybridization buffer (Illumina) and loaded into TruSeq PE v3 flowcells (Illumina) on an Illumina cBot followed by indexed paired-end sequencing (101+7+101 bp) on a Illumina HiSeq 2000 using TruSeq SBS Kit v3 chemistry.

GSM1101971

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252507,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01984810

GSM1101971

GSE45326

Biochain:R-1234142-P

Public on Sep 01 2013

Mar 19 2013

9606

Kidney

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252507

https://www.ncbi.nlm.nih.gov/biosample/SAMN01984810

tissue: liver

Palle Juul-Jensens Bouleward 99

Aarhus

Denmark

Aarhus University

Morten,Muhlig,Nielsen

Illumina Casava software used for basecalling, and Tophat and Cufflinks used for transcript FPKM estiamtes.,Genome_build: hg18,Supplementary_files_format_and_content: Total transcript FPKM values in the GTF file format

Normal tissue provided by Biochain. Total RNA was isolated by a modified guanidine thiocyanate technique according to BioCahin certificate of analysis F-753-1-6 revA.,Using 500 ng of total-RNA from each of the samples, RNA-Seq libraries were constructed by depletion of rRNA followed by synthesis of directional, paired-end and indexed RNA-Seq libraries. The rRNA depleted RNA was purified using the RNA Clean & Concentrator™-5 columns (Zymo Research). Speed-vac was used to reduce the remaining sample volume to 9.5μL followed by synthesis of directional, paired-end and indexed RNA-Seq libraries using the ScriptSeq kit (Epicentre). Briefly, rRNA depleted RNA was chemically fragmented and cDNA was synthesized from a tagged random hexamer. The cDNA was terminal tagged using a 3’-end blocked and tagged oligo followed by MiniElute (Qiagen) purification. The di-tagged cDNA was then used as template in a 10 cycle PCR reaction. Libraries were purified by agarose gel electrophoresis selecting elements of 200-600 bp in size. The RNA-Seq libraries were denaturated and diluted to 10 pM with pre-chilled Hybridization buffer (Illumina) and loaded into TruSeq PE v3 flowcells (Illumina) on an Illumina cBot followed by indexed paired-end sequencing (101+7+101 bp) on a Illumina HiSeq 2000 using TruSeq SBS Kit v3 chemistry.

GSM1101972

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252508,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01984811

GSM1101972

GSE45326

Biochain:R-1234149-P

Public on Sep 01 2013

Mar 19 2013

9606

Liver

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252508

https://www.ncbi.nlm.nih.gov/biosample/SAMN01984811

tissue: lung

Palle Juul-Jensens Bouleward 99

Aarhus

Denmark

Aarhus University

Morten,Muhlig,Nielsen

Illumina Casava software used for basecalling, and Tophat and Cufflinks used for transcript FPKM estiamtes.,Genome_build: hg18,Supplementary_files_format_and_content: Total transcript FPKM values in the GTF file format

Normal tissue provided by Biochain. Total RNA was isolated by a modified guanidine thiocyanate technique according to BioCahin certificate of analysis F-753-1-6 revA.,Using 500 ng of total-RNA from each of the samples, RNA-Seq libraries were constructed by depletion of rRNA followed by synthesis of directional, paired-end and indexed RNA-Seq libraries. The rRNA depleted RNA was purified using the RNA Clean & Concentrator™-5 columns (Zymo Research). Speed-vac was used to reduce the remaining sample volume to 9.5μL followed by synthesis of directional, paired-end and indexed RNA-Seq libraries using the ScriptSeq kit (Epicentre). Briefly, rRNA depleted RNA was chemically fragmented and cDNA was synthesized from a tagged random hexamer. The cDNA was terminal tagged using a 3’-end blocked and tagged oligo followed by MiniElute (Qiagen) purification. The di-tagged cDNA was then used as template in a 10 cycle PCR reaction. Libraries were purified by agarose gel electrophoresis selecting elements of 200-600 bp in size. The RNA-Seq libraries were denaturated and diluted to 10 pM with pre-chilled Hybridization buffer (Illumina) and loaded into TruSeq PE v3 flowcells (Illumina) on an Illumina cBot followed by indexed paired-end sequencing (101+7+101 bp) on a Illumina HiSeq 2000 using TruSeq SBS Kit v3 chemistry.

GSM1101973

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252509,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01984812

GSM1101973

GSE45326

Biochain:R-1234152-P

Public on Sep 01 2013

Mar 19 2013

9606

Lung

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252509

https://www.ncbi.nlm.nih.gov/biosample/SAMN01984812

tissue: muscle

Palle Juul-Jensens Bouleward 99

Aarhus

Denmark

Aarhus University

Morten,Muhlig,Nielsen

Illumina Casava software used for basecalling, and Tophat and Cufflinks used for transcript FPKM estiamtes.,Genome_build: hg18,Supplementary_files_format_and_content: Total transcript FPKM values in the GTF file format

Normal tissue provided by Biochain. Total RNA was isolated by a modified guanidine thiocyanate technique according to BioCahin certificate of analysis F-753-1-6 revA.,Using 500 ng of total-RNA from each of the samples, RNA-Seq libraries were constructed by depletion of rRNA followed by synthesis of directional, paired-end and indexed RNA-Seq libraries. The rRNA depleted RNA was purified using the RNA Clean & Concentrator™-5 columns (Zymo Research). Speed-vac was used to reduce the remaining sample volume to 9.5μL followed by synthesis of directional, paired-end and indexed RNA-Seq libraries using the ScriptSeq kit (Epicentre). Briefly, rRNA depleted RNA was chemically fragmented and cDNA was synthesized from a tagged random hexamer. The cDNA was terminal tagged using a 3’-end blocked and tagged oligo followed by MiniElute (Qiagen) purification. The di-tagged cDNA was then used as template in a 10 cycle PCR reaction. Libraries were purified by agarose gel electrophoresis selecting elements of 200-600 bp in size. The RNA-Seq libraries were denaturated and diluted to 10 pM with pre-chilled Hybridization buffer (Illumina) and loaded into TruSeq PE v3 flowcells (Illumina) on an Illumina cBot followed by indexed paired-end sequencing (101+7+101 bp) on a Illumina HiSeq 2000 using TruSeq SBS Kit v3 chemistry.

GSM1101974

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252510,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01984813

GSM1101974

GSE45326

Biochain:R-1234171-P

Public on Sep 01 2013

Mar 19 2013

9606

Muscle

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252510

https://www.ncbi.nlm.nih.gov/biosample/SAMN01984813

tissue: ovary

Palle Juul-Jensens Bouleward 99

Aarhus

Denmark

Aarhus University

Morten,Muhlig,Nielsen

Illumina Casava software used for basecalling, and Tophat and Cufflinks used for transcript FPKM estiamtes.,Genome_build: hg18,Supplementary_files_format_and_content: Total transcript FPKM values in the GTF file format

Normal tissue provided by Biochain. Total RNA was isolated by a modified guanidine thiocyanate technique according to BioCahin certificate of analysis F-753-1-6 revA.,Using 500 ng of total-RNA from each of the samples, RNA-Seq libraries were constructed by depletion of rRNA followed by synthesis of directional, paired-end and indexed RNA-Seq libraries. The rRNA depleted RNA was purified using the RNA Clean & Concentrator™-5 columns (Zymo Research). Speed-vac was used to reduce the remaining sample volume to 9.5μL followed by synthesis of directional, paired-end and indexed RNA-Seq libraries using the ScriptSeq kit (Epicentre). Briefly, rRNA depleted RNA was chemically fragmented and cDNA was synthesized from a tagged random hexamer. The cDNA was terminal tagged using a 3’-end blocked and tagged oligo followed by MiniElute (Qiagen) purification. The di-tagged cDNA was then used as template in a 10 cycle PCR reaction. Libraries were purified by agarose gel electrophoresis selecting elements of 200-600 bp in size. The RNA-Seq libraries were denaturated and diluted to 10 pM with pre-chilled Hybridization buffer (Illumina) and loaded into TruSeq PE v3 flowcells (Illumina) on an Illumina cBot followed by indexed paired-end sequencing (101+7+101 bp) on a Illumina HiSeq 2000 using TruSeq SBS Kit v3 chemistry.

GSM1101975

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252511,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01984814

GSM1101975

GSE45326

Biochain:R-1234183-P

Public on Sep 01 2013

Mar 19 2013

9606

Ovary

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252511

https://www.ncbi.nlm.nih.gov/biosample/SAMN01984814

tissue: prostate

Palle Juul-Jensens Bouleward 99

Aarhus

Denmark

Aarhus University

Morten,Muhlig,Nielsen

Illumina Casava software used for basecalling, and Tophat and Cufflinks used for transcript FPKM estiamtes.,Genome_build: hg18,Supplementary_files_format_and_content: Total transcript FPKM values in the GTF file format

Normal tissue provided by Biochain. Total RNA was isolated by a modified guanidine thiocyanate technique according to BioCahin certificate of analysis F-753-1-6 revA.,Using 500 ng of total-RNA from each of the samples, RNA-Seq libraries were constructed by depletion of rRNA followed by synthesis of directional, paired-end and indexed RNA-Seq libraries. The rRNA depleted RNA was purified using the RNA Clean & Concentrator™-5 columns (Zymo Research). Speed-vac was used to reduce the remaining sample volume to 9.5μL followed by synthesis of directional, paired-end and indexed RNA-Seq libraries using the ScriptSeq kit (Epicentre). Briefly, rRNA depleted RNA was chemically fragmented and cDNA was synthesized from a tagged random hexamer. The cDNA was terminal tagged using a 3’-end blocked and tagged oligo followed by MiniElute (Qiagen) purification. The di-tagged cDNA was then used as template in a 10 cycle PCR reaction. Libraries were purified by agarose gel electrophoresis selecting elements of 200-600 bp in size. The RNA-Seq libraries were denaturated and diluted to 10 pM with pre-chilled Hybridization buffer (Illumina) and loaded into TruSeq PE v3 flowcells (Illumina) on an Illumina cBot followed by indexed paired-end sequencing (101+7+101 bp) on a Illumina HiSeq 2000 using TruSeq SBS Kit v3 chemistry.

GSM1101976

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252513,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01984815

GSM1101976

GSE45326

Biochain:R-1234201-P

Public on Sep 01 2013

Mar 19 2013

9606

Prostate

SRA

https://www.ncbi.nlm.nih.gov/sra?term=SRX252513

https://www.ncbi.nlm.nih.gov/biosample/SAMN01984815

tissue: skin

Palle Juul-Jensens Bouleward 99

Aarhus

Denmark

Aarhus University

Morten,Muhlig,Nielsen

Illumina Casava software used for basecalling, and Tophat and Cufflinks used for transcript FPKM estiamtes.,Genome_build: hg18,Supplementary_files_format_and_content: Total transcript FPKM values in the GTF file format

Normal tissue provided by Biochain. Total RNA was isolated by a modified guanidine thiocyanate technique according to BioCahin certificate of analysis F-753-1-6 revA.,Using 500 ng of total-RNA from each of the samples, RNA-Seq libraries were constructed by depletion of rRNA followed by synthesis of directional, paired-end and indexed RNA-Seq libraries. The rRNA depleted RNA was purified using the RNA Clean & Concentrator™-5 columns (Zymo Research). Speed-vac was used to reduce the remaining sample volume to 9.5μL followed by synthesis of directional, paired-end and indexed RNA-Seq libraries using the ScriptSeq kit (Epicentre). Briefly, rRNA depleted RNA was chemically fragmented and cDNA was synthesized from a tagged random hexamer. The cDNA was terminal tagged using a 3’-end blocked and tagged oligo followed by MiniElute (Qiagen) purification. The di-tagged cDNA was then used as template in a 10 cycle PCR reaction. Libraries were purified by agarose gel electrophoresis selecting elements of 200-600 bp in size. The RNA-Seq libraries were denaturated and diluted to 10 pM with pre-chilled Hybridization buffer (Illumina) and loaded into TruSeq PE v3 flowcells (Illumina) on an Illumina cBot followed by indexed paired-end sequencing (101+7+101 bp) on a Illumina HiSeq 2000 using TruSeq SBS Kit v3 chemistry.

GSM1101977

Illumina HiSeq 2000

May 15 2019

cDNA

transcriptomic

RNA-Seq

total RNA

Homo sapiens

GPL11154

SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX252512,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01984816

GSM1101977

GSE45326