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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126686 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053681,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268782 | GSM1126686 | GSE46224 | 0.130408 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM+LVAD3_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268782 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053681 |
|
1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126687 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053650,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268783 | GSM1126687 | GSE46224 | 0.137188 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM+LVAD4_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268783 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053650 |
|
1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126688 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053651,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268784 | GSM1126688 | GSE46224 | 0.318616 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM+LVAD5_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268784 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053651 |
|
1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126689 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053652,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268785 | GSM1126689 | GSE46224 | 0 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM+LVAD6_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268785 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053652 |
|
1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126690 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053653,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268786 | GSM1126690 | GSE46224 | 0.053896 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM+LVAD7_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268786 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053653 |
|
1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126691 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053654,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268787 | GSM1126691 | GSE46224 | 0.04742 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM+LVAD8_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268787 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053654 |
|
1 | cell type: tumor cells,library: 4sU RNA | 270 Dongan | Shanghai | China | Fudan University | Shenglin,,Huang | Illumina Casava1.7 software used for basecalling.,Reads were mapped to human reference genome GRCh37/hg19 by using TopHat 1.3.1,The expression levels of mRNAs and geRNAs were calculated with FPKM (Fragments Per Kilobase per Million fragments mapped) by using Cufflink 2.0.2,Genome_build: hg19,Supplementary_files_format_and_content: bigwig files | Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturerâs instructions. Nuclear and cytoplasmic RNA were separated and extracted using the PARIS⢠Kit (Ambion). Poly(A) RNA was purified with two rounds of hybridization to Dynal oligo(dT) beads (Invitrogen). Nuclear and cytoplasmic RNA samples were treated with RiboMinus⢠Eukaryote Kit (Invitrogen) to remove ribosomal RNA before constructing RNA-seq libraries.The 4sU-labeled RNA was isolated by using organomercurial affinity matrix.,Strand-specific RNA-seq libraries were constructed from various RNA samples. Specifically, the 4sU-labeled RNA, poly(A) RNA, nuclear RNA (ribosome minus), and cytoplasmic RNA (ribosome minus) were used for library construction. Briefly, RNA samples (about 200 ng) were fragmented and then used for first- and second-strand cDNA synthesis with random hexamer primers. For second-strand cDNA synthesis, dUTP mix (without dTTP) was used which allows for the removal of the second strand. The cDNA fragments were treated with End-It DNA End Repair Kit (Epicentre) to repair the ends, then modified with Klenow fragment 3â to 5â exo- (NEB) to add an âAâ base at the 3âend of the DNA fragments, and finally ligated to adapters with a âTâ overhang. Ligated cDNA products were size selected (300-600 bp) and treated with uracil DNA glycosylase (NEB) to remove the second-strand cDNA. Purified first-strand cDNA was subjected to 15 cycles of PCR amplification. Library quality was determined on Bioanalyzer 2100 (Agilent). Finally sequencing was performed on Illumina HiSeq 2000 (2 à 100 bp paired-end). | GSM1126809 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053911,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX269414 | GSM1126809 | GSE46228 | 0 | HelaS3 cells | Public on Dec 31 2013 | Apr 19 2013 | 9606 | 4sU_RNA_repeat1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX269414 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053911 |
|
1 | cell type: tumor cells,library: 4sU RNA | 270 Dongan | Shanghai | China | Fudan University | Shenglin,,Huang | Illumina Casava1.7 software used for basecalling.,Reads were mapped to human reference genome GRCh37/hg19 by using TopHat 1.3.1,The expression levels of mRNAs and geRNAs were calculated with FPKM (Fragments Per Kilobase per Million fragments mapped) by using Cufflink 2.0.2,Genome_build: hg19,Supplementary_files_format_and_content: bigwig files | Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturerâs instructions. Nuclear and cytoplasmic RNA were separated and extracted using the PARIS⢠Kit (Ambion). Poly(A) RNA was purified with two rounds of hybridization to Dynal oligo(dT) beads (Invitrogen). Nuclear and cytoplasmic RNA samples were treated with RiboMinus⢠Eukaryote Kit (Invitrogen) to remove ribosomal RNA before constructing RNA-seq libraries.The 4sU-labeled RNA was isolated by using organomercurial affinity matrix.,Strand-specific RNA-seq libraries were constructed from various RNA samples. Specifically, the 4sU-labeled RNA, poly(A) RNA, nuclear RNA (ribosome minus), and cytoplasmic RNA (ribosome minus) were used for library construction. Briefly, RNA samples (about 200 ng) were fragmented and then used for first- and second-strand cDNA synthesis with random hexamer primers. For second-strand cDNA synthesis, dUTP mix (without dTTP) was used which allows for the removal of the second strand. The cDNA fragments were treated with End-It DNA End Repair Kit (Epicentre) to repair the ends, then modified with Klenow fragment 3â to 5â exo- (NEB) to add an âAâ base at the 3âend of the DNA fragments, and finally ligated to adapters with a âTâ overhang. Ligated cDNA products were size selected (300-600 bp) and treated with uracil DNA glycosylase (NEB) to remove the second-strand cDNA. Purified first-strand cDNA was subjected to 15 cycles of PCR amplification. Library quality was determined on Bioanalyzer 2100 (Agilent). Finally sequencing was performed on Illumina HiSeq 2000 (2 à 100 bp paired-end). | GSM1126810 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053912,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX269415 | GSM1126810 | GSE46228 | 0.10889 | HelaS3 cells | Public on Dec 31 2013 | Apr 19 2013 | 9606 | 4sU_RNA_repeat2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX269415 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053912 |
|
1 | cell type: tumor cells,library: polyA RNA | 270 Dongan | Shanghai | China | Fudan University | Shenglin,,Huang | Illumina Casava1.7 software used for basecalling.,Reads were mapped to human reference genome GRCh37/hg19 by using TopHat 1.3.1,The expression levels of mRNAs and geRNAs were calculated with FPKM (Fragments Per Kilobase per Million fragments mapped) by using Cufflink 2.0.2,Genome_build: hg19,Supplementary_files_format_and_content: bigwig files | Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturerâs instructions. Nuclear and cytoplasmic RNA were separated and extracted using the PARIS⢠Kit (Ambion). Poly(A) RNA was purified with two rounds of hybridization to Dynal oligo(dT) beads (Invitrogen). Nuclear and cytoplasmic RNA samples were treated with RiboMinus⢠Eukaryote Kit (Invitrogen) to remove ribosomal RNA before constructing RNA-seq libraries.The 4sU-labeled RNA was isolated by using organomercurial affinity matrix.,Strand-specific RNA-seq libraries were constructed from various RNA samples. Specifically, the 4sU-labeled RNA, poly(A) RNA, nuclear RNA (ribosome minus), and cytoplasmic RNA (ribosome minus) were used for library construction. Briefly, RNA samples (about 200 ng) were fragmented and then used for first- and second-strand cDNA synthesis with random hexamer primers. For second-strand cDNA synthesis, dUTP mix (without dTTP) was used which allows for the removal of the second strand. The cDNA fragments were treated with End-It DNA End Repair Kit (Epicentre) to repair the ends, then modified with Klenow fragment 3â to 5â exo- (NEB) to add an âAâ base at the 3âend of the DNA fragments, and finally ligated to adapters with a âTâ overhang. Ligated cDNA products were size selected (300-600 bp) and treated with uracil DNA glycosylase (NEB) to remove the second-strand cDNA. Purified first-strand cDNA was subjected to 15 cycles of PCR amplification. Library quality was determined on Bioanalyzer 2100 (Agilent). Finally sequencing was performed on Illumina HiSeq 2000 (2 à 100 bp paired-end). | GSM1126811 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053913,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX269416 | GSM1126811 | GSE46228 | 0 | HelaS3 cells | Public on Dec 31 2013 | Apr 19 2013 | 9606 | polyA_RNA_repeat1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX269416 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053913 |
|
1 | cell type: tumor cells,library: polyA RNA | 270 Dongan | Shanghai | China | Fudan University | Shenglin,,Huang | Illumina Casava1.7 software used for basecalling.,Reads were mapped to human reference genome GRCh37/hg19 by using TopHat 1.3.1,The expression levels of mRNAs and geRNAs were calculated with FPKM (Fragments Per Kilobase per Million fragments mapped) by using Cufflink 2.0.2,Genome_build: hg19,Supplementary_files_format_and_content: bigwig files | Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturerâs instructions. Nuclear and cytoplasmic RNA were separated and extracted using the PARIS⢠Kit (Ambion). Poly(A) RNA was purified with two rounds of hybridization to Dynal oligo(dT) beads (Invitrogen). Nuclear and cytoplasmic RNA samples were treated with RiboMinus⢠Eukaryote Kit (Invitrogen) to remove ribosomal RNA before constructing RNA-seq libraries.The 4sU-labeled RNA was isolated by using organomercurial affinity matrix.,Strand-specific RNA-seq libraries were constructed from various RNA samples. Specifically, the 4sU-labeled RNA, poly(A) RNA, nuclear RNA (ribosome minus), and cytoplasmic RNA (ribosome minus) were used for library construction. Briefly, RNA samples (about 200 ng) were fragmented and then used for first- and second-strand cDNA synthesis with random hexamer primers. For second-strand cDNA synthesis, dUTP mix (without dTTP) was used which allows for the removal of the second strand. The cDNA fragments were treated with End-It DNA End Repair Kit (Epicentre) to repair the ends, then modified with Klenow fragment 3â to 5â exo- (NEB) to add an âAâ base at the 3âend of the DNA fragments, and finally ligated to adapters with a âTâ overhang. Ligated cDNA products were size selected (300-600 bp) and treated with uracil DNA glycosylase (NEB) to remove the second-strand cDNA. Purified first-strand cDNA was subjected to 15 cycles of PCR amplification. Library quality was determined on Bioanalyzer 2100 (Agilent). Finally sequencing was performed on Illumina HiSeq 2000 (2 à 100 bp paired-end). | GSM1126812 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053914,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX269417 | GSM1126812 | GSE46228 | 0 | HelaS3 cells | Public on Dec 31 2013 | Apr 19 2013 | 9606 | polyA_RNA_repeat2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX269417 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053914 |
|
1 | cell type: tumor cells,library: nucleus RNA | 270 Dongan | Shanghai | China | Fudan University | Shenglin,,Huang | Illumina Casava1.7 software used for basecalling.,Reads were mapped to human reference genome GRCh37/hg19 by using TopHat 1.3.1,The expression levels of mRNAs and geRNAs were calculated with FPKM (Fragments Per Kilobase per Million fragments mapped) by using Cufflink 2.0.2,Genome_build: hg19,Supplementary_files_format_and_content: bigwig files | Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturerâs instructions. Nuclear and cytoplasmic RNA were separated and extracted using the PARIS⢠Kit (Ambion). Poly(A) RNA was purified with two rounds of hybridization to Dynal oligo(dT) beads (Invitrogen). Nuclear and cytoplasmic RNA samples were treated with RiboMinus⢠Eukaryote Kit (Invitrogen) to remove ribosomal RNA before constructing RNA-seq libraries.The 4sU-labeled RNA was isolated by using organomercurial affinity matrix.,Strand-specific RNA-seq libraries were constructed from various RNA samples. Specifically, the 4sU-labeled RNA, poly(A) RNA, nuclear RNA (ribosome minus), and cytoplasmic RNA (ribosome minus) were used for library construction. Briefly, RNA samples (about 200 ng) were fragmented and then used for first- and second-strand cDNA synthesis with random hexamer primers. For second-strand cDNA synthesis, dUTP mix (without dTTP) was used which allows for the removal of the second strand. The cDNA fragments were treated with End-It DNA End Repair Kit (Epicentre) to repair the ends, then modified with Klenow fragment 3â to 5â exo- (NEB) to add an âAâ base at the 3âend of the DNA fragments, and finally ligated to adapters with a âTâ overhang. Ligated cDNA products were size selected (300-600 bp) and treated with uracil DNA glycosylase (NEB) to remove the second-strand cDNA. Purified first-strand cDNA was subjected to 15 cycles of PCR amplification. Library quality was determined on Bioanalyzer 2100 (Agilent). Finally sequencing was performed on Illumina HiSeq 2000 (2 à 100 bp paired-end). | GSM1126813 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053915,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX269418 | GSM1126813 | GSE46228 | 0.000675 | HelaS3 cells | Public on Dec 31 2013 | Apr 19 2013 | 9606 | Nucleus_RNA_repeat1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX269418 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053915 |
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1 | cell type: tumor cells,library: nucleus RNA | 270 Dongan | Shanghai | China | Fudan University | Shenglin,,Huang | Illumina Casava1.7 software used for basecalling.,Reads were mapped to human reference genome GRCh37/hg19 by using TopHat 1.3.1,The expression levels of mRNAs and geRNAs were calculated with FPKM (Fragments Per Kilobase per Million fragments mapped) by using Cufflink 2.0.2,Genome_build: hg19,Supplementary_files_format_and_content: bigwig files | Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturerâs instructions. Nuclear and cytoplasmic RNA were separated and extracted using the PARIS⢠Kit (Ambion). Poly(A) RNA was purified with two rounds of hybridization to Dynal oligo(dT) beads (Invitrogen). Nuclear and cytoplasmic RNA samples were treated with RiboMinus⢠Eukaryote Kit (Invitrogen) to remove ribosomal RNA before constructing RNA-seq libraries.The 4sU-labeled RNA was isolated by using organomercurial affinity matrix.,Strand-specific RNA-seq libraries were constructed from various RNA samples. Specifically, the 4sU-labeled RNA, poly(A) RNA, nuclear RNA (ribosome minus), and cytoplasmic RNA (ribosome minus) were used for library construction. Briefly, RNA samples (about 200 ng) were fragmented and then used for first- and second-strand cDNA synthesis with random hexamer primers. For second-strand cDNA synthesis, dUTP mix (without dTTP) was used which allows for the removal of the second strand. The cDNA fragments were treated with End-It DNA End Repair Kit (Epicentre) to repair the ends, then modified with Klenow fragment 3â to 5â exo- (NEB) to add an âAâ base at the 3âend of the DNA fragments, and finally ligated to adapters with a âTâ overhang. Ligated cDNA products were size selected (300-600 bp) and treated with uracil DNA glycosylase (NEB) to remove the second-strand cDNA. Purified first-strand cDNA was subjected to 15 cycles of PCR amplification. Library quality was determined on Bioanalyzer 2100 (Agilent). Finally sequencing was performed on Illumina HiSeq 2000 (2 à 100 bp paired-end). | GSM1126814 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053916,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX269419 | GSM1126814 | GSE46228 | 0 | HelaS3 cells | Public on Dec 31 2013 | Apr 19 2013 | 9606 | Nucleus_RNA_repeat2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX269419 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053916 |
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1 | cell type: tumor cells,library: cyto RNA | 270 Dongan | Shanghai | China | Fudan University | Shenglin,,Huang | Illumina Casava1.7 software used for basecalling.,Reads were mapped to human reference genome GRCh37/hg19 by using TopHat 1.3.1,The expression levels of mRNAs and geRNAs were calculated with FPKM (Fragments Per Kilobase per Million fragments mapped) by using Cufflink 2.0.2,Genome_build: hg19,Supplementary_files_format_and_content: bigwig files | Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturerâs instructions. Nuclear and cytoplasmic RNA were separated and extracted using the PARIS⢠Kit (Ambion). Poly(A) RNA was purified with two rounds of hybridization to Dynal oligo(dT) beads (Invitrogen). Nuclear and cytoplasmic RNA samples were treated with RiboMinus⢠Eukaryote Kit (Invitrogen) to remove ribosomal RNA before constructing RNA-seq libraries.The 4sU-labeled RNA was isolated by using organomercurial affinity matrix.,Strand-specific RNA-seq libraries were constructed from various RNA samples. Specifically, the 4sU-labeled RNA, poly(A) RNA, nuclear RNA (ribosome minus), and cytoplasmic RNA (ribosome minus) were used for library construction. Briefly, RNA samples (about 200 ng) were fragmented and then used for first- and second-strand cDNA synthesis with random hexamer primers. For second-strand cDNA synthesis, dUTP mix (without dTTP) was used which allows for the removal of the second strand. The cDNA fragments were treated with End-It DNA End Repair Kit (Epicentre) to repair the ends, then modified with Klenow fragment 3â to 5â exo- (NEB) to add an âAâ base at the 3âend of the DNA fragments, and finally ligated to adapters with a âTâ overhang. Ligated cDNA products were size selected (300-600 bp) and treated with uracil DNA glycosylase (NEB) to remove the second-strand cDNA. Purified first-strand cDNA was subjected to 15 cycles of PCR amplification. Library quality was determined on Bioanalyzer 2100 (Agilent). Finally sequencing was performed on Illumina HiSeq 2000 (2 à 100 bp paired-end). | GSM1126815 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053917,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX269420 | GSM1126815 | GSE46228 | 0.006441 | HelaS3 cells | Public on Dec 31 2013 | Apr 19 2013 | 9606 | Cyto_RNA_repeat1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX269420 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053917 |
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1 | cell type: tumor cells,library: cyto RNA | 270 Dongan | Shanghai | China | Fudan University | Shenglin,,Huang | Illumina Casava1.7 software used for basecalling.,Reads were mapped to human reference genome GRCh37/hg19 by using TopHat 1.3.1,The expression levels of mRNAs and geRNAs were calculated with FPKM (Fragments Per Kilobase per Million fragments mapped) by using Cufflink 2.0.2,Genome_build: hg19,Supplementary_files_format_and_content: bigwig files | Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturerâs instructions. Nuclear and cytoplasmic RNA were separated and extracted using the PARIS⢠Kit (Ambion). Poly(A) RNA was purified with two rounds of hybridization to Dynal oligo(dT) beads (Invitrogen). Nuclear and cytoplasmic RNA samples were treated with RiboMinus⢠Eukaryote Kit (Invitrogen) to remove ribosomal RNA before constructing RNA-seq libraries.The 4sU-labeled RNA was isolated by using organomercurial affinity matrix.,Strand-specific RNA-seq libraries were constructed from various RNA samples. Specifically, the 4sU-labeled RNA, poly(A) RNA, nuclear RNA (ribosome minus), and cytoplasmic RNA (ribosome minus) were used for library construction. Briefly, RNA samples (about 200 ng) were fragmented and then used for first- and second-strand cDNA synthesis with random hexamer primers. For second-strand cDNA synthesis, dUTP mix (without dTTP) was used which allows for the removal of the second strand. The cDNA fragments were treated with End-It DNA End Repair Kit (Epicentre) to repair the ends, then modified with Klenow fragment 3â to 5â exo- (NEB) to add an âAâ base at the 3âend of the DNA fragments, and finally ligated to adapters with a âTâ overhang. Ligated cDNA products were size selected (300-600 bp) and treated with uracil DNA glycosylase (NEB) to remove the second-strand cDNA. Purified first-strand cDNA was subjected to 15 cycles of PCR amplification. Library quality was determined on Bioanalyzer 2100 (Agilent). Finally sequencing was performed on Illumina HiSeq 2000 (2 à 100 bp paired-end). | GSM1126816 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053918,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX269421 | GSM1126816 | GSE46228 | 0.009694 | HelaS3 cells | Public on Dec 31 2013 | Apr 19 2013 | 9606 | Cyto_RNA_repeat2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX269421 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053918 |
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1 | tissue: adipose,treatment: control | 423 Guardian Drive | Philadelphia | USA | University of Pennsylvania | Yichuan,,Liu | Generate gene expression by cufflink v1.3.0,Generate alternative splicing files by MATS2.1.0,Genome_build: hg19,Supplementary_files_format_and_content: Standard cufflink outputs, tab-delimited text files including FPKM values and FDR adjusted p-values.,Supplementary_files_format_and_content: A_adipose_gene_exp.xls contains the differentially expressed genes from cuffdiff at variant read depths. The read depths were ranged from 5M reads to 500M reads (full set). In the excel file one tab has the cuffdiff result for one read depth, e.g. adipose_100M indicates the differentially expressed gene results for adipose tissue at read depth 100M reads.,Supplementary_files_format_and_content: A_adipose_gene_exp_simluation_100M.xls contains the differentially expressed genes for certain read depth (100M reads here) for 10 times simulation. The purpose is to evaluate sampling variations and to see whether the sequenced reads are representative. Each tab in the excel file contains the differentially expressed genes for each simulation rounds, as a result, 10 tabs in this file. Similar description for A_adipose_gene_exp_simulation_10M.xls file, the only difference is the read depth in simulation is 10M reads.,Supplementary_files_format_and_content: MATS_A_adipose.xls represents the alternative-splicing (AS) results from Multivariate Analysis of Transcript Splicing (MATS). Similar to A_adipose_gene_exp.xls, it contains the AS results for adipose tissue at variant depths from 5M to 500M reads. Each tab represents the AS results for one depth.,Supplementary_files_format_and_content: MATS_A_adipose_simulation_100M.xls and MATS_A_adipose_simulation_10M.xls represents the AS results for 10 times simulation at read depths 100M and 10M reads. Similar to A_adipose_gene_exp_simulation_100M.xls and A_adipose_gene_exp_simulation_10M.xls, each tab contains the AS result for one simulation rounds, as a result, totally 10 tabs. | For adipose tissue, the RNA was extracted using RNeasy lipid total RNA mini kit (Qiagen, Valencia, CA). Extracted RNA samples underwent quality control (QC) assessment using the Agilent Bioanalyzer (Agilent, Santa Clara, CA). Poly-A library preparation and RNA sequencing were performed at the Penn Genome Frontiers Instituteâs High-Throughput Sequencing Facility per Illuminaâs (San Diego, CA) standard protocols. Briefly, we generated first-strand cDNA using random hexamer-primed reverse transcription, followed by second-strand cDNA synthesis using RNase H and DNA polymerase, and ligation of sequencing adapters using the Illumina paired-end sample preparation kit. Fragments of ~350 bp were selected gel electrophoresis, followed by 15 cycles of PCR amplification. The prepared libraries were then sequenced using Illuminaâs HiSeq 2000 at four lanes per sample (~456 million to 701 million 2 Ã 101 bp paired-end reads per sample). | GSM1128650 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02055492,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271431 | GSM1128650 | GSE46323 | 0.101407 | adipose_preLPS | Public on Jul 12 2013 | Apr 23 2013 | 9606 | A_adipose_preLPS (Sample 1) | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271431 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02055492 |
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1 | tissue: adipose,treatment: LPS | 423 Guardian Drive | Philadelphia | USA | University of Pennsylvania | Yichuan,,Liu | Generate gene expression by cufflink v1.3.0,Generate alternative splicing files by MATS2.1.0,Genome_build: hg19,Supplementary_files_format_and_content: Standard cufflink outputs, tab-delimited text files including FPKM values and FDR adjusted p-values.,Supplementary_files_format_and_content: A_adipose_gene_exp.xls contains the differentially expressed genes from cuffdiff at variant read depths. The read depths were ranged from 5M reads to 500M reads (full set). In the excel file one tab has the cuffdiff result for one read depth, e.g. adipose_100M indicates the differentially expressed gene results for adipose tissue at read depth 100M reads.,Supplementary_files_format_and_content: A_adipose_gene_exp_simluation_100M.xls contains the differentially expressed genes for certain read depth (100M reads here) for 10 times simulation. The purpose is to evaluate sampling variations and to see whether the sequenced reads are representative. Each tab in the excel file contains the differentially expressed genes for each simulation rounds, as a result, 10 tabs in this file. Similar description for A_adipose_gene_exp_simulation_10M.xls file, the only difference is the read depth in simulation is 10M reads.,Supplementary_files_format_and_content: MATS_A_adipose.xls represents the alternative-splicing (AS) results from Multivariate Analysis of Transcript Splicing (MATS). Similar to A_adipose_gene_exp.xls, it contains the AS results for adipose tissue at variant depths from 5M to 500M reads. Each tab represents the AS results for one depth.,Supplementary_files_format_and_content: MATS_A_adipose_simulation_100M.xls and MATS_A_adipose_simulation_10M.xls represents the AS results for 10 times simulation at read depths 100M and 10M reads. Similar to A_adipose_gene_exp_simulation_100M.xls and A_adipose_gene_exp_simulation_10M.xls, each tab contains the AS result for one simulation rounds, as a result, totally 10 tabs. | For adipose tissue, the RNA was extracted using RNeasy lipid total RNA mini kit (Qiagen, Valencia, CA). Extracted RNA samples underwent quality control (QC) assessment using the Agilent Bioanalyzer (Agilent, Santa Clara, CA). Poly-A library preparation and RNA sequencing were performed at the Penn Genome Frontiers Instituteâs High-Throughput Sequencing Facility per Illuminaâs (San Diego, CA) standard protocols. Briefly, we generated first-strand cDNA using random hexamer-primed reverse transcription, followed by second-strand cDNA synthesis using RNase H and DNA polymerase, and ligation of sequencing adapters using the Illumina paired-end sample preparation kit. Fragments of ~350 bp were selected gel electrophoresis, followed by 15 cycles of PCR amplification. The prepared libraries were then sequenced using Illuminaâs HiSeq 2000 at four lanes per sample (~456 million to 701 million 2 Ã 101 bp paired-end reads per sample). | GSM1128651 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02055493,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271432 | GSM1128651 | GSE46323 | 0.252086 | adipose_postLPS | Public on Jul 12 2013 | Apr 23 2013 | 9606 | A_adipose_postLPS (Sample 2) | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271432 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02055493 |
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1 | total rna input: 1000 ng,rna state: formalin-fixed, paraffin-embedded (FFPE) | 320 Charles Street | Cambridge | USA | Broad Institute of MIT & Harvard | Joshua,Z,Levin | **********************************************************************,,PROCESSED DATA FILE NAME: GSE40705_FFPE_isoform.txt,PROCESSED DATA FILE NAME: GSE40705_FFPE_gene.txt,Removed rRNA reads by aligning reads to rRNA transcripts using BWA version 0.6.1 using default parameters,We created a set of reads that did not map to rRNA to be used for further processing. To do this, reads where neither mate aligned to rRNA were extracted for further use using samtools 0.1.9 using the following commands: samtools view -S -b -f 4 -F 264 rRNA.sam > rRNA.1.bam; samtools view -S -b -f 8 -F 260 rRNA.sam > rRNA.2.bam; samtools view -S -b -f 12 -F 256 rRNA.sam > rRNA.3.bam,Output bam files were merged and reads were extracted using Picard,These reads were aligned to the UCSC transcriptome twice. The first alignment was done to create a set of uniquely mapped reads so that they could be downsampled to a fixed number of reads which are known to map to the transcriptome. This was done using bowtie version 0.12.7 allowing for one hit per read. The following parameters were used: -q --phred33-quals -v 2 -e 99999999 -l 25 -I 1 -X 1000 -p 16 -k 1 -m 200,This alignment was then downsampled to a fixed number of reads using Picard,The downsampled portion of the reads were then aligned to the UCSC transcriptome using bowtie version 0.12.7 allowing for multiple hits per read. This was the second, final alignment. The following parameters were used: bowtie -q --phred33-quals -v 2 -e 99999999 -l 25 -I 1 -X 1000 -p 15 -a -m 200,Transcripts and genes were quanitifed using RSEM version 1.1.17 run with default settings using the final Bowtie alignment,Genome_build: UCSC Genome Browser17 knownGene transcript dataset (version 05-Feb-2012),Supplementary_files_format_and_content: Processed data files are tab-delimited files that consist of the transcripts per million (TPM) expression level values as calculated by RSEM. Results are calculated at the gene (sample_gene.txt) and isoform (sample_isoform.txt) file. Each file contains TPM values calculated for each of the three protocols for the sample (RNaseH, RiboZero, and Total RNA) | Library construction method: RNase H rRNA-depletion (Morlan et al. PLOS One, 2012) | GSM1129240 | Illumina HiSeq 2500 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL16791 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056214,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271883 | GSM1129240 | GSE40705 | 0.020799 | human normal kidney section (Cybrdi) | Public on May 15 2013 | Apr 24 2013 | 9606 | FFPE_RNaseH | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271883 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056214 |
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1 | total rna input: 1000 ng,rna state: formalin-fixed, paraffin-embedded (FFPE) | 320 Charles Street | Cambridge | USA | Broad Institute of MIT & Harvard | Joshua,Z,Levin | **********************************************************************,,PROCESSED DATA FILE NAME: GSE40705_FFPE_isoform.txt,PROCESSED DATA FILE NAME: GSE40705_FFPE_gene.txt,Removed rRNA reads by aligning reads to rRNA transcripts using BWA version 0.6.1 using default parameters,We created a set of reads that did not map to rRNA to be used for further processing. To do this, reads where neither mate aligned to rRNA were extracted for further use using samtools 0.1.9 using the following commands: samtools view -S -b -f 4 -F 264 rRNA.sam > rRNA.1.bam; samtools view -S -b -f 8 -F 260 rRNA.sam > rRNA.2.bam; samtools view -S -b -f 12 -F 256 rRNA.sam > rRNA.3.bam,Output bam files were merged and reads were extracted using Picard,These reads were aligned to the UCSC transcriptome twice. The first alignment was done to create a set of uniquely mapped reads so that they could be downsampled to a fixed number of reads which are known to map to the transcriptome. This was done using bowtie version 0.12.7 allowing for one hit per read. The following parameters were used: -q --phred33-quals -v 2 -e 99999999 -l 25 -I 1 -X 1000 -p 16 -k 1 -m 200,This alignment was then downsampled to a fixed number of reads using Picard,The downsampled portion of the reads were then aligned to the UCSC transcriptome using bowtie version 0.12.7 allowing for multiple hits per read. This was the second, final alignment. The following parameters were used: bowtie -q --phred33-quals -v 2 -e 99999999 -l 25 -I 1 -X 1000 -p 15 -a -m 200,Transcripts and genes were quanitifed using RSEM version 1.1.17 run with default settings using the final Bowtie alignment,Genome_build: UCSC Genome Browser17 knownGene transcript dataset (version 05-Feb-2012),Supplementary_files_format_and_content: Processed data files are tab-delimited files that consist of the transcripts per million (TPM) expression level values as calculated by RSEM. Results are calculated at the gene (sample_gene.txt) and isoform (sample_isoform.txt) file. Each file contains TPM values calculated for each of the three protocols for the sample (RNaseH, RiboZero, and Total RNA) | Library construction method: Ribo-Zero (Epicentre) | GSM1129241 | Illumina HiSeq 2500 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL16791 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056215,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271884 | GSM1129241 | GSE40705 | 0.005212 | human normal kidney section (Cybrdi) | Public on May 15 2013 | Apr 24 2013 | 9606 | FFPE_RiboZero | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271884 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056215 |
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1 | total rna input: 1000 ng,rna state: formalin-fixed, paraffin-embedded (FFPE) | 320 Charles Street | Cambridge | USA | Broad Institute of MIT & Harvard | Joshua,Z,Levin | **********************************************************************,,PROCESSED DATA FILE NAME: GSE40705_FFPE_isoform.txt,PROCESSED DATA FILE NAME: GSE40705_FFPE_gene.txt,Removed rRNA reads by aligning reads to rRNA transcripts using BWA version 0.6.1 using default parameters,We created a set of reads that did not map to rRNA to be used for further processing. To do this, reads where neither mate aligned to rRNA were extracted for further use using samtools 0.1.9 using the following commands: samtools view -S -b -f 4 -F 264 rRNA.sam > rRNA.1.bam; samtools view -S -b -f 8 -F 260 rRNA.sam > rRNA.2.bam; samtools view -S -b -f 12 -F 256 rRNA.sam > rRNA.3.bam,Output bam files were merged and reads were extracted using Picard,These reads were aligned to the UCSC transcriptome twice. The first alignment was done to create a set of uniquely mapped reads so that they could be downsampled to a fixed number of reads which are known to map to the transcriptome. This was done using bowtie version 0.12.7 allowing for one hit per read. The following parameters were used: -q --phred33-quals -v 2 -e 99999999 -l 25 -I 1 -X 1000 -p 16 -k 1 -m 200,This alignment was then downsampled to a fixed number of reads using Picard,The downsampled portion of the reads were then aligned to the UCSC transcriptome using bowtie version 0.12.7 allowing for multiple hits per read. This was the second, final alignment. The following parameters were used: bowtie -q --phred33-quals -v 2 -e 99999999 -l 25 -I 1 -X 1000 -p 15 -a -m 200,Transcripts and genes were quanitifed using RSEM version 1.1.17 run with default settings using the final Bowtie alignment,Genome_build: UCSC Genome Browser17 knownGene transcript dataset (version 05-Feb-2012),Supplementary_files_format_and_content: Processed data files are tab-delimited files that consist of the transcripts per million (TPM) expression level values as calculated by RSEM. Results are calculated at the gene (sample_gene.txt) and isoform (sample_isoform.txt) file. Each file contains TPM values calculated for each of the three protocols for the sample (RNaseH, RiboZero, and Total RNA) | Library construction method: Standard | GSM1129242 | Illumina HiSeq 2500 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL16791 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056216,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271885 | GSM1129242 | GSE40705 | 0.013072 | human normal kidney section (Cybrdi) | Public on May 15 2013 | Apr 24 2013 | 9606 | FFPE_Total | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271885 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056216 |
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1 | total rna input: 1000 ng,rna state: partially degraded | 320 Charles Street | Cambridge | USA | Broad Institute of MIT & Harvard | Joshua,Z,Levin | **********************************************************************,,PROCESSED DATA FILE NAME: GSE40705_Pancreas_gene.txt,PROCESSED DATA FILE NAME: GSE40705_Pancreas_isoform.txt,Removed rRNA reads by aligning reads to rRNA transcripts using BWA version 0.6.1 using default parameters,We created a set of reads that did not map to rRNA to be used for further processing. To do this, reads where neither mate aligned to rRNA were extracted for further use using samtools 0.1.9 using the following commands: samtools view -S -b -f 4 -F 264 rRNA.sam > rRNA.1.bam; samtools view -S -b -f 8 -F 260 rRNA.sam > rRNA.2.bam; samtools view -S -b -f 12 -F 256 rRNA.sam > rRNA.3.bam,Output bam files were merged and reads were extracted using Picard,These reads were aligned to the UCSC transcriptome twice. The first alignment was done to create a set of uniquely mapped reads so that they could be downsampled to a fixed number of reads which are known to map to the transcriptome. This was done using bowtie version 0.12.7 allowing for one hit per read. The following parameters were used: -q --phred33-quals -v 2 -e 99999999 -l 25 -I 1 -X 1000 -p 16 -k 1 -m 200,This alignment was then downsampled to a fixed number of reads using Picard,The downsampled portion of the reads were then aligned to the UCSC transcriptome using bowtie version 0.12.7 allowing for multiple hits per read. This was the second, final alignment. The following parameters were used: bowtie -q --phred33-quals -v 2 -e 99999999 -l 25 -I 1 -X 1000 -p 15 -a -m 200,Transcripts and genes were quanitifed using RSEM version 1.1.17 run with default settings using the final Bowtie alignment,Genome_build: UCSC Genome Browser17 knownGene transcript dataset (version 05-Feb-2012),Supplementary_files_format_and_content: Processed data files are tab-delimited files that consist of the transcripts per million (TPM) expression level values as calculated by RSEM. Results are calculated at the gene (sample_gene.txt) and isoform (sample_isoform.txt) file. Each file contains TPM values calculated for each of the three protocols for the sample (RNaseH, RiboZero, and Total RNA) | Library construction method: RNase H rRNA-depletion (Morlan et al. PLOS One, 2012) | GSM1129243 | Illumina HiSeq 2500 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL16791 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056217,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271886 | GSM1129243 | GSE40705 | 0.008087 | human normal pancreas tissue (Zyagen) | Public on May 15 2013 | Apr 24 2013 | 9606 | Pancreas_RNaseH | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271886 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056217 |
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1 | total rna input: 1000 ng,rna state: partially degraded | 320 Charles Street | Cambridge | USA | Broad Institute of MIT & Harvard | Joshua,Z,Levin | **********************************************************************,,PROCESSED DATA FILE NAME: GSE40705_Pancreas_gene.txt,PROCESSED DATA FILE NAME: GSE40705_Pancreas_isoform.txt,Removed rRNA reads by aligning reads to rRNA transcripts using BWA version 0.6.1 using default parameters,We created a set of reads that did not map to rRNA to be used for further processing. To do this, reads where neither mate aligned to rRNA were extracted for further use using samtools 0.1.9 using the following commands: samtools view -S -b -f 4 -F 264 rRNA.sam > rRNA.1.bam; samtools view -S -b -f 8 -F 260 rRNA.sam > rRNA.2.bam; samtools view -S -b -f 12 -F 256 rRNA.sam > rRNA.3.bam,Output bam files were merged and reads were extracted using Picard,These reads were aligned to the UCSC transcriptome twice. The first alignment was done to create a set of uniquely mapped reads so that they could be downsampled to a fixed number of reads which are known to map to the transcriptome. This was done using bowtie version 0.12.7 allowing for one hit per read. The following parameters were used: -q --phred33-quals -v 2 -e 99999999 -l 25 -I 1 -X 1000 -p 16 -k 1 -m 200,This alignment was then downsampled to a fixed number of reads using Picard,The downsampled portion of the reads were then aligned to the UCSC transcriptome using bowtie version 0.12.7 allowing for multiple hits per read. This was the second, final alignment. The following parameters were used: bowtie -q --phred33-quals -v 2 -e 99999999 -l 25 -I 1 -X 1000 -p 15 -a -m 200,Transcripts and genes were quanitifed using RSEM version 1.1.17 run with default settings using the final Bowtie alignment,Genome_build: UCSC Genome Browser17 knownGene transcript dataset (version 05-Feb-2012),Supplementary_files_format_and_content: Processed data files are tab-delimited files that consist of the transcripts per million (TPM) expression level values as calculated by RSEM. Results are calculated at the gene (sample_gene.txt) and isoform (sample_isoform.txt) file. Each file contains TPM values calculated for each of the three protocols for the sample (RNaseH, RiboZero, and Total RNA) | Library construction method: Ribo-Zero (Epicentre) | GSM1129244 | Illumina HiSeq 2500 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL16791 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056218,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271887 | GSM1129244 | GSE40705 | 0 | human normal pancreas tissue (Zyagen) | Public on May 15 2013 | Apr 24 2013 | 9606 | Pancreas_RiboZero | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271887 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056218 |
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1 | total rna input: 1000 ng,rna state: partially degraded | 320 Charles Street | Cambridge | USA | Broad Institute of MIT & Harvard | Joshua,Z,Levin | **********************************************************************,,PROCESSED DATA FILE NAME: GSE40705_Pancreas_gene.txt,PROCESSED DATA FILE NAME: GSE40705_Pancreas_isoform.txt,Removed rRNA reads by aligning reads to rRNA transcripts using BWA version 0.6.1 using default parameters,We created a set of reads that did not map to rRNA to be used for further processing. To do this, reads where neither mate aligned to rRNA were extracted for further use using samtools 0.1.9 using the following commands: samtools view -S -b -f 4 -F 264 rRNA.sam > rRNA.1.bam; samtools view -S -b -f 8 -F 260 rRNA.sam > rRNA.2.bam; samtools view -S -b -f 12 -F 256 rRNA.sam > rRNA.3.bam,Output bam files were merged and reads were extracted using Picard,These reads were aligned to the UCSC transcriptome twice. The first alignment was done to create a set of uniquely mapped reads so that they could be downsampled to a fixed number of reads which are known to map to the transcriptome. This was done using bowtie version 0.12.7 allowing for one hit per read. The following parameters were used: -q --phred33-quals -v 2 -e 99999999 -l 25 -I 1 -X 1000 -p 16 -k 1 -m 200,This alignment was then downsampled to a fixed number of reads using Picard,The downsampled portion of the reads were then aligned to the UCSC transcriptome using bowtie version 0.12.7 allowing for multiple hits per read. This was the second, final alignment. The following parameters were used: bowtie -q --phred33-quals -v 2 -e 99999999 -l 25 -I 1 -X 1000 -p 15 -a -m 200,Transcripts and genes were quanitifed using RSEM version 1.1.17 run with default settings using the final Bowtie alignment,Genome_build: UCSC Genome Browser17 knownGene transcript dataset (version 05-Feb-2012),Supplementary_files_format_and_content: Processed data files are tab-delimited files that consist of the transcripts per million (TPM) expression level values as calculated by RSEM. Results are calculated at the gene (sample_gene.txt) and isoform (sample_isoform.txt) file. Each file contains TPM values calculated for each of the three protocols for the sample (RNaseH, RiboZero, and Total RNA) | Library construction method: Standard | GSM1129245 | Illumina HiSeq 2500 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL16791 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056219,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271888 | GSM1129245 | GSE40705 | 0.03268 | human normal pancreas tissue (Zyagen) | Public on May 15 2013 | Apr 24 2013 | 9606 | Pancreas_Total | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271888 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056219 |
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1 | cell type: OCI-Ly7 cell line,treatment: treated with 2uM GSK343 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129307 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056252,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271803 | GSM1129307 | GSE45982 | 0 | OCI-Ly7 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | OCI-Ly7 GSK343 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271803 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056252 |
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1 | cell type: OCI-Ly7 cell line,treatment: treated with 2uM GSK669 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129308 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056253,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271804 | GSM1129308 | GSE45982 | 0.005468 | OCI-Ly7 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | OCI-Ly7 GSK669 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271804 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056253 |
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1 | cell type: Farage cell line,treatment: treated with 2uM GSK343 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129309 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056254,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271805 | GSM1129309 | GSE45982 | 0.000775 | Farage cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | Farage GSK343 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271805 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056254 |
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1 | cell type: Farage cell line,treatment: treated with 2uM GSK669 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129310 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056255,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271806 | GSM1129310 | GSE45982 | 0.071266 | Farage cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | Farage GSK669 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271806 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056255 |
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1 | cell type: SUDHL5 cell line,treatment: treated with 2uM GSK343 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129311 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056256,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271807 | GSM1129311 | GSE45982 | 0.000141 | SUDHL5 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | SUDHL5 GSK343 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271807 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056256 |
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1 | cell type: SUDHL5 cell line,treatment: treated with 2uM GSK669 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129312 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056257,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271808 | GSM1129312 | GSE45982 | 0.082344 | SUDHL5 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | SUDHL5 GSK669 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271808 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056257 |
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1 | cell type: OCI-Ly1 cell line,treatment: treated with 2uM GSK343 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129313 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056258,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271809 | GSM1129313 | GSE45982 | 0.010064 | OCI-Ly1 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | OCI-Ly1 GSK343 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271809 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056258 |
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1 | cell type: OCI-Ly1 cell line,treatment: treated with 2uM GSK669 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129314 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056259,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271810 | GSM1129314 | GSE45982 | 0.082116 | OCI-Ly1 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | OCI-Ly1 GSK669 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271810 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056259 |
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1 | cell type: WSUDLCL2 cell line,treatment: treated with 2uM GSK343 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129315 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056260,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271811 | GSM1129315 | GSE45982 | 0 | WSUDLCL2 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | WSUDLCL2 GSK343 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271811 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056260 |
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1 | cell type: WSUDLCL2 cell line,treatment: treated with 2uM GSK669 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129316 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056261,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271812 | GSM1129316 | GSE45982 | 0.006006 | WSUDLCL2 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | WSUDLCL2 GSK669 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271812 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056261 |
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1 | cell type: Pfeiffer cell line,treatment: treated with 2uM GSK343 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129317 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056262,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271813 | GSM1129317 | GSE45982 | 0.005017 | Pfeiffer cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | Pfeiffer GSK343 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271813 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056262 |
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1 | cell type: Pfeiffer cell line,treatment: treated with 2uM GSK669 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129318 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056263,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271814 | GSM1129318 | GSE45982 | 0 | Pfeiffer cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | Pfeiffer GSK669 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271814 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056263 |
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1 | cell type: OCI-Ly7 cell line,treatment: transduced with anti-EZH2 shRNA #2 for EZH2 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129319 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056264,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271815 | GSM1129319 | GSE45982 | 0.005382 | OCI-Ly7 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | OCI-Ly7 shEZH2 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271815 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056264 |
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1 | cell type: OCI-Ly7 cell line,treatment: transduced with anti-EZH2 shRNA #3 for EZH2 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129320 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056265,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271816 | GSM1129320 | GSE45982 | 0.003826 | OCI-Ly7 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | OCI-Ly7 shEZH2 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271816 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056265 |
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1 | cell type: OCI-Ly7 cell line,treatment: transuced with control scrambled shRNA for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129321 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056266,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271817 | GSM1129321 | GSE45982 | 0.001336 | OCI-Ly7 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | OCI-Ly7 scrambled | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271817 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056266 |
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1 | cell type: Farage cell line,treatment: transduced with anti-EZH2 shRNA #2 for EZH2 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129322 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056267,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271818 | GSM1129322 | GSE45982 | 0.000552 | Farage cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | Farage shEZH2 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271818 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056267 |
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1 | cell type: Farage cell line,treatment: transduced with anti-EZH2 shRNA #3 for EZH2 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129323 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056268,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271819 | GSM1129323 | GSE45982 | 0 | Farage cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | Farage shEZH2 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271819 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056268 |
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1 | cell type: Farage cell line,treatment: transduced with control scrambled shRNA for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129324 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056269,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271820 | GSM1129324 | GSE45982 | 0.00107 | Farage cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | Farage scrambled | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271820 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056269 |
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1 | cell type: SUDHL5 cell line,treatment: transduced with anti-EZH2 shRNA #2 for EZH2 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129325 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056270,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271821 | GSM1129325 | GSE45982 | 0.030331 | SUDHL5 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | SUDHL5 shEZH2 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271821 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056270 |
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1 | cell type: SUDHL5 cell line,treatment: transduced with anti-EZH2 shRNA #3 for EZH2 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129326 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056271,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271822 | GSM1129326 | GSE45982 | 0.000819 | SUDHL5 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | SUDHL5 shEZH2 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271822 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056271 |
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1 | cell type: SUDHL5 cell line,treatment: transuced with control scrambled shRNA for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129327 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056272,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271823 | GSM1129327 | GSE45982 | 0 | SUDHL5 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | SUDHL5 scrambled | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271823 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056272 |
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1 | cell type: OCI-Ly1 cell line,treatment: transduced with anti-EZH2 shRNA #2 for EZH2 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129328 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056273,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271824 | GSM1129328 | GSE45982 | 0.001483 | OCI-Ly1 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | OCI-Ly1 shEZH2 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271824 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056273 |
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1 | cell type: OCI-Ly1 cell line,treatment: transduced with anti-EZH2 shRNA #3 for EZH2 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129329 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056274,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271825 | GSM1129329 | GSE45982 | 0.001483 | OCI-Ly1 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | OCI-Ly1 shEZH2 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271825 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056274 |
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1 | cell type: OCI-Ly1 cell line,treatment: transuced with control scrambled shRNA for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129330 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056275,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271826 | GSM1129330 | GSE45982 | 0.000025 | OCI-Ly1 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | OCI-Ly1 scrambled | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271826 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056275 |
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1 | cell type: WSUDLCL2 cell line,treatment: transduced with anti-EZH2 shRNA #2 for EZH2 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129331 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056222,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271827 | GSM1129331 | GSE45982 | 0.011602 | WSUDLCL2 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | WSUDLCL2 shEZH2 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271827 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056222 |
|
1 | cell type: WSUDLCL2 cell line,treatment: transduced with anti-EZH2 shRNA #3 for EZH2 for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129332 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056223,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271828 | GSM1129332 | GSE45982 | 0 | WSUDLCL2 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | WSUDLCL2 shEZH2 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271828 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056223 |
|
1 | cell type: WSUDLCL2 cell line,treatment: transuced with control scrambled shRNA for 7 days | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg19,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129333 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056224,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271829 | GSM1129333 | GSE45982 | 0 | WSUDLCL2 cell line | Public on May 13 2013 | Apr 25 2013 | 9606 | WSUDLCL2 scrambled | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271829 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056224 |
|
1 | cell type: Tonsillar naive B cells,treatment: NA,purification: Cells purified from normal fresh human tonsillectomy specimens by magnetic bead cell separation based on the expression the phenotypic marker IgD | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg18,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129340 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056231,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271836 | GSM1129340 | GSE45982 | 0.296645 | Tonsillar Naïve B cells | Public on May 13 2013 | Apr 25 2013 | 9606 | NB 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271836 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056231 |
|
1 | cell type: Tonsillar naive B cells,treatment: NA,purification: Cells purified from normal fresh human tonsillectomy specimens by magnetic bead cell separation based on the expression the phenotypic marker IgD | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg18,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129341 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056232,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271837 | GSM1129341 | GSE45982 | 0.143056 | Tonsillar Naïve B cells | Public on May 13 2013 | Apr 25 2013 | 9606 | NB 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271837 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056232 |
|
1 | cell type: Tonsillar naive B cells,treatment: NA,purification: Cells purified from normal fresh human tonsillectomy specimens by magnetic bead cell separation based on the expression the phenotypic marker IgD | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg18,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129342 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056233,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271838 | GSM1129342 | GSE45982 | 0.083446 | Tonsillar Naïve B cells | Public on May 13 2013 | Apr 25 2013 | 9606 | NB 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271838 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056233 |
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1 | cell type: Tonsillar naive B cells,treatment: NA,purification: Cells purified from normal fresh human tonsillectomy specimens by magnetic bead cell separation based on the expression the phenotypic marker IgD | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg18,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129343 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056234,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271839 | GSM1129343 | GSE45982 | 0.17362 | Tonsillar Naïve B cells | Public on May 13 2013 | Apr 25 2013 | 9606 | NB 4 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271839 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056234 |
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1 | cell type: Tonsillar Germinal Center B cells,treatment: NA,purification: Cells purified from normal fresh human tonsillectomy specimens by magnetic bead cell separation based on the expression the phenotypic marker CD77 | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg18,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129344 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056235,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271840 | GSM1129344 | GSE45982 | 0.013896 | Tonsillar Germinal Center B cells | Public on May 13 2013 | Apr 25 2013 | 9606 | GCB 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271840 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056235 |
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1 | cell type: Tonsillar Germinal Center B cells,treatment: NA,purification: Cells purified from normal fresh human tonsillectomy specimens by magnetic bead cell separation based on the expression the phenotypic marker CD77 | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg18,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129345 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056236,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271841 | GSM1129345 | GSE45982 | 0 | Tonsillar Germinal Center B cells | Public on May 13 2013 | Apr 25 2013 | 9606 | GCB 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271841 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056236 |
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1 | cell type: Tonsillar Germinal Center B cells,treatment: NA,purification: Cells purified from normal fresh human tonsillectomy specimens by magnetic bead cell separation based on the expression the phenotypic marker CD77 | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg18,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129346 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056237,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271842 | GSM1129346 | GSE45982 | 0.077466 | Tonsillar Germinal Center B cells | Public on May 13 2013 | Apr 25 2013 | 9606 | GCB 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271842 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056237 |
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1 | cell type: Tonsillar Germinal Center B cells,treatment: NA,purification: Cells purified from normal fresh human tonsillectomy specimens by magnetic bead cell separation based on the expression the phenotypic marker CD77 | 445 E 69th St | New York | USA | Weill Cornell Medical College | Matt,,Teater | genome build: hg18,Illumina Casava1.8 software used for basecalling.,RNA-seq data was aligned to transcripts using TopHat with default parameters. ChIP-seq data was aligned to the appropriate genome using ELAND.,FPKM were obtained using CuffLinks with upper-quartile and GC normalization,H3K4me3 ChIP-seq reads were called into peaks using the ChIPseeqer framework (p<10-15 and fold-change over input threshold 2) (Giannopoulou and Elemento, 2011) and H3K27me3 and EZH2 ChIP-seq reads were quantified in 1kb bins genome-wide, identifying regions of enrichment as consecutive bins with read counts greater than one standard deviation of the genome-wide mean.,Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript; WIG files were generatedand peak files were called using ChIPseeqer framework (http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml) | RNA was prepared using Trizol extraction (Invitrogen) according to the manufacturerâs protocol.,ChIP-seq and RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT⢠dsDNA HS Assay (Life Technologies) | GSM1129347 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056238,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX271843 | GSM1129347 | GSE45982 | 0.193818 | Tonsillar Germinal Center B cells | Public on May 13 2013 | Apr 25 2013 | 9606 | GCB 4 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX271843 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056238 |
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1 | subjects: 10 healthy female volunteers,age of subjects: about 60 years,tissue: skin (epidermal suction blister samples) | Im Neuenheimer Feld 580 | Heidelberg | Germany | German Center for Cancer Research | Guenter,,Raddatz | Illumina Casava1.8.1 software used for basecalling.,Preprocessing, read trimming: shore 0.6.2,Preprocessing, quality filtering: shore 0.6.2,Transcriptome-mapping: tophat 2.0,Evaluation of differential expression: DESeq,Genome_build: hg19,Supplementary_files_format_and_content: Matrix-format created by DESeq containing the expression levels and p-values for differential expression | Epidermal suction blister samples were collected according to the current version of the Declaration of Helsinki and the guideline of the International Conference on Harmonization Good Clinical Practice (ICH GCP) was observed as applicable to a non-drug study. All volunteers provided written, informed consent. Suction blister samples were obtained at the study center of Beiersdorf AG and approved by the Beiersdorf AG Legal Review Board. Briefly, epidermis samples were detached from the forearms of 10 healthy female volunteers by applying a negative pressure of 150â250 mmHg for 2 h. Subsequently, suction blister roofs were taken and immediately stored at -20 °C. Before RNA isolation, suction blister samples were homogenized using a TissueLyser (Retsch). Total RNA from suction blister samples was isolated using the Fibrous Tissue Kit (Qiagen) according to the manufacturerâs instructions. The Poly(A)Purist⢠MAG Kit (Ambion) was used for mRNA selection.,Sequencing libraries were prepared using 1µg of DNAse-treated human total RNA in the first step of the TruSeq RNA Sample Preparation v2 protocol (Illumina, Part# 15026495 Rev. A) as recommended by the manufacturer. | GSM1131156 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02086418,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272491 | GSM1131156 | GSE46486,GSE46487 | 0.028736 | skin | Public on Dec 20 2013 | Apr 29 2013 | 9606 | Skin sample from old subjects | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272491 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02086418 |
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1 | cell type: cumulus granulosa cells,stimulation protocol: GnRH antagonist, rFSH, hCG,etiology of infertility: male factor | Akadeemia tee 15 | Tallinn | Estonia | Tallinn University of Technology | Agne,,Velthut-Meikas | Base calling and filtering was done using instrument software real time analysis (RTA v1.12.4.2) with default parameters.,Adapter sequences were removed with cutAdapt v0.9.3.,Bowtie v0.12.7 was used to map sequences to human genome 19 (Hg19) allowing no mismatches between the seed and target and reporting only the best aligned match. Aligned sequenced fragments were concatenated into transcripts using the TopHat v1.2.0 algorithm.,The BAM files from TopHat were converted to SAM format by SAMtools v.0.1.18. To get the number of reads per each gene the SAM files and the reference genome were used as input for HTSeq (http://www-huber.embl.de/users/anders/HTSeq), where intersection-nonempty mode was used.,Differential mRNA expression analysis was performed using the R/Bioconductor package EdgeR.,Genome_build: UCSC hg19,Supplementary_files_format_and_content: RNA counts per gene for each sample generated by HTSeq. | Total RNA was extracted using the miRNeasy Mini Kit (Qiagen), according to the manufacturerâs instructions.,RNA population containing the poly(A) tail was enriched by Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific) and library was prepared with mRNA Library Prep Master Mix Set 1 for Illumina (New England Biolabs) according to the manufacturer´s protocols with a few optimized modifications: a) all the purification steps were carried out with Agencourt AMPure XP (Beckman Coulter Inc.) beads, except for purification of fragmented RNA where RNeasy MinElute kit (Qiagen) was used; b) fragmentation incubation time was shortened to 2 minutes to gain longer fragments suitable for long sequencing runs; c) size selection by agarose gel electrophoresis was not performed, the average length of the fragment was 420 bp, including 300 bp of insert and 120 bp of adapter sequences; and d) the template amount for PCR was 15 ng and 10 cycles were carried out. The library preparation stage included annealing of unique adapters to individual samples for further sample indexing and pooling of all six poly(A) RNA samples. Adapters as well as PCR primers were from NEXTflex DNA Barcodes (Bioo Scientific Corporation). 13 pM of the sample pool was used for template hybridization, clustering and amplification (corresponds to 2.17 pM of individual sample). | GSM1131192 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087547,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272866 | GSM1131192 | GSE46490,GSE46508 | 0.004144 | cumulus granulosa cells | Public on Aug 05 2013 | Apr 29 2013 | 9606 | CGC1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272866 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087547 |
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1 | cell type: cumulus granulosa cells,stimulation protocol: GnRH antagonist, rFSH, hCG,etiology of infertility: male factor | Akadeemia tee 15 | Tallinn | Estonia | Tallinn University of Technology | Agne,,Velthut-Meikas | Base calling and filtering was done using instrument software real time analysis (RTA v1.12.4.2) with default parameters.,Adapter sequences were removed with cutAdapt v0.9.3.,Bowtie v0.12.7 was used to map sequences to human genome 19 (Hg19) allowing no mismatches between the seed and target and reporting only the best aligned match. Aligned sequenced fragments were concatenated into transcripts using the TopHat v1.2.0 algorithm.,The BAM files from TopHat were converted to SAM format by SAMtools v.0.1.18. To get the number of reads per each gene the SAM files and the reference genome were used as input for HTSeq (http://www-huber.embl.de/users/anders/HTSeq), where intersection-nonempty mode was used.,Differential mRNA expression analysis was performed using the R/Bioconductor package EdgeR.,Genome_build: UCSC hg19,Supplementary_files_format_and_content: RNA counts per gene for each sample generated by HTSeq. | Total RNA was extracted using the miRNeasy Mini Kit (Qiagen), according to the manufacturerâs instructions.,RNA population containing the poly(A) tail was enriched by Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific) and library was prepared with mRNA Library Prep Master Mix Set 1 for Illumina (New England Biolabs) according to the manufacturer´s protocols with a few optimized modifications: a) all the purification steps were carried out with Agencourt AMPure XP (Beckman Coulter Inc.) beads, except for purification of fragmented RNA where RNeasy MinElute kit (Qiagen) was used; b) fragmentation incubation time was shortened to 2 minutes to gain longer fragments suitable for long sequencing runs; c) size selection by agarose gel electrophoresis was not performed, the average length of the fragment was 420 bp, including 300 bp of insert and 120 bp of adapter sequences; and d) the template amount for PCR was 15 ng and 10 cycles were carried out. The library preparation stage included annealing of unique adapters to individual samples for further sample indexing and pooling of all six poly(A) RNA samples. Adapters as well as PCR primers were from NEXTflex DNA Barcodes (Bioo Scientific Corporation). 13 pM of the sample pool was used for template hybridization, clustering and amplification (corresponds to 2.17 pM of individual sample). | GSM1131193 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087548,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272867 | GSM1131193 | GSE46490,GSE46508 | 0.004781 | cumulus granulosa cells | Public on Aug 05 2013 | Apr 29 2013 | 9606 | CGC2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272867 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087548 |
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1 | cell type: cumulus granulosa cells,stimulation protocol: GnRH antagonist, rFSH, hCG,etiology of infertility: male factor | Akadeemia tee 15 | Tallinn | Estonia | Tallinn University of Technology | Agne,,Velthut-Meikas | Base calling and filtering was done using instrument software real time analysis (RTA v1.12.4.2) with default parameters.,Adapter sequences were removed with cutAdapt v0.9.3.,Bowtie v0.12.7 was used to map sequences to human genome 19 (Hg19) allowing no mismatches between the seed and target and reporting only the best aligned match. Aligned sequenced fragments were concatenated into transcripts using the TopHat v1.2.0 algorithm.,The BAM files from TopHat were converted to SAM format by SAMtools v.0.1.18. To get the number of reads per each gene the SAM files and the reference genome were used as input for HTSeq (http://www-huber.embl.de/users/anders/HTSeq), where intersection-nonempty mode was used.,Differential mRNA expression analysis was performed using the R/Bioconductor package EdgeR.,Genome_build: UCSC hg19,Supplementary_files_format_and_content: RNA counts per gene for each sample generated by HTSeq. | Total RNA was extracted using the miRNeasy Mini Kit (Qiagen), according to the manufacturerâs instructions.,RNA population containing the poly(A) tail was enriched by Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific) and library was prepared with mRNA Library Prep Master Mix Set 1 for Illumina (New England Biolabs) according to the manufacturer´s protocols with a few optimized modifications: a) all the purification steps were carried out with Agencourt AMPure XP (Beckman Coulter Inc.) beads, except for purification of fragmented RNA where RNeasy MinElute kit (Qiagen) was used; b) fragmentation incubation time was shortened to 2 minutes to gain longer fragments suitable for long sequencing runs; c) size selection by agarose gel electrophoresis was not performed, the average length of the fragment was 420 bp, including 300 bp of insert and 120 bp of adapter sequences; and d) the template amount for PCR was 15 ng and 10 cycles were carried out. The library preparation stage included annealing of unique adapters to individual samples for further sample indexing and pooling of all six poly(A) RNA samples. Adapters as well as PCR primers were from NEXTflex DNA Barcodes (Bioo Scientific Corporation). 13 pM of the sample pool was used for template hybridization, clustering and amplification (corresponds to 2.17 pM of individual sample). | GSM1131194 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087549,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272868 | GSM1131194 | GSE46490,GSE46508 | 0.003729 | cumulus granulosa cells | Public on Aug 05 2013 | Apr 29 2013 | 9606 | CGC3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272868 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087549 |
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1 | cell type: mural granulosa cells,stimulation protocol: GnRH antagonist, rFSH, hCG,etiology of infertility: male factor | Akadeemia tee 15 | Tallinn | Estonia | Tallinn University of Technology | Agne,,Velthut-Meikas | Base calling and filtering was done using instrument software real time analysis (RTA v1.12.4.2) with default parameters.,Adapter sequences were removed with cutAdapt v0.9.3.,Bowtie v0.12.7 was used to map sequences to human genome 19 (Hg19) allowing no mismatches between the seed and target and reporting only the best aligned match. Aligned sequenced fragments were concatenated into transcripts using the TopHat v1.2.0 algorithm.,The BAM files from TopHat were converted to SAM format by SAMtools v.0.1.18. To get the number of reads per each gene the SAM files and the reference genome were used as input for HTSeq (http://www-huber.embl.de/users/anders/HTSeq), where intersection-nonempty mode was used.,Differential mRNA expression analysis was performed using the R/Bioconductor package EdgeR.,Genome_build: UCSC hg19,Supplementary_files_format_and_content: RNA counts per gene for each sample generated by HTSeq. | Total RNA was extracted using the miRNeasy Mini Kit (Qiagen), according to the manufacturerâs instructions.,RNA population containing the poly(A) tail was enriched by Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific) and library was prepared with mRNA Library Prep Master Mix Set 1 for Illumina (New England Biolabs) according to the manufacturer´s protocols with a few optimized modifications: a) all the purification steps were carried out with Agencourt AMPure XP (Beckman Coulter Inc.) beads, except for purification of fragmented RNA where RNeasy MinElute kit (Qiagen) was used; b) fragmentation incubation time was shortened to 2 minutes to gain longer fragments suitable for long sequencing runs; c) size selection by agarose gel electrophoresis was not performed, the average length of the fragment was 420 bp, including 300 bp of insert and 120 bp of adapter sequences; and d) the template amount for PCR was 15 ng and 10 cycles were carried out. The library preparation stage included annealing of unique adapters to individual samples for further sample indexing and pooling of all six poly(A) RNA samples. Adapters as well as PCR primers were from NEXTflex DNA Barcodes (Bioo Scientific Corporation). 13 pM of the sample pool was used for template hybridization, clustering and amplification (corresponds to 2.17 pM of individual sample). | GSM1131195 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087550,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272869 | GSM1131195 | GSE46490,GSE46508 | 0.010517 | mural granulosa cells | Public on Aug 05 2013 | Apr 29 2013 | 9606 | MGC1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272869 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087550 |
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1 | cell type: mural granulosa cells,stimulation protocol: GnRH antagonist, rFSH, hCG,etiology of infertility: male factor | Akadeemia tee 15 | Tallinn | Estonia | Tallinn University of Technology | Agne,,Velthut-Meikas | Base calling and filtering was done using instrument software real time analysis (RTA v1.12.4.2) with default parameters.,Adapter sequences were removed with cutAdapt v0.9.3.,Bowtie v0.12.7 was used to map sequences to human genome 19 (Hg19) allowing no mismatches between the seed and target and reporting only the best aligned match. Aligned sequenced fragments were concatenated into transcripts using the TopHat v1.2.0 algorithm.,The BAM files from TopHat were converted to SAM format by SAMtools v.0.1.18. To get the number of reads per each gene the SAM files and the reference genome were used as input for HTSeq (http://www-huber.embl.de/users/anders/HTSeq), where intersection-nonempty mode was used.,Differential mRNA expression analysis was performed using the R/Bioconductor package EdgeR.,Genome_build: UCSC hg19,Supplementary_files_format_and_content: RNA counts per gene for each sample generated by HTSeq. | Total RNA was extracted using the miRNeasy Mini Kit (Qiagen), according to the manufacturerâs instructions.,RNA population containing the poly(A) tail was enriched by Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific) and library was prepared with mRNA Library Prep Master Mix Set 1 for Illumina (New England Biolabs) according to the manufacturer´s protocols with a few optimized modifications: a) all the purification steps were carried out with Agencourt AMPure XP (Beckman Coulter Inc.) beads, except for purification of fragmented RNA where RNeasy MinElute kit (Qiagen) was used; b) fragmentation incubation time was shortened to 2 minutes to gain longer fragments suitable for long sequencing runs; c) size selection by agarose gel electrophoresis was not performed, the average length of the fragment was 420 bp, including 300 bp of insert and 120 bp of adapter sequences; and d) the template amount for PCR was 15 ng and 10 cycles were carried out. The library preparation stage included annealing of unique adapters to individual samples for further sample indexing and pooling of all six poly(A) RNA samples. Adapters as well as PCR primers were from NEXTflex DNA Barcodes (Bioo Scientific Corporation). 13 pM of the sample pool was used for template hybridization, clustering and amplification (corresponds to 2.17 pM of individual sample). | GSM1131196 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087551,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272870 | GSM1131196 | GSE46490,GSE46508 | 0.003334 | mural granulosa cells | Public on Aug 05 2013 | Apr 29 2013 | 9606 | MGC2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272870 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087551 |
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1 | cell type: mural granulosa cells,stimulation protocol: GnRH antagonist, rFSH, hCG,etiology of infertility: male factor | Akadeemia tee 15 | Tallinn | Estonia | Tallinn University of Technology | Agne,,Velthut-Meikas | Base calling and filtering was done using instrument software real time analysis (RTA v1.12.4.2) with default parameters.,Adapter sequences were removed with cutAdapt v0.9.3.,Bowtie v0.12.7 was used to map sequences to human genome 19 (Hg19) allowing no mismatches between the seed and target and reporting only the best aligned match. Aligned sequenced fragments were concatenated into transcripts using the TopHat v1.2.0 algorithm.,The BAM files from TopHat were converted to SAM format by SAMtools v.0.1.18. To get the number of reads per each gene the SAM files and the reference genome were used as input for HTSeq (http://www-huber.embl.de/users/anders/HTSeq), where intersection-nonempty mode was used.,Differential mRNA expression analysis was performed using the R/Bioconductor package EdgeR.,Genome_build: UCSC hg19,Supplementary_files_format_and_content: RNA counts per gene for each sample generated by HTSeq. | Total RNA was extracted using the miRNeasy Mini Kit (Qiagen), according to the manufacturerâs instructions.,RNA population containing the poly(A) tail was enriched by Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific) and library was prepared with mRNA Library Prep Master Mix Set 1 for Illumina (New England Biolabs) according to the manufacturer´s protocols with a few optimized modifications: a) all the purification steps were carried out with Agencourt AMPure XP (Beckman Coulter Inc.) beads, except for purification of fragmented RNA where RNeasy MinElute kit (Qiagen) was used; b) fragmentation incubation time was shortened to 2 minutes to gain longer fragments suitable for long sequencing runs; c) size selection by agarose gel electrophoresis was not performed, the average length of the fragment was 420 bp, including 300 bp of insert and 120 bp of adapter sequences; and d) the template amount for PCR was 15 ng and 10 cycles were carried out. The library preparation stage included annealing of unique adapters to individual samples for further sample indexing and pooling of all six poly(A) RNA samples. Adapters as well as PCR primers were from NEXTflex DNA Barcodes (Bioo Scientific Corporation). 13 pM of the sample pool was used for template hybridization, clustering and amplification (corresponds to 2.17 pM of individual sample). | GSM1131197 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087552,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272871 | GSM1131197 | GSE46490,GSE46508 | 0.003164 | mural granulosa cells | Public on Aug 05 2013 | Apr 29 2013 | 9606 | MGC3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272871 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087552 |
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1 | cell type: primary human umbilical vein endothelial cells,passage: 4-6,infected with: a lentivirus containing human PR,treated with: none | 621 Charles E. Young Dr. S. | Los Angeles | USA | University of California-Los Angeles | Lauren,,Goddard | Debarcoding of the multiplex runs was performed using in house shell script,Reads were then processed and aligned to the human genome (hg19) using TopHat v2.0.4 (Trapnell et al., 2009) with default parameters.,The aligned read files were further processed with Cufflinks v2.0.1 (Trapnell et al., 2010) to calculate RPKP values. Assemblies for all samples were merged using CuffMerge and differential expression was determined using Cuffdiff. Genes with a p-value smaller than 0.01 where considered as differentially expressed.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample and Excel table final lists of differentially expressed genes | Total RNA was extracted using RNeasy Kit (Qiagen, Valencia, CA) according to manufacturer instructions.,The library for sequencing was constructed using an Illumina Multiplex System according to manufacturer's instructions (Illumina, San Diego, CA). Libraries were sequenced using HIseq-2000 (Illumina, San Diego, CA) to obtain 50 bp long reads. | GSM1131338 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087533,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272849 | GSM1131338 | GSE46502,GSE46503 | 0.002169 | primary HUVECs | Public on Jan 01 2014 | Apr 30 2013 | 9606 | PR | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272849 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087533 |
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1 | cell type: primary human umbilical vein endothelial cells,passage: 4-6,infected with: a lentivirus containing human PR,treated with: Progesterone | 621 Charles E. Young Dr. S. | Los Angeles | USA | University of California-Los Angeles | Lauren,,Goddard | Debarcoding of the multiplex runs was performed using in house shell script,Reads were then processed and aligned to the human genome (hg19) using TopHat v2.0.4 (Trapnell et al., 2009) with default parameters.,The aligned read files were further processed with Cufflinks v2.0.1 (Trapnell et al., 2010) to calculate RPKP values. Assemblies for all samples were merged using CuffMerge and differential expression was determined using Cuffdiff. Genes with a p-value smaller than 0.01 where considered as differentially expressed.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample and Excel table final lists of differentially expressed genes | Total RNA was extracted using RNeasy Kit (Qiagen, Valencia, CA) according to manufacturer instructions.,The library for sequencing was constructed using an Illumina Multiplex System according to manufacturer's instructions (Illumina, San Diego, CA). Libraries were sequenced using HIseq-2000 (Illumina, San Diego, CA) to obtain 50 bp long reads. | GSM1131339 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087534,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272850 | GSM1131339 | GSE46502,GSE46503 | 0.003186 | primary HUVECs | Public on Jan 01 2014 | Apr 30 2013 | 9606 | PR+P | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272850 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087534 |
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1 | cell type: primary human umbilical vein endothelial cells,passage: 4-6,infected with: a lentivirus containing human PR,treated with: LPS (1μM) for 4 hrs | 621 Charles E. Young Dr. S. | Los Angeles | USA | University of California-Los Angeles | Lauren,,Goddard | Debarcoding of the multiplex runs was performed using in house shell script,Reads were then processed and aligned to the human genome (hg19) using TopHat v2.0.4 (Trapnell et al., 2009) with default parameters.,The aligned read files were further processed with Cufflinks v2.0.1 (Trapnell et al., 2010) to calculate RPKP values. Assemblies for all samples were merged using CuffMerge and differential expression was determined using Cuffdiff. Genes with a p-value smaller than 0.01 where considered as differentially expressed.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample and Excel table final lists of differentially expressed genes | Total RNA was extracted using RNeasy Kit (Qiagen, Valencia, CA) according to manufacturer instructions.,The library for sequencing was constructed using an Illumina Multiplex System according to manufacturer's instructions (Illumina, San Diego, CA). Libraries were sequenced using HIseq-2000 (Illumina, San Diego, CA) to obtain 50 bp long reads. | GSM1131340 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087535,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272851 | GSM1131340 | GSE46502,GSE46503 | 0.002169 | primary HUVECs | Public on Jan 01 2014 | Apr 30 2013 | 9606 | PR+LPS_4h | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272851 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087535 |
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1 | cell type: primary human umbilical vein endothelial cells,passage: 4-6,infected with: a lentivirus containing human PR,treated with: LPS (1μM) for 8 hrs | 621 Charles E. Young Dr. S. | Los Angeles | USA | University of California-Los Angeles | Lauren,,Goddard | Debarcoding of the multiplex runs was performed using in house shell script,Reads were then processed and aligned to the human genome (hg19) using TopHat v2.0.4 (Trapnell et al., 2009) with default parameters.,The aligned read files were further processed with Cufflinks v2.0.1 (Trapnell et al., 2010) to calculate RPKP values. Assemblies for all samples were merged using CuffMerge and differential expression was determined using Cuffdiff. Genes with a p-value smaller than 0.01 where considered as differentially expressed.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample and Excel table final lists of differentially expressed genes | Total RNA was extracted using RNeasy Kit (Qiagen, Valencia, CA) according to manufacturer instructions.,The library for sequencing was constructed using an Illumina Multiplex System according to manufacturer's instructions (Illumina, San Diego, CA). Libraries were sequenced using HIseq-2000 (Illumina, San Diego, CA) to obtain 50 bp long reads. | GSM1131341 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087536,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272852 | GSM1131341 | GSE46502,GSE46503 | 0.007664 | primary HUVECs | Public on Jan 01 2014 | Apr 30 2013 | 9606 | PR+LPS_8h | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272852 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087536 |
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1 | cell type: primary human umbilical vein endothelial cells,passage: 4-6,infected with: a lentivirus containing human PR,treated with: LPS (1μM) + progesterone (100nM) for 4 hrs | 621 Charles E. Young Dr. S. | Los Angeles | USA | University of California-Los Angeles | Lauren,,Goddard | Debarcoding of the multiplex runs was performed using in house shell script,Reads were then processed and aligned to the human genome (hg19) using TopHat v2.0.4 (Trapnell et al., 2009) with default parameters.,The aligned read files were further processed with Cufflinks v2.0.1 (Trapnell et al., 2010) to calculate RPKP values. Assemblies for all samples were merged using CuffMerge and differential expression was determined using Cuffdiff. Genes with a p-value smaller than 0.01 where considered as differentially expressed.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample and Excel table final lists of differentially expressed genes | Total RNA was extracted using RNeasy Kit (Qiagen, Valencia, CA) according to manufacturer instructions.,The library for sequencing was constructed using an Illumina Multiplex System according to manufacturer's instructions (Illumina, San Diego, CA). Libraries were sequenced using HIseq-2000 (Illumina, San Diego, CA) to obtain 50 bp long reads. | GSM1131342 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087537,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272853 | GSM1131342 | GSE46502,GSE46503 | 0.002314 | primary HUVECs | Public on Jan 01 2014 | Apr 30 2013 | 9606 | PR+LPS+P_4h | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272853 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087537 |
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1 | cell type: primary human umbilical vein endothelial cells,passage: 4-6,infected with: a lentivirus containing human PR,treated with: LPS (1μM) + progesterone (100nM) for 8 hrs | 621 Charles E. Young Dr. S. | Los Angeles | USA | University of California-Los Angeles | Lauren,,Goddard | Debarcoding of the multiplex runs was performed using in house shell script,Reads were then processed and aligned to the human genome (hg19) using TopHat v2.0.4 (Trapnell et al., 2009) with default parameters.,The aligned read files were further processed with Cufflinks v2.0.1 (Trapnell et al., 2010) to calculate RPKP values. Assemblies for all samples were merged using CuffMerge and differential expression was determined using Cuffdiff. Genes with a p-value smaller than 0.01 where considered as differentially expressed.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample and Excel table final lists of differentially expressed genes | Total RNA was extracted using RNeasy Kit (Qiagen, Valencia, CA) according to manufacturer instructions.,The library for sequencing was constructed using an Illumina Multiplex System according to manufacturer's instructions (Illumina, San Diego, CA). Libraries were sequenced using HIseq-2000 (Illumina, San Diego, CA) to obtain 50 bp long reads. | GSM1131343 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087538,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272854 | GSM1131343 | GSE46502,GSE46503 | 0.001652 | primary HUVECs | Public on Jan 01 2014 | Apr 30 2013 | 9606 | PR+LPS+P_8h | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272854 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087538 |
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1 | location: Ascending colon,disease: sessile serrated polyp,Sex: Male | 30 North 1900 East | Salt Lake City | USA | University of Utah | Don,,Delker | Fastq files were aligned to human genome (Hg19) using novocraft novoalign application version 2.08.02,SAM files were converted to binary BAM files using USeq SamTranscriptomeParser application version 8.2.6,Data normalization, differential gene expression and statistical analyses were performed using USeq OverDispersedDefinedRegionScanSeqs application version 8.2.6,Visualization tracks for the Integrated Genome Browser were created using Useq Sam2USeq application version 8.2.6,Genome_build: Hg19,Supplementary_files_format_and_content: Tab-delimited text file with false discovery rate (FDR), fold change (polyp/control), mean RPKM (reads per kilobase gene length per million reads) for each gene, and individual reads for each sample | Colon biopsy samples were stored in RNAlater at 4°C overnight and RNA extracted with TRIzol,Illumina TruSeq RNA Sample Prep Kit | GSM1131538 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087588,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272897 | GSM1131538 | GSE46513 | 0.014532 | Colon | Public on Apr 29 2014 | Apr 30 2013 | 9606 | SSP1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272897 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087588 |
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1 | location: Ascending colon,disease: sessile serrated polyp,Sex: Female | 30 North 1900 East | Salt Lake City | USA | University of Utah | Don,,Delker | Fastq files were aligned to human genome (Hg19) using novocraft novoalign application version 2.08.02,SAM files were converted to binary BAM files using USeq SamTranscriptomeParser application version 8.2.6,Data normalization, differential gene expression and statistical analyses were performed using USeq OverDispersedDefinedRegionScanSeqs application version 8.2.6,Visualization tracks for the Integrated Genome Browser were created using Useq Sam2USeq application version 8.2.6,Genome_build: Hg19,Supplementary_files_format_and_content: Tab-delimited text file with false discovery rate (FDR), fold change (polyp/control), mean RPKM (reads per kilobase gene length per million reads) for each gene, and individual reads for each sample | Colon biopsy samples were stored in RNAlater at 4°C overnight and RNA extracted with TRIzol,Illumina TruSeq RNA Sample Prep Kit | GSM1131539 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087589,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272898 | GSM1131539 | GSE46513 | 0.006565 | Colon | Public on Apr 29 2014 | Apr 30 2013 | 9606 | SSP2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272898 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087589 |
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1 | location: Ascending colon,disease: sessile serrated polyp,Sex: Female | 30 North 1900 East | Salt Lake City | USA | University of Utah | Don,,Delker | Fastq files were aligned to human genome (Hg19) using novocraft novoalign application version 2.08.02,SAM files were converted to binary BAM files using USeq SamTranscriptomeParser application version 8.2.6,Data normalization, differential gene expression and statistical analyses were performed using USeq OverDispersedDefinedRegionScanSeqs application version 8.2.6,Visualization tracks for the Integrated Genome Browser were created using Useq Sam2USeq application version 8.2.6,Genome_build: Hg19,Supplementary_files_format_and_content: Tab-delimited text file with false discovery rate (FDR), fold change (polyp/control), mean RPKM (reads per kilobase gene length per million reads) for each gene, and individual reads for each sample | Colon biopsy samples were stored in RNAlater at 4°C overnight and RNA extracted with TRIzol,Illumina TruSeq RNA Sample Prep Kit | GSM1131540 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087583,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272899 | GSM1131540 | GSE46513 | 0.027483 | Colon | Public on Apr 29 2014 | Apr 30 2013 | 9606 | SSP3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272899 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087583 |
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1 | location: Ascending colon,disease: sessile serrated polyp,Sex: Female | 30 North 1900 East | Salt Lake City | USA | University of Utah | Don,,Delker | Fastq files were aligned to human genome (Hg19) using novocraft novoalign application version 2.08.02,SAM files were converted to binary BAM files using USeq SamTranscriptomeParser application version 8.2.6,Data normalization, differential gene expression and statistical analyses were performed using USeq OverDispersedDefinedRegionScanSeqs application version 8.2.6,Visualization tracks for the Integrated Genome Browser were created using Useq Sam2USeq application version 8.2.6,Genome_build: Hg19,Supplementary_files_format_and_content: Tab-delimited text file with false discovery rate (FDR), fold change (polyp/control), mean RPKM (reads per kilobase gene length per million reads) for each gene, and individual reads for each sample | Colon biopsy samples were stored in RNAlater at 4°C overnight and RNA extracted with TRIzol,Illumina TruSeq RNA Sample Prep Kit | GSM1131541 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087584,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272900 | GSM1131541 | GSE46513 | 0.014462 | Colon | Public on Apr 29 2014 | Apr 30 2013 | 9606 | SSP4 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272900 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087584 |
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1 | location: Ascending colon,disease: sessile serrated polyp,Sex: Male | 30 North 1900 East | Salt Lake City | USA | University of Utah | Don,,Delker | Fastq files were aligned to human genome (Hg19) using novocraft novoalign application version 2.08.02,SAM files were converted to binary BAM files using USeq SamTranscriptomeParser application version 8.2.6,Data normalization, differential gene expression and statistical analyses were performed using USeq OverDispersedDefinedRegionScanSeqs application version 8.2.6,Visualization tracks for the Integrated Genome Browser were created using Useq Sam2USeq application version 8.2.6,Genome_build: Hg19,Supplementary_files_format_and_content: Tab-delimited text file with false discovery rate (FDR), fold change (polyp/control), mean RPKM (reads per kilobase gene length per million reads) for each gene, and individual reads for each sample | Colon biopsy samples were stored in RNAlater at 4°C overnight and RNA extracted with TRIzol,Illumina TruSeq RNA Sample Prep Kit | GSM1131542 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087574,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272901 | GSM1131542 | GSE46513 | 0.016709 | Colon | Public on Apr 29 2014 | Apr 30 2013 | 9606 | SSP5 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272901 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087574 |
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1 | location: Ascending colon,disease: sessile serrated polyp,Sex: Female | 30 North 1900 East | Salt Lake City | USA | University of Utah | Don,,Delker | Fastq files were aligned to human genome (Hg19) using novocraft novoalign application version 2.08.02,SAM files were converted to binary BAM files using USeq SamTranscriptomeParser application version 8.2.6,Data normalization, differential gene expression and statistical analyses were performed using USeq OverDispersedDefinedRegionScanSeqs application version 8.2.6,Visualization tracks for the Integrated Genome Browser were created using Useq Sam2USeq application version 8.2.6,Genome_build: Hg19,Supplementary_files_format_and_content: Tab-delimited text file with false discovery rate (FDR), fold change (polyp/control), mean RPKM (reads per kilobase gene length per million reads) for each gene, and individual reads for each sample | Colon biopsy samples were stored in RNAlater at 4°C overnight and RNA extracted with TRIzol,Illumina TruSeq RNA Sample Prep Kit | GSM1131543 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087575,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272902 | GSM1131543 | GSE46513 | 0.015323 | Colon | Public on Apr 29 2014 | Apr 30 2013 | 9606 | SSP6 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272902 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087575 |
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1 | location: Ascending colon,disease: sessile serrated polyp,Sex: Female | 30 North 1900 East | Salt Lake City | USA | University of Utah | Don,,Delker | Fastq files were aligned to human genome (Hg19) using novocraft novoalign application version 2.08.02,SAM files were converted to binary BAM files using USeq SamTranscriptomeParser application version 8.2.6,Data normalization, differential gene expression and statistical analyses were performed using USeq OverDispersedDefinedRegionScanSeqs application version 8.2.6,Visualization tracks for the Integrated Genome Browser were created using Useq Sam2USeq application version 8.2.6,Genome_build: Hg19,Supplementary_files_format_and_content: Tab-delimited text file with false discovery rate (FDR), fold change (polyp/control), mean RPKM (reads per kilobase gene length per million reads) for each gene, and individual reads for each sample | Colon biopsy samples were stored in RNAlater at 4°C overnight and RNA extracted with TRIzol,Illumina TruSeq RNA Sample Prep Kit | GSM1131544 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087576,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272903 | GSM1131544 | GSE46513 | 0.030117 | Colon | Public on Apr 29 2014 | Apr 30 2013 | 9606 | SSP7 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272903 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087576 |
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1 | location: Cecum,disease: patient matched uninvolved colon,Sex: Male | 30 North 1900 East | Salt Lake City | USA | University of Utah | Don,,Delker | Fastq files were aligned to human genome (Hg19) using novocraft novoalign application version 2.08.02,SAM files were converted to binary BAM files using USeq SamTranscriptomeParser application version 8.2.6,Data normalization, differential gene expression and statistical analyses were performed using USeq OverDispersedDefinedRegionScanSeqs application version 8.2.6,Visualization tracks for the Integrated Genome Browser were created using Useq Sam2USeq application version 8.2.6,Genome_build: Hg19,Supplementary_files_format_and_content: Tab-delimited text file with false discovery rate (FDR), fold change (polyp/control), mean RPKM (reads per kilobase gene length per million reads) for each gene, and individual reads for each sample | Colon biopsy samples were stored in RNAlater at 4°C overnight and RNA extracted with TRIzol,Illumina TruSeq RNA Sample Prep Kit | GSM1131545 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087577,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272904 | GSM1131545 | GSE46513 | 0.014532 | Colon | Public on Apr 29 2014 | Apr 30 2013 | 9606 | CTRL1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272904 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087577 |
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1 | location: Cecum,disease: patient matched uninvolved colon,Sex: Female | 30 North 1900 East | Salt Lake City | USA | University of Utah | Don,,Delker | Fastq files were aligned to human genome (Hg19) using novocraft novoalign application version 2.08.02,SAM files were converted to binary BAM files using USeq SamTranscriptomeParser application version 8.2.6,Data normalization, differential gene expression and statistical analyses were performed using USeq OverDispersedDefinedRegionScanSeqs application version 8.2.6,Visualization tracks for the Integrated Genome Browser were created using Useq Sam2USeq application version 8.2.6,Genome_build: Hg19,Supplementary_files_format_and_content: Tab-delimited text file with false discovery rate (FDR), fold change (polyp/control), mean RPKM (reads per kilobase gene length per million reads) for each gene, and individual reads for each sample | Colon biopsy samples were stored in RNAlater at 4°C overnight and RNA extracted with TRIzol,Illumina TruSeq RNA Sample Prep Kit | GSM1131546 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087578,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272905 | GSM1131546 | GSE46513 | 0.009003 | Colon | Public on Apr 29 2014 | Apr 30 2013 | 9606 | CTRL2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272905 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087578 |
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1 | location: Ascending colon,disease: patient matched uninvolved colon,Sex: Female | 30 North 1900 East | Salt Lake City | USA | University of Utah | Don,,Delker | Fastq files were aligned to human genome (Hg19) using novocraft novoalign application version 2.08.02,SAM files were converted to binary BAM files using USeq SamTranscriptomeParser application version 8.2.6,Data normalization, differential gene expression and statistical analyses were performed using USeq OverDispersedDefinedRegionScanSeqs application version 8.2.6,Visualization tracks for the Integrated Genome Browser were created using Useq Sam2USeq application version 8.2.6,Genome_build: Hg19,Supplementary_files_format_and_content: Tab-delimited text file with false discovery rate (FDR), fold change (polyp/control), mean RPKM (reads per kilobase gene length per million reads) for each gene, and individual reads for each sample | Colon biopsy samples were stored in RNAlater at 4°C overnight and RNA extracted with TRIzol,Illumina TruSeq RNA Sample Prep Kit | GSM1131547 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087579,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272906 | GSM1131547 | GSE46513 | 0.045064 | Colon | Public on Apr 29 2014 | Apr 30 2013 | 9606 | CTRL3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272906 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087579 |
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1 | location: Ascending colon,disease: patient matched uninvolved colon,Sex: Male | 30 North 1900 East | Salt Lake City | USA | University of Utah | Don,,Delker | Fastq files were aligned to human genome (Hg19) using novocraft novoalign application version 2.08.02,SAM files were converted to binary BAM files using USeq SamTranscriptomeParser application version 8.2.6,Data normalization, differential gene expression and statistical analyses were performed using USeq OverDispersedDefinedRegionScanSeqs application version 8.2.6,Visualization tracks for the Integrated Genome Browser were created using Useq Sam2USeq application version 8.2.6,Genome_build: Hg19,Supplementary_files_format_and_content: Tab-delimited text file with false discovery rate (FDR), fold change (polyp/control), mean RPKM (reads per kilobase gene length per million reads) for each gene, and individual reads for each sample | Colon biopsy samples were stored in RNAlater at 4°C overnight and RNA extracted with TRIzol,Illumina TruSeq RNA Sample Prep Kit | GSM1131548 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087580,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272907 | GSM1131548 | GSE46513 | 0.018017 | Colon | Public on Apr 29 2014 | Apr 30 2013 | 9606 | CTRL4 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272907 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087580 |
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1 | location: Cecum,disease: patient matched uninvolved colon,Sex: Female | 30 North 1900 East | Salt Lake City | USA | University of Utah | Don,,Delker | Fastq files were aligned to human genome (Hg19) using novocraft novoalign application version 2.08.02,SAM files were converted to binary BAM files using USeq SamTranscriptomeParser application version 8.2.6,Data normalization, differential gene expression and statistical analyses were performed using USeq OverDispersedDefinedRegionScanSeqs application version 8.2.6,Visualization tracks for the Integrated Genome Browser were created using Useq Sam2USeq application version 8.2.6,Genome_build: Hg19,Supplementary_files_format_and_content: Tab-delimited text file with false discovery rate (FDR), fold change (polyp/control), mean RPKM (reads per kilobase gene length per million reads) for each gene, and individual reads for each sample | Colon biopsy samples were stored in RNAlater at 4°C overnight and RNA extracted with TRIzol,Illumina TruSeq RNA Sample Prep Kit | GSM1131549 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087581,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272908 | GSM1131549 | GSE46513 | 0.017455 | Colon | Public on Apr 29 2014 | Apr 30 2013 | 9606 | CTRL5 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272908 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087581 |
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1 | location: Ascending colon,disease: patient matched uninvolved colon,Sex: Female | 30 North 1900 East | Salt Lake City | USA | University of Utah | Don,,Delker | Fastq files were aligned to human genome (Hg19) using novocraft novoalign application version 2.08.02,SAM files were converted to binary BAM files using USeq SamTranscriptomeParser application version 8.2.6,Data normalization, differential gene expression and statistical analyses were performed using USeq OverDispersedDefinedRegionScanSeqs application version 8.2.6,Visualization tracks for the Integrated Genome Browser were created using Useq Sam2USeq application version 8.2.6,Genome_build: Hg19,Supplementary_files_format_and_content: Tab-delimited text file with false discovery rate (FDR), fold change (polyp/control), mean RPKM (reads per kilobase gene length per million reads) for each gene, and individual reads for each sample | Colon biopsy samples were stored in RNAlater at 4°C overnight and RNA extracted with TRIzol,Illumina TruSeq RNA Sample Prep Kit | GSM1131550 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087582,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272909 | GSM1131550 | GSE46513 | 0.052077 | Colon | Public on Apr 29 2014 | Apr 30 2013 | 9606 | CTRL6 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272909 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087582 |
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1 | location: Ascending colon,disease: normal colon (patient with no polyps),Sex: Male | 30 North 1900 East | Salt Lake City | USA | University of Utah | Don,,Delker | Fastq files were aligned to human genome (Hg19) using novocraft novoalign application version 2.08.02,SAM files were converted to binary BAM files using USeq SamTranscriptomeParser application version 8.2.6,Data normalization, differential gene expression and statistical analyses were performed using USeq OverDispersedDefinedRegionScanSeqs application version 8.2.6,Visualization tracks for the Integrated Genome Browser were created using Useq Sam2USeq application version 8.2.6,Genome_build: Hg19,Supplementary_files_format_and_content: Tab-delimited text file with false discovery rate (FDR), fold change (polyp/control), mean RPKM (reads per kilobase gene length per million reads) for each gene, and individual reads for each sample | Colon biopsy samples were stored in RNAlater at 4°C overnight and RNA extracted with TRIzol,Illumina TruSeq RNA Sample Prep Kit | GSM1131551 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087572,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272910 | GSM1131551 | GSE46513 | 0.024512 | Colon | Public on Apr 29 2014 | Apr 30 2013 | 9606 | CTRL7 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272910 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087572 |
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1 | location: Ascending colon,disease: normal colon (patient with no polyps),Sex: Male | 30 North 1900 East | Salt Lake City | USA | University of Utah | Don,,Delker | Fastq files were aligned to human genome (Hg19) using novocraft novoalign application version 2.08.02,SAM files were converted to binary BAM files using USeq SamTranscriptomeParser application version 8.2.6,Data normalization, differential gene expression and statistical analyses were performed using USeq OverDispersedDefinedRegionScanSeqs application version 8.2.6,Visualization tracks for the Integrated Genome Browser were created using Useq Sam2USeq application version 8.2.6,Genome_build: Hg19,Supplementary_files_format_and_content: Tab-delimited text file with false discovery rate (FDR), fold change (polyp/control), mean RPKM (reads per kilobase gene length per million reads) for each gene, and individual reads for each sample | Colon biopsy samples were stored in RNAlater at 4°C overnight and RNA extracted with TRIzol,Illumina TruSeq RNA Sample Prep Kit | GSM1131552 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087573,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272911 | GSM1131552 | GSE46513 | 0.047722 | Colon | Public on Apr 29 2014 | Apr 30 2013 | 9606 | CTRL8 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272911 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087573 |
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1 | cell line: BJAB,cell type: EBV-negative Burkitt's lymphoma cells,ectopic barts: no (empty retroviral vector),ip antibody: anti-human Ago2 (11A9) antibody,ip antibody info: PMID:18430891 | 1111 Highland Ave | Madison | USA | University of Wisconsin-Madison | Bill,,Sugden | Primary analysis performed using RTA 1.12.4.2 followed by secondary analysis with CASAVA 1.8.1,Sequence analysis was conducted using CLC Genomics Workbench Version 4.9; reads were mapped to hg18 human genome build,Unique exon reads for each gene were then used to create expression values for each gene with the following formula: Expression Value = (unique exon reads)(10^9)/(exon length)(total unique exon reads),A table was constructed consisting of genes with the respective associated expression values for each condition.,Genome_build: hg18,Supplementary_files_format_and_content: text file contains genes and associated enrichment values for each sample. Fold change (Column 4) is the ratio of the respective values BJAB_3628/BJAB_3626 (Column_3/Column_2) | 1Ã10^8 cells were washed with PBS and lysed with 500 µl of PLB buffer (10 mM HEPES, pH 7.0, 100 mM KCl, 0.5% NP-40, 5 mM MgCl2, 200 U/ml RNase inhibitor (Ambion), 1 mM DTT, proteinase inhibitor cocktail) at 4°C for 30 min. Following centrifugation, the lysate was incubated with anti-human Ago2 (11A9) antibody (Provided by Dr. Gunter Meister [Rüdel S, et al. (2008) A multifunctional human Argonaute2-specific monoclonal antibody. RNA 6: 1244â2153.]) conjugated dynabeads (Invitrogen) in 500 µl of NET-2 buffer (20 mM EDTA, pH 8.0, 1 mM DTT, and 200 U/ml RNase inhibitor in NT-2 buffer (150 mM Tris-HCl, pH 7.0, 100 mM Tris-HCl, pH 8.0, 750 mM NaCl, 0.25% NP-40, 5 mM MgCl2)) at 4°C for overnight. The protein-dynabead complexes were washed 6 times with NT-2 buffer, once with NTmS buffer (150 mM Tris-HCl, pH 7.0, 100 mM Tris-HCl, pH 8.0, 0.25% NP-40, 5 mM MgCl2) and resuspended with 1à Turbo DNase buffer and 2 U of Turbo DNase (Ambion) at 37°C for 30 min. The activity of DNase was eliminated with 15 mM of EDTA followed by addition of same volume of proteinase K buffer (2.4 mg/ml of proteinase K and 2% SDS in NT-2 buffer) at 55°C for 30 min. The RNA was extracted with acid-phenol/chloroform (pH 4.5) once, chloroform once and precipitated and resuspended in RNAse-free water.,Libraries were generated using Illuminaâs mRNA Seq kit (lot#5701543) Rev. D according to manufacturer's protocol. Briefly, samples were fragmented then precipitated at -80°C, followed by first strand & second strand cDNA synthesis. After end repair and adenylation of 3' ends, adapters were ligated to cDNA molecules. Following ligation, cDNA was purified using E-gel Size Select 2% agarose gels. Enrichment of purified cDNA was done via LMPCR (15 cycles) followed by purification using ZymoResearch DNA Clean & Concentrator columns (25ul elution volume). Libraries were validated on Agilent 1000 DNA chip and Quant-iT quantification. | GSM1131553 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087570,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272893 | GSM1131553 | GSE46514 | 0.001083 | BJAB cells_empty_RISC-IP | Public on May 01 2013 | Apr 30 2013 | 9606 | 3626Ago | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272893 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087570 |
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1 | cell line: BJAB,cell type: EBV-negative Burkitt's lymphoma cells,ectopic barts: yes (expressing EBV's BART miRNAs),ip antibody: anti-human Ago2 (11A9) antibody,ip antibody info: PMID:18430891 | 1111 Highland Ave | Madison | USA | University of Wisconsin-Madison | Bill,,Sugden | Primary analysis performed using RTA 1.12.4.2 followed by secondary analysis with CASAVA 1.8.1,Sequence analysis was conducted using CLC Genomics Workbench Version 4.9; reads were mapped to hg18 human genome build,Unique exon reads for each gene were then used to create expression values for each gene with the following formula: Expression Value = (unique exon reads)(10^9)/(exon length)(total unique exon reads),A table was constructed consisting of genes with the respective associated expression values for each condition.,Genome_build: hg18,Supplementary_files_format_and_content: text file contains genes and associated enrichment values for each sample. Fold change (Column 4) is the ratio of the respective values BJAB_3628/BJAB_3626 (Column_3/Column_2) | 1Ã10^8 cells were washed with PBS and lysed with 500 µl of PLB buffer (10 mM HEPES, pH 7.0, 100 mM KCl, 0.5% NP-40, 5 mM MgCl2, 200 U/ml RNase inhibitor (Ambion), 1 mM DTT, proteinase inhibitor cocktail) at 4°C for 30 min. Following centrifugation, the lysate was incubated with anti-human Ago2 (11A9) antibody (Provided by Dr. Gunter Meister [Rüdel S, et al. (2008) A multifunctional human Argonaute2-specific monoclonal antibody. RNA 6: 1244â2153.]) conjugated dynabeads (Invitrogen) in 500 µl of NET-2 buffer (20 mM EDTA, pH 8.0, 1 mM DTT, and 200 U/ml RNase inhibitor in NT-2 buffer (150 mM Tris-HCl, pH 7.0, 100 mM Tris-HCl, pH 8.0, 750 mM NaCl, 0.25% NP-40, 5 mM MgCl2)) at 4°C for overnight. The protein-dynabead complexes were washed 6 times with NT-2 buffer, once with NTmS buffer (150 mM Tris-HCl, pH 7.0, 100 mM Tris-HCl, pH 8.0, 0.25% NP-40, 5 mM MgCl2) and resuspended with 1à Turbo DNase buffer and 2 U of Turbo DNase (Ambion) at 37°C for 30 min. The activity of DNase was eliminated with 15 mM of EDTA followed by addition of same volume of proteinase K buffer (2.4 mg/ml of proteinase K and 2% SDS in NT-2 buffer) at 55°C for 30 min. The RNA was extracted with acid-phenol/chloroform (pH 4.5) once, chloroform once and precipitated and resuspended in RNAse-free water.,Libraries were generated using Illuminaâs mRNA Seq kit (lot#5701543) Rev. D according to manufacturer's protocol. Briefly, samples were fragmented then precipitated at -80°C, followed by first strand & second strand cDNA synthesis. After end repair and adenylation of 3' ends, adapters were ligated to cDNA molecules. Following ligation, cDNA was purified using E-gel Size Select 2% agarose gels. Enrichment of purified cDNA was done via LMPCR (15 cycles) followed by purification using ZymoResearch DNA Clean & Concentrator columns (25ul elution volume). Libraries were validated on Agilent 1000 DNA chip and Quant-iT quantification. | GSM1131554 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087571,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272894 | GSM1131554 | GSE46514 | 0 | BJAB cells_BARTs_RISC-IP | Public on May 01 2013 | Apr 30 2013 | 9606 | 3628Ago | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272894 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087571 |
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1 | tissue: brain,Sex: female,pathology: normal | 423 Guardian Dr, 1404 Blockley Hall | Philadelphia | USA | University of Pennsylvania | Paul,,Ryvkin | Illumina Casava1.7 software used for basecalling.,Sequenced reads were trimmed for adapter sequence using cutadapt v0.9 with options "-e 0.06 -O 6 -m 14 -n 2",Reads were mapped to the genome (hg19) using bowtie with options "--best --strata -v 2 -k 100" and non-unique mappers were removed. Reads with a mismatch rate > 6% were discarded.,Reads mapping to known ribosomal RNA sequences via Bowtie were discarded.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files containing read counts for each trimmed, rRNA-masked sequence | RNA was harvested from frozen brain tissue using Trizol reagent.,Illumina small RNA Sample Prep kit (#FC-102-1009) was used to construct libraries from 30ug total RNA. Instead of initial size fractionation, rRNAs were depleted by one round of Ribominus (Invitrogen). | GSM1131743 | Illumina HiSeq 2000 | May 15 2019 | other | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087660,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272963 | GSM1131743 | GSE46523 | 0.031166 | Dorsolateral prefrontal cortex | Public on Jul 01 2013 | Apr 30 2013 | 9606 | Normal Brain 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272963 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087660 |
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1 | tissue: brain,Sex: female,pathology: normal | 423 Guardian Dr, 1404 Blockley Hall | Philadelphia | USA | University of Pennsylvania | Paul,,Ryvkin | Illumina Casava1.7 software used for basecalling.,Sequenced reads were trimmed for adapter sequence using cutadapt v0.9 with options "-e 0.06 -O 6 -m 14 -n 2",Reads were mapped to the genome (hg19) using bowtie with options "--best --strata -v 2 -k 100" and non-unique mappers were removed. Reads with a mismatch rate > 6% were discarded.,Reads mapping to known ribosomal RNA sequences via Bowtie were discarded.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files containing read counts for each trimmed, rRNA-masked sequence | RNA was harvested from frozen brain tissue using Trizol reagent.,Illumina small RNA Sample Prep kit (#FC-102-1009) was used to construct libraries from 30ug total RNA. Instead of initial size fractionation, rRNAs were depleted by one round of Ribominus (Invitrogen). | GSM1131744 | Illumina HiSeq 2000 | May 15 2019 | other | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087661,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272964 | GSM1131744 | GSE46523 | 0.002445 | Dorsolateral prefrontal cortex | Public on Jul 01 2013 | Apr 30 2013 | 9606 | Normal Brain 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272964 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087661 |
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1 | tissue: brain,Sex: female,pathology: normal | 423 Guardian Dr, 1404 Blockley Hall | Philadelphia | USA | University of Pennsylvania | Paul,,Ryvkin | Illumina Casava1.7 software used for basecalling.,Sequenced reads were trimmed for adapter sequence using cutadapt v0.9 with options "-e 0.06 -O 6 -m 14 -n 2",Reads were mapped to the genome (hg19) using bowtie with options "--best --strata -v 2 -k 100" and non-unique mappers were removed. Reads with a mismatch rate > 6% were discarded.,Reads mapping to known ribosomal RNA sequences via Bowtie were discarded.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files containing read counts for each trimmed, rRNA-masked sequence | RNA was harvested from frozen brain tissue using Trizol reagent.,Illumina small RNA Sample Prep kit (#FC-102-1009) was used to construct libraries from 30ug total RNA. Instead of initial size fractionation, rRNAs were depleted by one round of Ribominus (Invitrogen). | GSM1131745 | Illumina HiSeq 2000 | May 15 2019 | other | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087662,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272965 | GSM1131745 | GSE46523 | 0.004048 | Dorsolateral prefrontal cortex | Public on Jul 01 2013 | Apr 30 2013 | 9606 | Normal Brain 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272965 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087662 |
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1 | tissue: brain,Sex: female,pathology: normal | 423 Guardian Dr, 1404 Blockley Hall | Philadelphia | USA | University of Pennsylvania | Paul,,Ryvkin | Illumina Casava1.7 software used for basecalling.,Sequenced reads were trimmed for adapter sequence using cutadapt v0.9 with options "-e 0.06 -O 6 -m 14 -n 2",Reads were mapped to the genome (hg19) using bowtie with options "--best --strata -v 2 -k 100" and non-unique mappers were removed. Reads with a mismatch rate > 6% were discarded.,Reads mapping to known ribosomal RNA sequences via Bowtie were discarded.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files containing read counts for each trimmed, rRNA-masked sequence | RNA was harvested from frozen brain tissue using Trizol reagent.,Illumina small RNA Sample Prep kit (#FC-102-1009) was used to construct libraries from 30ug total RNA. Instead of initial size fractionation, rRNAs were depleted by one round of Ribominus (Invitrogen). | GSM1131746 | Illumina HiSeq 2000 | May 15 2019 | other | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087663,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272966 | GSM1131746 | GSE46523 | 0.010535 | Dorsolateral prefrontal cortex | Public on Jul 01 2013 | Apr 30 2013 | 9606 | Normal Brain 4 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272966 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087663 |
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1 | tissue: brain,Sex: male,pathology: normal | 423 Guardian Dr, 1404 Blockley Hall | Philadelphia | USA | University of Pennsylvania | Paul,,Ryvkin | Illumina Casava1.7 software used for basecalling.,Sequenced reads were trimmed for adapter sequence using cutadapt v0.9 with options "-e 0.06 -O 6 -m 14 -n 2",Reads were mapped to the genome (hg19) using bowtie with options "--best --strata -v 2 -k 100" and non-unique mappers were removed. Reads with a mismatch rate > 6% were discarded.,Reads mapping to known ribosomal RNA sequences via Bowtie were discarded.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files containing read counts for each trimmed, rRNA-masked sequence | RNA was harvested from frozen brain tissue using Trizol reagent.,Illumina small RNA Sample Prep kit (#FC-102-1009) was used to construct libraries from 30ug total RNA. Instead of initial size fractionation, rRNAs were depleted by one round of Ribominus (Invitrogen). | GSM1131747 | Illumina HiSeq 2000 | May 15 2019 | other | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02087664,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272967 | GSM1131747 | GSE46523 | 0.030673 | Dorsolateral prefrontal cortex | Public on Jul 01 2013 | Apr 30 2013 | 9606 | Normal Brain 5 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272967 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02087664 |
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1 | sample group: patients,tissue: 14 day neurons | 1300 Morris Park Ave., F103 | Bronx | USA | Albert Einstein College of Medicine | Herb,,Lachman | Paired-end RNA-seq was carried out on an Illumina HiSeq 2000. We obtained 90-101 bp mate-paired reads from cDNA fragments with an average size of 250-bp (standard deviation for the distribution of inner distances between mate pairs is approximately 100 bp). RNA-seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version 2.0.8) [PMID:19289445]. We counted the number of fragments mapped to each gene annotated in the GENCODE database (version 18), which included multiple categories of annotated transcripts, and quantified transcript abundance as FPKM (fragments per kilobase of exon per million fragments mapped).,Genome_build: GRCh37/hg19,Supplementary_files_format_and_content: text file including FPKM for each sample. | RNA-seq was carried out on and day 14 neurons at the Columbia Genome Center. Total RNA was isolated from cells using the miRNeasy Kit (Qiagen) according to the manufacturerâs protocol. An additional DNAse1 digestion step was performed to ensure that the samples were not contaminated with genomic DNA. RNA purity was assessed using the Agilant 2100 Bioanalyzer (Beijing Genomics Institute). Each RNA sample had an A260:A280 ratio above 1.8, a RIN>9, and a A260:A230 ratio above 2.2.,Briefly, total RNA was converted to cDNA using oligo dT, which was then used for Illumina sequencing library preparation. | GSM1132421 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02116149,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX273280 | GSM1132421 | GSE46562 | 0.007022 | schizohrenia neurons | Public on Nov 01 2013 | May 01 2013 | 9606 | 1804 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX273280 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02116149 |
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1 | sample group: patients,tissue: 14 day neurons | 1300 Morris Park Ave., F103 | Bronx | USA | Albert Einstein College of Medicine | Herb,,Lachman | Paired-end RNA-seq was carried out on an Illumina HiSeq 2000. We obtained 90-101 bp mate-paired reads from cDNA fragments with an average size of 250-bp (standard deviation for the distribution of inner distances between mate pairs is approximately 100 bp). RNA-seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version 2.0.8) [PMID:19289445]. We counted the number of fragments mapped to each gene annotated in the GENCODE database (version 18), which included multiple categories of annotated transcripts, and quantified transcript abundance as FPKM (fragments per kilobase of exon per million fragments mapped).,Genome_build: GRCh37/hg19,Supplementary_files_format_and_content: text file including FPKM for each sample. | RNA-seq was carried out on and day 14 neurons at the Columbia Genome Center. Total RNA was isolated from cells using the miRNeasy Kit (Qiagen) according to the manufacturerâs protocol. An additional DNAse1 digestion step was performed to ensure that the samples were not contaminated with genomic DNA. RNA purity was assessed using the Agilant 2100 Bioanalyzer (Beijing Genomics Institute). Each RNA sample had an A260:A280 ratio above 1.8, a RIN>9, and a A260:A230 ratio above 2.2.,Briefly, total RNA was converted to cDNA using oligo dT, which was then used for Illumina sequencing library preparation. | GSM1132422 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02116150,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX273281 | GSM1132422 | GSE46562 | 0.010801 | schizohrenia neurons | Public on Nov 01 2013 | May 01 2013 | 9606 | 22q11-30 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX273281 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02116150 |
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1 | sample group: patients,tissue: 14 day neurons | 1300 Morris Park Ave., F103 | Bronx | USA | Albert Einstein College of Medicine | Herb,,Lachman | Paired-end RNA-seq was carried out on an Illumina HiSeq 2000. We obtained 90-101 bp mate-paired reads from cDNA fragments with an average size of 250-bp (standard deviation for the distribution of inner distances between mate pairs is approximately 100 bp). RNA-seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version 2.0.8) [PMID:19289445]. We counted the number of fragments mapped to each gene annotated in the GENCODE database (version 18), which included multiple categories of annotated transcripts, and quantified transcript abundance as FPKM (fragments per kilobase of exon per million fragments mapped).,Genome_build: GRCh37/hg19,Supplementary_files_format_and_content: text file including FPKM for each sample. | RNA-seq was carried out on and day 14 neurons at the Columbia Genome Center. Total RNA was isolated from cells using the miRNeasy Kit (Qiagen) according to the manufacturerâs protocol. An additional DNAse1 digestion step was performed to ensure that the samples were not contaminated with genomic DNA. RNA purity was assessed using the Agilant 2100 Bioanalyzer (Beijing Genomics Institute). Each RNA sample had an A260:A280 ratio above 1.8, a RIN>9, and a A260:A230 ratio above 2.2.,Briefly, total RNA was converted to cDNA using oligo dT, which was then used for Illumina sequencing library preparation. | GSM1132423 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02116151,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX273282 | GSM1132423 | GSE46562 | 0.00755 | schizohrenia neurons | Public on Nov 01 2013 | May 01 2013 | 9606 | 537 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX273282 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02116151 |
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1 | sample group: patients,tissue: 14 day neurons | 1300 Morris Park Ave., F103 | Bronx | USA | Albert Einstein College of Medicine | Herb,,Lachman | Paired-end RNA-seq was carried out on an Illumina HiSeq 2000. We obtained 90-101 bp mate-paired reads from cDNA fragments with an average size of 250-bp (standard deviation for the distribution of inner distances between mate pairs is approximately 100 bp). RNA-seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version 2.0.8) [PMID:19289445]. We counted the number of fragments mapped to each gene annotated in the GENCODE database (version 18), which included multiple categories of annotated transcripts, and quantified transcript abundance as FPKM (fragments per kilobase of exon per million fragments mapped).,Genome_build: GRCh37/hg19,Supplementary_files_format_and_content: text file including FPKM for each sample. | RNA-seq was carried out on and day 14 neurons at the Columbia Genome Center. Total RNA was isolated from cells using the miRNeasy Kit (Qiagen) according to the manufacturerâs protocol. An additional DNAse1 digestion step was performed to ensure that the samples were not contaminated with genomic DNA. RNA purity was assessed using the Agilant 2100 Bioanalyzer (Beijing Genomics Institute). Each RNA sample had an A260:A280 ratio above 1.8, a RIN>9, and a A260:A230 ratio above 2.2.,Briefly, total RNA was converted to cDNA using oligo dT, which was then used for Illumina sequencing library preparation. | GSM1132424 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02116152,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX273283 | GSM1132424 | GSE46562 | 0.008323 | schizohrenia neurons | Public on Nov 01 2013 | May 01 2013 | 9606 | 22q11-15 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX273283 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02116152 |
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1 | sample group: control,tissue: 14 day neurons | 1300 Morris Park Ave., F103 | Bronx | USA | Albert Einstein College of Medicine | Herb,,Lachman | Paired-end RNA-seq was carried out on an Illumina HiSeq 2000. We obtained 90-101 bp mate-paired reads from cDNA fragments with an average size of 250-bp (standard deviation for the distribution of inner distances between mate pairs is approximately 100 bp). RNA-seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version 2.0.8) [PMID:19289445]. We counted the number of fragments mapped to each gene annotated in the GENCODE database (version 18), which included multiple categories of annotated transcripts, and quantified transcript abundance as FPKM (fragments per kilobase of exon per million fragments mapped).,Genome_build: GRCh37/hg19,Supplementary_files_format_and_content: text file including FPKM for each sample. | RNA-seq was carried out on and day 14 neurons at the Columbia Genome Center. Total RNA was isolated from cells using the miRNeasy Kit (Qiagen) according to the manufacturerâs protocol. An additional DNAse1 digestion step was performed to ensure that the samples were not contaminated with genomic DNA. RNA purity was assessed using the Agilant 2100 Bioanalyzer (Beijing Genomics Institute). Each RNA sample had an A260:A280 ratio above 1.8, a RIN>9, and a A260:A230 ratio above 2.2.,Briefly, total RNA was converted to cDNA using oligo dT, which was then used for Illumina sequencing library preparation. | GSM1132425 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02116153,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX273284 | GSM1132425 | GSE46562 | 0.008344 | control neurons | Public on Nov 01 2013 | May 01 2013 | 9606 | iPSC5 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX273284 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02116153 |
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1 | sample group: control,tissue: 14 day neurons | 1300 Morris Park Ave., F103 | Bronx | USA | Albert Einstein College of Medicine | Herb,,Lachman | Paired-end RNA-seq was carried out on an Illumina HiSeq 2000. We obtained 90-101 bp mate-paired reads from cDNA fragments with an average size of 250-bp (standard deviation for the distribution of inner distances between mate pairs is approximately 100 bp). RNA-seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version 2.0.8) [PMID:19289445]. We counted the number of fragments mapped to each gene annotated in the GENCODE database (version 18), which included multiple categories of annotated transcripts, and quantified transcript abundance as FPKM (fragments per kilobase of exon per million fragments mapped).,Genome_build: GRCh37/hg19,Supplementary_files_format_and_content: text file including FPKM for each sample. | RNA-seq was carried out on and day 14 neurons at the Columbia Genome Center. Total RNA was isolated from cells using the miRNeasy Kit (Qiagen) according to the manufacturerâs protocol. An additional DNAse1 digestion step was performed to ensure that the samples were not contaminated with genomic DNA. RNA purity was assessed using the Agilant 2100 Bioanalyzer (Beijing Genomics Institute). Each RNA sample had an A260:A280 ratio above 1.8, a RIN>9, and a A260:A230 ratio above 2.2.,Briefly, total RNA was converted to cDNA using oligo dT, which was then used for Illumina sequencing library preparation. | GSM1132426 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02116154,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX273285 | GSM1132426 | GSE46562 | 0.007918 | control neurons | Public on Nov 01 2013 | May 01 2013 | 9606 | iPSC6 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX273285 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02116154 |
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1 | sample group: control,tissue: 14 day neurons | 1300 Morris Park Ave., F103 | Bronx | USA | Albert Einstein College of Medicine | Herb,,Lachman | Paired-end RNA-seq was carried out on an Illumina HiSeq 2000. We obtained 90-101 bp mate-paired reads from cDNA fragments with an average size of 250-bp (standard deviation for the distribution of inner distances between mate pairs is approximately 100 bp). RNA-seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version 2.0.8) [PMID:19289445]. We counted the number of fragments mapped to each gene annotated in the GENCODE database (version 18), which included multiple categories of annotated transcripts, and quantified transcript abundance as FPKM (fragments per kilobase of exon per million fragments mapped).,Genome_build: GRCh37/hg19,Supplementary_files_format_and_content: text file including FPKM for each sample. | RNA-seq was carried out on and day 14 neurons at the Columbia Genome Center. Total RNA was isolated from cells using the miRNeasy Kit (Qiagen) according to the manufacturerâs protocol. An additional DNAse1 digestion step was performed to ensure that the samples were not contaminated with genomic DNA. RNA purity was assessed using the Agilant 2100 Bioanalyzer (Beijing Genomics Institute). Each RNA sample had an A260:A280 ratio above 1.8, a RIN>9, and a A260:A230 ratio above 2.2.,Briefly, total RNA was converted to cDNA using oligo dT, which was then used for Illumina sequencing library preparation. | GSM1132427 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02116155,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX273286 | GSM1132427 | GSE46562 | 0.006809 | control neurons | Public on Nov 01 2013 | May 01 2013 | 9606 | iPSC2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX273286 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02116155 |
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1 | group: alzheimer patient,gender: female,age: 77 | Building 60 | Homburg | Germany | Saarland University | Andreas,,Keller | Demultiplexing of the raw sequencing data and generation of the fastq files was done using CASAVA v.1.8.2,The raw reads were preprocessed by cutting the 3' adapter sequence using the program fastx_clipper from the FASTX-Toolkit,mirbase v18 counts and counts for novel predicted miRNAs were collected using the miRDeep2 pipeline,miRNAs with less than 50 read counts summed up across all samples of each group (ad or control) were excluded from further analysis,the counts were normalized by quantile normalization,Genome_build: hg19,Supplementary_files_format_and_content: Excel table containing the raw mirbase and novel mirna counts and the quantile normalized counts | Total RNA including miRNA was isolated using the PAXgene Blood miRNA Kit (Qiagen) following the manufacturerâs recommendations.,For the library preparation, 200 ng of total RNA was used per sample. Preparation was performed following the protocol of the TruSeq Small RNA Sample Prep Kit (Illumina). Libraries were then pooled in batches of six samples in equal amounts and clustered with a concentration of 9 pmol in one lane each of a single read flowcell using the cBot (Illumina). | GSM1132688 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02116274,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX273417 | GSM1132688 | GSE46579 | 0.244624 | whole blood | Public on Jun 17 2013 | May 02 2013 | 9606 | AD sample 0 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX273417 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02116274 |