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1 | tissue: lung fibroblasts,transfection: Scramble siRNA | 7 Divinity Ave | Cambridge | USA | Harvard University | Cole,,Trapnell | All reads aligned with TopHat version 1.4.0 using the following options: "-a 5" against hg19 and annotated UCSC coding transcripts.,Aligments were processed with Cuffdiff version 2.0.0 using default options.,Genome_build: hg19,Supplementary_files_format_and_content: Cuffdiff expression tracking | Total RNA from human cell lines or human fat was extracted with Trizol (Invitrogen) and purified via the RNeasy mini kit (Qiagen) according to the manufacturersâ instructions. RNA quality was assessed using an Aglient Bioanalyzer. RNA-Seq libraries were prepared with the TruSeq mRNA-Seq kit (v1) according to manufacturer's instructions. Sequenced insert length for all libraries was approximately 180bp with a standard deviation of 50bp.,TruSeq RNA-Seq kit v1 | GSM925762 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX145662,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00990704 | GSM925762 | GSE37703,GSE37704 | 0.005064 | LFB_scramble_hiseq_repA | Public on Dec 11 2012 | May 02 2012 | 9606 | LFB_scramble_hiseq_repA | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX145662 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00990704 |
|
1 | tissue: lung fibroblasts,transfection: Scramble siRNA | 7 Divinity Ave | Cambridge | USA | Harvard University | Cole,,Trapnell | All reads aligned with TopHat version 1.4.0 using the following options: "-a 5" against hg19 and annotated UCSC coding transcripts.,Aligments were processed with Cuffdiff version 2.0.0 using default options.,Genome_build: hg19,Supplementary_files_format_and_content: Cuffdiff expression tracking | Total RNA from human cell lines or human fat was extracted with Trizol (Invitrogen) and purified via the RNeasy mini kit (Qiagen) according to the manufacturersâ instructions. RNA quality was assessed using an Aglient Bioanalyzer. RNA-Seq libraries were prepared with the TruSeq mRNA-Seq kit (v1) according to manufacturer's instructions. Sequenced insert length for all libraries was approximately 180bp with a standard deviation of 50bp.,TruSeq RNA-Seq kit v1 | GSM925763 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX145663,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00990705 | GSM925763 | GSE37703,GSE37704 | 0.013418 | LFB_scramble_hiseq_repB | Public on Dec 11 2012 | May 02 2012 | 9606 | LFB_scramble_hiseq_repB | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX145663 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00990705 |
|
1 | tissue: lung fibroblasts,transfection: Scramble siRNA | 7 Divinity Ave | Cambridge | USA | Harvard University | Cole,,Trapnell | All reads aligned with TopHat version 1.4.0 using the following options: "-a 5" against hg19 and annotated UCSC coding transcripts.,Aligments were processed with Cuffdiff version 2.0.0 using default options.,Genome_build: hg19,Supplementary_files_format_and_content: Cuffdiff expression tracking | Total RNA from human cell lines or human fat was extracted with Trizol (Invitrogen) and purified via the RNeasy mini kit (Qiagen) according to the manufacturersâ instructions. RNA quality was assessed using an Aglient Bioanalyzer. RNA-Seq libraries were prepared with the TruSeq mRNA-Seq kit (v1) according to manufacturer's instructions. Sequenced insert length for all libraries was approximately 180bp with a standard deviation of 50bp.,TruSeq RNA-Seq kit v1 | GSM925764 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX145664,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00990706 | GSM925764 | GSE37703,GSE37704 | 0.01614 | LFB_scramble_hiseq_repC | Public on Dec 11 2012 | May 02 2012 | 9606 | LFB_scramble_hiseq_repC | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX145664 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00990706 |
|
1 | tissue: lung fibroblasts,transfection: HOXA1 knockdown | 7 Divinity Ave | Cambridge | USA | Harvard University | Cole,,Trapnell | All reads aligned with TopHat version 1.4.0 using the following options: "-a 5" against hg19 and annotated UCSC coding transcripts.,Aligments were processed with Cuffdiff version 2.0.0 using default options.,Genome_build: hg19,Supplementary_files_format_and_content: Cuffdiff expression tracking | Total RNA from human cell lines or human fat was extracted with Trizol (Invitrogen) and purified via the RNeasy mini kit (Qiagen) according to the manufacturersâ instructions. RNA quality was assessed using an Aglient Bioanalyzer. RNA-Seq libraries were prepared with the TruSeq mRNA-Seq kit (v1) according to manufacturer's instructions. Sequenced insert length for all libraries was approximately 180bp with a standard deviation of 50bp.,TruSeq RNA-Seq kit v1 | GSM925765 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX145665,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00990707 | GSM925765 | GSE37703,GSE37704 | 0.005064 | LFB_HOXA1KD_hiseq_repA | Public on Dec 11 2012 | May 02 2012 | 9606 | LFB_HOXA1KD_hiseq_repA | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX145665 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00990707 |
|
1 | disease: pancreatic cancer,cell type: peripheral blood mononuclear cells | 180 Feng Lin Rd | Shanghai | China | Zhongshan Hospital, Fudan University | xiaolin,,wang | Basecalls performed using CASAVA version 1.4,The 50nt sequence tags from HiSeq sequencing will go through the data cleaning first, which includes getting rid of the low quality tags and several kinds of contaminants from the 50nt tags,Align small RNA tags to the human miRNA precursor/mature miRNA of corresponding species in miRBase17 using BLAST 2.2.25 ,with the following configurations:blastall -p blastn -F F -e 0.01,Normalize the expression of miRNA in two samples to get the expression of transcript per million (TPM). Normalization formula: Normalized expression = Actual miRNA count/Total count of clean reads*1000000,Calculate fold-change and P-value from the normalized expression,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample | Peripheral blood mononuclear cells (PBMCs) were isolated with lymphocyte separation medium following the manufacturerââ¬â¢s instruction (Sigama,USA).,Peripheral blood (5 ml) was drawn into EDTA tubes, transferred to the laboratory within 30 min for blood processing.,Total RNA was extracted by Trizol Reagent according to the instructions from the manufacturer (invitrogen, USA).,Small RNA library was prepared according to the prescribed procedure and standards of the Illumina Sample Preparation Protocol.In brief, total RNA was purified by electrophoretic separation on a 15% TBE-urea denaturing PAGE gel and small RNA regions corresponding to the 18-30 nucleotide bands in the marker lane were excised and recovered. The 18-30 nt small RNAs were 5' and 3' RNA adapter-ligated by T4 RNA ligase and at each step length validated and purified by urea PAGE gel electrophoretic separation. The adapter-ligated small RNA was subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen) and PCR amplified, using primers that anneal to the ends of the adapters. The amplified cDNA constructs, too, were purified and recovered. | GSM925875 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX145684,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00990716 | GSM925875 | GSE37710 | 0.3539 | peripheral blood mononuclear cells | Public on May 04 2012 | May 02 2012 | 9606 | PDAC smallRNAseq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX145684 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00990716 |
|
1 | disease: benign pancreatic/peripancreatic diseases,cell type: peripheral blood mononuclear cells | 180 Feng Lin Rd | Shanghai | China | Zhongshan Hospital, Fudan University | xiaolin,,wang | Basecalls performed using CASAVA version 1.4,The 50nt sequence tags from HiSeq sequencing will go through the data cleaning first, which includes getting rid of the low quality tags and several kinds of contaminants from the 50nt tags,Align small RNA tags to the human miRNA precursor/mature miRNA of corresponding species in miRBase17 using BLAST 2.2.25 ,with the following configurations:blastall -p blastn -F F -e 0.01,Normalize the expression of miRNA in two samples to get the expression of transcript per million (TPM). Normalization formula: Normalized expression = Actual miRNA count/Total count of clean reads*1000000,Calculate fold-change and P-value from the normalized expression,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample | Peripheral blood mononuclear cells (PBMCs) were isolated with lymphocyte separation medium following the manufacturerââ¬â¢s instruction (Sigama,USA).,Peripheral blood (5 ml) was drawn into EDTA tubes, transferred to the laboratory within 30 min for blood processing.,Total RNA was extracted by Trizol Reagent according to the instructions from the manufacturer (invitrogen, USA).,Small RNA library was prepared according to the prescribed procedure and standards of the Illumina Sample Preparation Protocol.In brief, total RNA was purified by electrophoretic separation on a 15% TBE-urea denaturing PAGE gel and small RNA regions corresponding to the 18-30 nucleotide bands in the marker lane were excised and recovered. The 18-30 nt small RNAs were 5' and 3' RNA adapter-ligated by T4 RNA ligase and at each step length validated and purified by urea PAGE gel electrophoretic separation. The adapter-ligated small RNA was subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen) and PCR amplified, using primers that anneal to the ends of the adapters. The amplified cDNA constructs, too, were purified and recovered. | GSM925876 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX145685,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00990717 | GSM925876 | GSE37710 | 0.019104 | peripheral blood mononuclear cells | Public on May 04 2012 | May 02 2012 | 9606 | BPD smallRNAseq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX145685 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00990717 |
|
1 | disease: healthy,cell type: peripheral blood mononuclear cells | 180 Feng Lin Rd | Shanghai | China | Zhongshan Hospital, Fudan University | xiaolin,,wang | Basecalls performed using CASAVA version 1.4,The 50nt sequence tags from HiSeq sequencing will go through the data cleaning first, which includes getting rid of the low quality tags and several kinds of contaminants from the 50nt tags,Align small RNA tags to the human miRNA precursor/mature miRNA of corresponding species in miRBase17 using BLAST 2.2.25 ,with the following configurations:blastall -p blastn -F F -e 0.01,Normalize the expression of miRNA in two samples to get the expression of transcript per million (TPM). Normalization formula: Normalized expression = Actual miRNA count/Total count of clean reads*1000000,Calculate fold-change and P-value from the normalized expression,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample | Peripheral blood mononuclear cells (PBMCs) were isolated with lymphocyte separation medium following the manufacturerââ¬â¢s instruction (Sigama,USA).,Peripheral blood (5 ml) was drawn into EDTA tubes, transferred to the laboratory within 30 min for blood processing.,Total RNA was extracted by Trizol Reagent according to the instructions from the manufacturer (invitrogen, USA).,Small RNA library was prepared according to the prescribed procedure and standards of the Illumina Sample Preparation Protocol.In brief, total RNA was purified by electrophoretic separation on a 15% TBE-urea denaturing PAGE gel and small RNA regions corresponding to the 18-30 nucleotide bands in the marker lane were excised and recovered. The 18-30 nt small RNAs were 5' and 3' RNA adapter-ligated by T4 RNA ligase and at each step length validated and purified by urea PAGE gel electrophoretic separation. The adapter-ligated small RNA was subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen) and PCR amplified, using primers that anneal to the ends of the adapters. The amplified cDNA constructs, too, were purified and recovered. | GSM925877 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX145686,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00990718 | GSM925877 | GSE37710 | 0.191465 | peripheral blood mononuclear cells | Public on May 04 2012 | May 02 2012 | 9606 | Healthy smallRNAseq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX145686 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00990718 |
|
1 | cell line: THP1,cell type: human monocytic leukemia | 1470 Madison Avenue | New York | USA | Icahn School of Medicine at Mount Sinai | Brian,,Brown | Illumina Casava1.8 software used for basecalling.,Sequence reads were filtered for low quality and mapped to the hg19 genome.,Supplementary_files_format_and_content: Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated following the protocol from Mortazavi et al, Nat Methods, 2008. Briefly, all reads falling in the exons of a given gene were counted and normalized by the length of the gene and the total reads of the run. | Total RNA was extracted from 3x106 THP1 cells following Qiazol protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. | GSM927668 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX146004,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00990957 | GSM927668 | GSE37769,GSE37771 | 0.201191 | THP1 cells | Public on Jul 01 2012 | May 04 2012 | 9606 | THP1_mRNAseq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX146004 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00990957 |
|
1 | cell line: MCF-7,cell type: epithelial breast cancer cells,genotype/variation: overexpression of miR-23b,transiently transfected with: miR-23b | Falmer, JMS Building | Brighton | United Kingdom | University of Sussex | Leandro,,Castellano | Basecalls performed using CASAVA version 1.4,Sequence reads were mapped to the hg19 genome assembly using Partek flow (Partek incorporated),Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Partek Genomic Suite (Partek Incorporated),Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample | Total RNA has been extracted using TRIzol (invitrigen). Libraries were prepared using the True-seq RNA preparation kit (Illumina) following the manufacturer instructions | GSM929909 | Illumina HiSeq 2000 | Feb 21 2023 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX147670,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00993197 | GSM929909 | GSE37918 | 0.001377 | MCF-7_miR-23b | Public on May 01 2013 | May 10 2012 | 9606 | MCF-7-miR-23b | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX147670 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00993197 |
|
1 | cell line: MCF-7,cell type: epithelial breast cancer cells,genotype/variation: control | Falmer, JMS Building | Brighton | United Kingdom | University of Sussex | Leandro,,Castellano | Basecalls performed using CASAVA version 1.4,Sequence reads were mapped to the hg19 genome assembly using Partek flow (Partek incorporated),Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Partek Genomic Suite (Partek Incorporated),Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample | Total RNA has been extracted using TRIzol (invitrigen). Libraries were prepared using the True-seq RNA preparation kit (Illumina) following the manufacturer instructions | GSM929910 | Illumina HiSeq 2000 | Feb 21 2023 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX147671,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00993198 | GSM929910 | GSE37918 | 0 | MCF-7_miR-nc | Public on May 01 2013 | May 10 2012 | 9606 | MCF-7-miR-nc | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX147671 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00993198 |
|
1 | cell line: MDA-MB-231,cell type: mesenchymal-like breast cancer cells,genotype/variation: reduced miR-23b activity,stably transfected with: miR-23b with specific sponge vector | Falmer, JMS Building | Brighton | United Kingdom | University of Sussex | Leandro,,Castellano | Basecalls performed using CASAVA version 1.4,Sequence reads were mapped to the hg19 genome assembly using Partek flow (Partek incorporated),Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Partek Genomic Suite (Partek Incorporated),Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample | Total RNA has been extracted using TRIzol (invitrigen). Libraries were prepared using the True-seq RNA preparation kit (Illumina) following the manufacturer instructions | GSM929912 | Illumina HiSeq 2000 | Feb 21 2023 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX147673,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00993200 | GSM929912 | GSE37918 | 0.007663 | MDA-MB-231_sponge-miR-23b | Public on May 01 2013 | May 10 2012 | 9606 | MDA-MB-231-sp-23b | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX147673 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00993200 |
|
1 | cell line: MDA-MB-231,cell type: mesenchymal-like breast cancer cells,genotype/variation: control | Falmer, JMS Building | Brighton | United Kingdom | University of Sussex | Leandro,,Castellano | Basecalls performed using CASAVA version 1.4,Sequence reads were mapped to the hg19 genome assembly using Partek flow (Partek incorporated),Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Partek Genomic Suite (Partek Incorporated),Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample | Total RNA has been extracted using TRIzol (invitrigen). Libraries were prepared using the True-seq RNA preparation kit (Illumina) following the manufacturer instructions | GSM929913 | Illumina HiSeq 2000 | Feb 21 2023 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX147674,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00993201 | GSM929913 | GSE37918 | 0.0028 | MDA-MB-231_control | Public on May 01 2013 | May 10 2012 | 9606 | MDA-MB-231-control | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX147674 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00993201 |
|
1 | cell line: HEK293,cell line stably expressing: HIS/FLAG/HA-tagged ALKBH5,par-clip antibody: FLAG,culture medium: DMEM | Robert-Rössle-StraÃe 10 | Berlin | Germany | Max-Delbrück-Center for Molecular Medicine | Markus,,Landthaler | Adapters were removed with FAR 1.81 (the felxible adapter remover: http://sourceforge.net/projects/theflexibleadap/) aligned to hg18 and a set of RefSeq pre-mRNA sequences with BWA 0.5.8c.,Unique alignments were converted to a pileup and read clusters scored for characteristic conversions and read variability with a custom script.,After stringent-false positive filtering (using antisense clusters as a decoy database) remaining clusters were output as bed files. See Lebedeva et al. 2011 Mol Cell 43, 340â352 for details,Genome_build: hg18,Supplementary_files_format_and_content: bed file reporting binding sites | PAR-CLIP and small RNA cloning (Hafner et al. 2010 Cell 141, 129â141) | GSM936506 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149417,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998308 | GSM936506 | GSE38157,GSE38201 | 0.25856 | HEK293 cell culture | Public on Jun 01 2012 | May 24 2012 | 9606 | PARCLIP_ALKBH5 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149417 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998308 |
|
1 | cell line: HEK293,cell line stably expressing: HIS/FLAG/HA-tagged C17orf85,par-clip antibody: FLAG,culture medium: DMEM | Robert-Rössle-StraÃe 10 | Berlin | Germany | Max-Delbrück-Center for Molecular Medicine | Markus,,Landthaler | Adapters were removed with FAR 1.81 (the felxible adapter remover: http://sourceforge.net/projects/theflexibleadap/) aligned to hg18 and a set of RefSeq pre-mRNA sequences with BWA 0.5.8c.,Unique alignments were converted to a pileup and read clusters scored for characteristic conversions and read variability with a custom script.,After stringent-false positive filtering (using antisense clusters as a decoy database) remaining clusters were output as bed files. See Lebedeva et al. 2011 Mol Cell 43, 340â352 for details,Genome_build: hg18,Supplementary_files_format_and_content: bed file reporting binding sites | PAR-CLIP and small RNA cloning (Hafner et al. 2010 Cell 141, 129â141) | GSM936507 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149418,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998309 | GSM936507 | GSE38157,GSE38201 | 0.365782 | HEK293 cell culture | Public on Jun 01 2012 | May 24 2012 | 9606 | PARCLIP_C17orf85 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149418 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998309 |
|
1 | cell line: HEK293,cell line stably expressing: HIS/FLAG/HA-tagged C22orf28,par-clip antibody: FLAG,culture medium: DMEM | Robert-Rössle-StraÃe 10 | Berlin | Germany | Max-Delbrück-Center for Molecular Medicine | Markus,,Landthaler | Adapters were removed with FAR 1.81 (the felxible adapter remover: http://sourceforge.net/projects/theflexibleadap/) aligned to hg18 and a set of RefSeq pre-mRNA sequences with BWA 0.5.8c.,Unique alignments were converted to a pileup and read clusters scored for characteristic conversions and read variability with a custom script.,After stringent-false positive filtering (using antisense clusters as a decoy database) remaining clusters were output as bed files. See Lebedeva et al. 2011 Mol Cell 43, 340â352 for details,Genome_build: hg18,Supplementary_files_format_and_content: bed file reporting binding sites | PAR-CLIP and small RNA cloning (Hafner et al. 2010 Cell 141, 129â141) | GSM936508 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149419,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998310 | GSM936508 | GSE38157,GSE38201 | 0.23442 | HEK293 cell culture | Public on Jun 01 2012 | May 24 2012 | 9606 | PARCLIP_C22orf28 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149419 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998310 |
|
1 | cell line: HEK293,cell line stably expressing: HIS/FLAG/HA-tagged CAPRIN1,par-clip antibody: FLAG,culture medium: DMEM | Robert-Rössle-StraÃe 10 | Berlin | Germany | Max-Delbrück-Center for Molecular Medicine | Markus,,Landthaler | Adapters were removed with FAR 1.81 (the felxible adapter remover: http://sourceforge.net/projects/theflexibleadap/) aligned to hg18 and a set of RefSeq pre-mRNA sequences with BWA 0.5.8c.,Unique alignments were converted to a pileup and read clusters scored for characteristic conversions and read variability with a custom script.,After stringent-false positive filtering (using antisense clusters as a decoy database) remaining clusters were output as bed files. See Lebedeva et al. 2011 Mol Cell 43, 340â352 for details,Genome_build: hg18,Supplementary_files_format_and_content: bed file reporting binding sites | PAR-CLIP and small RNA cloning (Hafner et al. 2010 Cell 141, 129â141) | GSM936509 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149420,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998311 | GSM936509 | GSE38157,GSE38201 | 0.268641 | HEK293 cell culture | Public on Jun 01 2012 | May 24 2012 | 9606 | PARCLIP_CAPRIN1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149420 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998311 |
|
1 | cell line: HEK293,cell line stably expressing: HIS/FLAG/HA-tagged ZC3H7B,par-clip antibody: FLAG,culture medium: DMEM | Robert-Rössle-StraÃe 10 | Berlin | Germany | Max-Delbrück-Center for Molecular Medicine | Markus,,Landthaler | Adapters were removed with FAR 1.81 (the felxible adapter remover: http://sourceforge.net/projects/theflexibleadap/) aligned to hg18 and a set of RefSeq pre-mRNA sequences with BWA 0.5.8c.,Unique alignments were converted to a pileup and read clusters scored for characteristic conversions and read variability with a custom script.,After stringent-false positive filtering (using antisense clusters as a decoy database) remaining clusters were output as bed files. See Lebedeva et al. 2011 Mol Cell 43, 340â352 for details,Genome_build: hg18,Supplementary_files_format_and_content: bed file reporting binding sites | PAR-CLIP and small RNA cloning (Hafner et al. 2010 Cell 141, 129â141) | GSM936510 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149421,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998312 | GSM936510 | GSE38157,GSE38201 | 0.548697 | HEK293 cell culture | Public on Jun 01 2012 | May 24 2012 | 9606 | PARCLIP_ZC3H7B | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149421 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998312 |
|
1 | treatment: 8 hour 100 nM bisphenol A,replicate: 1,cell line: T-47D | 601 Genome Way | Huntsville | USA | HudsonAlpha Institute | Jason,,Gertz | To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters:-n 2 -a -m 10 -X 3000. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.,Genome_build: hg19,Supplementary_files_format_and_content: The processed data files contain the official gene symbol, refseq id and RPKM value | mRNA was harvested using an mRNA-direct kit (Invitrogen), followed by DNase treatment. Non-directional libraries were then constructed as described in Gertz J, Varley KE, Davis NS, Baas BJ et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012 Jan;22(1):134-41. | GSM937160 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149607,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998512 | GSM937160 | GSE38234 | 0.000257 | Breast cancer cell line | Public on Jun 13 2012 | May 24 2012 | 9606 | T47D_BPA_R1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149607 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998512 |
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1 | treatment: 8 hour 0.02% DMSO,replicate: 1,cell line: T-47D | 601 Genome Way | Huntsville | USA | HudsonAlpha Institute | Jason,,Gertz | To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters:-n 2 -a -m 10 -X 3000. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.,Genome_build: hg19,Supplementary_files_format_and_content: The processed data files contain the official gene symbol, refseq id and RPKM value | mRNA was harvested using an mRNA-direct kit (Invitrogen), followed by DNase treatment. Non-directional libraries were then constructed as described in Gertz J, Varley KE, Davis NS, Baas BJ et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012 Jan;22(1):134-41. | GSM937162 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149608,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998513 | GSM937162 | GSE38234 | 0.012193 | Breast cancer cell line | Public on Jun 13 2012 | May 24 2012 | 9606 | T47D_DMSO_R1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149608 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998513 |
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1 | treatment: 8 hour 10 nM 17β-estradiol,replicate: 1,cell line: T-47D | 601 Genome Way | Huntsville | USA | HudsonAlpha Institute | Jason,,Gertz | To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters:-n 2 -a -m 10 -X 3000. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.,Genome_build: hg19,Supplementary_files_format_and_content: The processed data files contain the official gene symbol, refseq id and RPKM value | mRNA was harvested using an mRNA-direct kit (Invitrogen), followed by DNase treatment. Non-directional libraries were then constructed as described in Gertz J, Varley KE, Davis NS, Baas BJ et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012 Jan;22(1):134-41. | GSM937163 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149609,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998514 | GSM937163 | GSE38234 | 0 | Breast cancer cell line | Public on Jun 13 2012 | May 24 2012 | 9606 | T47D_E2_R1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149609 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998514 |
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1 | treatment: 8 hour 100 nM genistein,replicate: 1,cell line: T-47D | 601 Genome Way | Huntsville | USA | HudsonAlpha Institute | Jason,,Gertz | To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters:-n 2 -a -m 10 -X 3000. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.,Genome_build: hg19,Supplementary_files_format_and_content: The processed data files contain the official gene symbol, refseq id and RPKM value | mRNA was harvested using an mRNA-direct kit (Invitrogen), followed by DNase treatment. Non-directional libraries were then constructed as described in Gertz J, Varley KE, Davis NS, Baas BJ et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012 Jan;22(1):134-41. | GSM937164 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149610,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998515 | GSM937164 | GSE38234 | 0.001184 | Breast cancer cell line | Public on Jun 13 2012 | May 24 2012 | 9606 | T47D_GEN_R1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149610 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998515 |
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1 | treatment: 8 hour 100 nM bisphenol A,replicate: 2,cell line: T-47D | 601 Genome Way | Huntsville | USA | HudsonAlpha Institute | Jason,,Gertz | To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters:-n 2 -a -m 10 -X 3000. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.,Genome_build: hg19,Supplementary_files_format_and_content: The processed data files contain the official gene symbol, refseq id and RPKM value | mRNA was harvested using an mRNA-direct kit (Invitrogen), followed by DNase treatment. Non-directional libraries were then constructed as described in Gertz J, Varley KE, Davis NS, Baas BJ et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012 Jan;22(1):134-41. | GSM937166 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149611,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998516 | GSM937166 | GSE38234 | 0.00083 | Breast cancer cell line | Public on Jun 13 2012 | May 24 2012 | 9606 | T47D_BPA_R2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149611 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998516 |
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1 | treatment: 8 hour 0.02% DMSO,replicate: 2,cell line: T-47D | 601 Genome Way | Huntsville | USA | HudsonAlpha Institute | Jason,,Gertz | To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters:-n 2 -a -m 10 -X 3000. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.,Genome_build: hg19,Supplementary_files_format_and_content: The processed data files contain the official gene symbol, refseq id and RPKM value | mRNA was harvested using an mRNA-direct kit (Invitrogen), followed by DNase treatment. Non-directional libraries were then constructed as described in Gertz J, Varley KE, Davis NS, Baas BJ et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012 Jan;22(1):134-41. | GSM937167 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149612,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998517 | GSM937167 | GSE38234 | 0.003647 | Breast cancer cell line | Public on Jun 13 2012 | May 24 2012 | 9606 | T47D_DMSO_R2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149612 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998517 |
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1 | treatment: 8 hour 10 nM 17β-estradiol,replicate: 2,cell line: T-47D | 601 Genome Way | Huntsville | USA | HudsonAlpha Institute | Jason,,Gertz | To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters:-n 2 -a -m 10 -X 3000. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.,Genome_build: hg19,Supplementary_files_format_and_content: The processed data files contain the official gene symbol, refseq id and RPKM value | mRNA was harvested using an mRNA-direct kit (Invitrogen), followed by DNase treatment. Non-directional libraries were then constructed as described in Gertz J, Varley KE, Davis NS, Baas BJ et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012 Jan;22(1):134-41. | GSM937168 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149613,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998518 | GSM937168 | GSE38234 | 0.000611 | Breast cancer cell line | Public on Jun 13 2012 | May 24 2012 | 9606 | T47D_E2_R2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149613 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998518 |
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1 | treatment: 8 hour 100 nM genistein,replicate: 2,cell line: T-47D | 601 Genome Way | Huntsville | USA | HudsonAlpha Institute | Jason,,Gertz | To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters:-n 2 -a -m 10 -X 3000. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.,Genome_build: hg19,Supplementary_files_format_and_content: The processed data files contain the official gene symbol, refseq id and RPKM value | mRNA was harvested using an mRNA-direct kit (Invitrogen), followed by DNase treatment. Non-directional libraries were then constructed as described in Gertz J, Varley KE, Davis NS, Baas BJ et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012 Jan;22(1):134-41. | GSM937170 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149614,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998519 | GSM937170 | GSE38234 | 0.003647 | Breast cancer cell line | Public on Jun 13 2012 | May 24 2012 | 9606 | T47D_GEN_R2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149614 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998519 |
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1 | treatment: 8 hour 100 nM bisphenol A,replicate: 1,cell line: ECC-1 | 601 Genome Way | Huntsville | USA | HudsonAlpha Institute | Jason,,Gertz | To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters:-n 2 -a -m 10 -X 3000. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.,Genome_build: hg19,Supplementary_files_format_and_content: The processed data files contain the official gene symbol, refseq id and RPKM value | mRNA was harvested using an mRNA-direct kit (Invitrogen), followed by DNase treatment. Non-directional libraries were then constructed as described in Gertz J, Varley KE, Davis NS, Baas BJ et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012 Jan;22(1):134-41. | GSM937171 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149615,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998520 | GSM937171 | GSE38234 | 0.008342 | Endometrial cancer cell line | Public on Jun 13 2012 | May 24 2012 | 9606 | ECC1_BPA_R1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149615 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998520 |
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1 | treatment: 8 hour 0.02% DMSO,replicate: 1,cell line: ECC-1 | 601 Genome Way | Huntsville | USA | HudsonAlpha Institute | Jason,,Gertz | To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters:-n 2 -a -m 10 -X 3000. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.,Genome_build: hg19,Supplementary_files_format_and_content: The processed data files contain the official gene symbol, refseq id and RPKM value | mRNA was harvested using an mRNA-direct kit (Invitrogen), followed by DNase treatment. Non-directional libraries were then constructed as described in Gertz J, Varley KE, Davis NS, Baas BJ et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012 Jan;22(1):134-41. | GSM937172 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149616,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998521 | GSM937172 | GSE38234 | 0.01778 | Endometrial cancer cell line | Public on Jun 13 2012 | May 24 2012 | 9606 | ECC1_DMSO_R1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149616 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998521 |
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1 | treatment: 8 hour 10 nM 17β-estradiol,replicate: 1,cell line: ECC-1 | 601 Genome Way | Huntsville | USA | HudsonAlpha Institute | Jason,,Gertz | To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters:-n 2 -a -m 10 -X 3000. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.,Genome_build: hg19,Supplementary_files_format_and_content: The processed data files contain the official gene symbol, refseq id and RPKM value | mRNA was harvested using an mRNA-direct kit (Invitrogen), followed by DNase treatment. Non-directional libraries were then constructed as described in Gertz J, Varley KE, Davis NS, Baas BJ et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012 Jan;22(1):134-41. | GSM937174 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149617,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998522 | GSM937174 | GSE38234 | 0.010194 | Endometrial cancer cell line | Public on Jun 13 2012 | May 24 2012 | 9606 | ECC1_E2_R1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149617 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998522 |
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1 | treatment: 8 hour 100 nM genistein,replicate: 1,cell line: ECC-1 | 601 Genome Way | Huntsville | USA | HudsonAlpha Institute | Jason,,Gertz | To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters:-n 2 -a -m 10 -X 3000. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.,Genome_build: hg19,Supplementary_files_format_and_content: The processed data files contain the official gene symbol, refseq id and RPKM value | mRNA was harvested using an mRNA-direct kit (Invitrogen), followed by DNase treatment. Non-directional libraries were then constructed as described in Gertz J, Varley KE, Davis NS, Baas BJ et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012 Jan;22(1):134-41. | GSM937175 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149618,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998523 | GSM937175 | GSE38234 | 0.008902 | Endometrial cancer cell line | Public on Jun 13 2012 | May 24 2012 | 9606 | ECC1_GEN_R1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149618 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998523 |
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1 | treatment: 8 hour 100 nM bisphenol A,replicate: 2,cell line: ECC-1 | 601 Genome Way | Huntsville | USA | HudsonAlpha Institute | Jason,,Gertz | To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters:-n 2 -a -m 10 -X 3000. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.,Genome_build: hg19,Supplementary_files_format_and_content: The processed data files contain the official gene symbol, refseq id and RPKM value | mRNA was harvested using an mRNA-direct kit (Invitrogen), followed by DNase treatment. Non-directional libraries were then constructed as described in Gertz J, Varley KE, Davis NS, Baas BJ et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012 Jan;22(1):134-41. | GSM937176 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149619,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998524 | GSM937176 | GSE38234 | 0.006441 | Endometrial cancer cell line | Public on Jun 13 2012 | May 24 2012 | 9606 | ECC1_BPA_R2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149619 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998524 |
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1 | treatment: 8 hour 0.02% DMSO,replicate: 2,cell line: ECC-1 | 601 Genome Way | Huntsville | USA | HudsonAlpha Institute | Jason,,Gertz | To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters:-n 2 -a -m 10 -X 3000. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.,Genome_build: hg19,Supplementary_files_format_and_content: The processed data files contain the official gene symbol, refseq id and RPKM value | mRNA was harvested using an mRNA-direct kit (Invitrogen), followed by DNase treatment. Non-directional libraries were then constructed as described in Gertz J, Varley KE, Davis NS, Baas BJ et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012 Jan;22(1):134-41. | GSM937178 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149620,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998525 | GSM937178 | GSE38234 | 0.005596 | Endometrial cancer cell line | Public on Jun 13 2012 | May 24 2012 | 9606 | ECC1_DMSO_R2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149620 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998525 |
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1 | treatment: 8 hour 10 nM 17β-estradiol,replicate: 2,cell line: ECC-1 | 601 Genome Way | Huntsville | USA | HudsonAlpha Institute | Jason,,Gertz | To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters:-n 2 -a -m 10 -X 3000. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.,Genome_build: hg19,Supplementary_files_format_and_content: The processed data files contain the official gene symbol, refseq id and RPKM value | mRNA was harvested using an mRNA-direct kit (Invitrogen), followed by DNase treatment. Non-directional libraries were then constructed as described in Gertz J, Varley KE, Davis NS, Baas BJ et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012 Jan;22(1):134-41. | GSM937179 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149621,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998526 | GSM937179 | GSE38234 | 0.014469 | Endometrial cancer cell line | Public on Jun 13 2012 | May 24 2012 | 9606 | ECC1_E2_R2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149621 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998526 |
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1 | treatment: 8 hour 100 nM genistein,replicate: 2,cell line: ECC-1 | 601 Genome Way | Huntsville | USA | HudsonAlpha Institute | Jason,,Gertz | To calculate expression levels in each library, sequence reads were aligned to a database of all spliced RefSeq transcripts using Bowtie with the following parameters:-n 2 -a -m 10 -X 3000. The number of reads aligning to each transcript was multiplied by 1 million, then divided by the length of the transcript times the total number of aligned reads to calculate RPKM values.,Genome_build: hg19,Supplementary_files_format_and_content: The processed data files contain the official gene symbol, refseq id and RPKM value | mRNA was harvested using an mRNA-direct kit (Invitrogen), followed by DNase treatment. Non-directional libraries were then constructed as described in Gertz J, Varley KE, Davis NS, Baas BJ et al. Transposase mediated construction of RNA-seq libraries. Genome Res 2012 Jan;22(1):134-41. | GSM937180 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149622,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998527 | GSM937180 | GSE38234 | 0.006884 | Endometrial cancer cell line | Public on Jun 13 2012 | May 24 2012 | 9606 | ECC1_GEN_R2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149622 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998527 |
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1 | cell type: Human fibroblast | 9500 Gilman Dr. | La Jolla | USA | University of California, San Diego | Hai-Ri,,Li | Illumina OLB-1.9.0 software used for basecalling.,For gene counts for expression, sequenced reads were mapped to refMrna(hg19) using bowtie v0.12.7 and counted for each genes(Genomics. 2011;98(4):266-71),For bed files, sequenced reads were mapped to hg19 using bowtie v0.12.7 and the bed files were made based on the mapping information.,Genome_build: hg19,BJ.bed: hg19 | RNAs were extracted from cultured cells using TRIzol Reagent (Life Technologies, cat# 15596-026) . The cDNAs were synthesized with biotinylated P7-dT(20) oligos by reverse transcription and captured to solid phase. The second strand cDNAs were made with Adpator-hexamer by extension using DNA polymerase. The second strand cDNAs were PCR amplified with P7 and P5-index-Adaptor primers. The PCR products were size-selected, pooled and subjected to Illumina sequencers, reading target sequences followed by reading index (Genomics. 2011:98;266) | GSM937708 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149679,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998579 | GSM937708 | GSE38265 | 0.149942 | Human fibroblast | Public on Apr 25 2014 | May 25 2012 | 9606 | Parent BJ cell | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149679 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998579 |
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1 | karyotype: Normal,cell type: iPS cell derived from BJ | 9500 Gilman Dr. | La Jolla | USA | University of California, San Diego | Hai-Ri,,Li | Illumina OLB-1.9.0 software used for basecalling.,For gene counts for expression, sequenced reads were mapped to refMrna(hg19) using bowtie v0.12.7 and counted for each genes(Genomics. 2011;98(4):266-71),For bed files, sequenced reads were mapped to hg19 using bowtie v0.12.7 and the bed files were made based on the mapping information.,Genome_build: hg19,BJ-OKS-iM2.bed: hg19 | RNAs were extracted from cultured cells using TRIzol Reagent (Life Technologies, cat# 15596-026) . The cDNAs were synthesized with biotinylated P7-dT(20) oligos by reverse transcription and captured to solid phase. The second strand cDNAs were made with Adpator-hexamer by extension using DNA polymerase. The second strand cDNAs were PCR amplified with P7 and P5-index-Adaptor primers. The PCR products were size-selected, pooled and subjected to Illumina sequencers, reading target sequences followed by reading index (Genomics. 2011:98;266) | GSM937709 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149680,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998580 | GSM937709 | GSE38265 | 0.382293 | iPS cell derived from BJ | Public on Apr 25 2014 | May 25 2012 | 9606 | BJ-OKS-iM#2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149680 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998580 |
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1 | karyotype: Normal,cell type: iPS cell derived from BJ | 9500 Gilman Dr. | La Jolla | USA | University of California, San Diego | Hai-Ri,,Li | Illumina OLB-1.9.0 software used for basecalling.,For gene counts for expression, sequenced reads were mapped to refMrna(hg19) using bowtie v0.12.7 and counted for each genes(Genomics. 2011;98(4):266-71),For bed files, sequenced reads were mapped to hg19 using bowtie v0.12.7 and the bed files were made based on the mapping information.,Genome_build: hg19,BJ-OKS-iM21.bed: hg19 | RNAs were extracted from cultured cells using TRIzol Reagent (Life Technologies, cat# 15596-026) . The cDNAs were synthesized with biotinylated P7-dT(20) oligos by reverse transcription and captured to solid phase. The second strand cDNAs were made with Adpator-hexamer by extension using DNA polymerase. The second strand cDNAs were PCR amplified with P7 and P5-index-Adaptor primers. The PCR products were size-selected, pooled and subjected to Illumina sequencers, reading target sequences followed by reading index (Genomics. 2011:98;266) | GSM937710 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149681,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998581 | GSM937710 | GSE38265 | 0.383417 | iPS cell derived from BJ | Public on Apr 25 2014 | May 25 2012 | 9606 | BJ-OKS-iM#21 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149681 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998581 |
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1 | cell type: iPS cell derived from BJ | 9500 Gilman Dr. | La Jolla | USA | University of California, San Diego | Hai-Ri,,Li | Illumina OLB-1.9.0 software used for basecalling.,For gene counts for expression, sequenced reads were mapped to refMrna(hg19) using bowtie v0.12.7 and counted for each genes(Genomics. 2011;98(4):266-71),For bed files, sequenced reads were mapped to hg19 using bowtie v0.12.7 and the bed files were made based on the mapping information.,Genome_build: hg19,BJ-OKS-iG2.bed: hg19 | RNAs were extracted from cultured cells using TRIzol Reagent (Life Technologies, cat# 15596-026) . The cDNAs were synthesized with biotinylated P7-dT(20) oligos by reverse transcription and captured to solid phase. The second strand cDNAs were made with Adpator-hexamer by extension using DNA polymerase. The second strand cDNAs were PCR amplified with P7 and P5-index-Adaptor primers. The PCR products were size-selected, pooled and subjected to Illumina sequencers, reading target sequences followed by reading index (Genomics. 2011:98;266) | GSM937711 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149682,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998582 | GSM937711 | GSE38265 | 0.488298 | iPS cell derived from BJ | Public on Apr 25 2014 | May 25 2012 | 9606 | BJ-OKS-iG#2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149682 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998582 |
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1 | karyotype: Normal,cell type: iPS cell derived from BJ | 9500 Gilman Dr. | La Jolla | USA | University of California, San Diego | Hai-Ri,,Li | Illumina OLB-1.9.0 software used for basecalling.,For gene counts for expression, sequenced reads were mapped to refMrna(hg19) using bowtie v0.12.7 and counted for each genes(Genomics. 2011;98(4):266-71),For bed files, sequenced reads were mapped to hg19 using bowtie v0.12.7 and the bed files were made based on the mapping information.,Genome_build: hg19,BJ-OKS-iG5.bed: hg19 | RNAs were extracted from cultured cells using TRIzol Reagent (Life Technologies, cat# 15596-026) . The cDNAs were synthesized with biotinylated P7-dT(20) oligos by reverse transcription and captured to solid phase. The second strand cDNAs were made with Adpator-hexamer by extension using DNA polymerase. The second strand cDNAs were PCR amplified with P7 and P5-index-Adaptor primers. The PCR products were size-selected, pooled and subjected to Illumina sequencers, reading target sequences followed by reading index (Genomics. 2011:98;266) | GSM937712 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149683,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998583 | GSM937712 | GSE38265 | 0.361754 | iPS cell derived from BJ | Public on Apr 25 2014 | May 25 2012 | 9606 | BJ-OKS-iG#5 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149683 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998583 |
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1 | cell type: Human embryonic stem cell line | 9500 Gilman Dr. | La Jolla | USA | University of California, San Diego | Hai-Ri,,Li | Illumina OLB-1.9.0 software used for basecalling.,For gene counts for expression, sequenced reads were mapped to refMrna(hg19) using bowtie v0.12.7 and counted for each genes(Genomics. 2011;98(4):266-71),For bed files, sequenced reads were mapped to hg19 using bowtie v0.12.7 and the bed files were made based on the mapping information.,Genome_build: hg19,HUES9.bed: hg19 | RNAs were extracted from cultured cells using TRIzol Reagent (Life Technologies, cat# 15596-026) . The cDNAs were synthesized with biotinylated P7-dT(20) oligos by reverse transcription and captured to solid phase. The second strand cDNAs were made with Adpator-hexamer by extension using DNA polymerase. The second strand cDNAs were PCR amplified with P7 and P5-index-Adaptor primers. The PCR products were size-selected, pooled and subjected to Illumina sequencers, reading target sequences followed by reading index (Genomics. 2011:98;266) | GSM937713 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX149684,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00998584 | GSM937713 | GSE38265 | 0.475345 | Human embryonic stem cell line | Public on Apr 25 2014 | May 25 2012 | 9606 | HUES9 control ES cell | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX149684 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00998584 |
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1 | cell type: B-cells,cell line: GM12750,directional rnaseq: Non-directional,experiment: cDNAbaseline,treatment: no | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | We have only FPKM gene expression analysis for 5 samples in current study. For other samples, we generated BAM files and utilized sequence information from the BAM files for studying RNA-editing and other types of single nucleotide differences. We also attached a spreadsheet on the Series record containing the sum of all RDDs determined for the combined analysis from the different individuals in this study.,Low quality bases at the 3' ends of reads defined by Illumina were trimmed, and the resulting reads were aligned to the human reference genome (hg18) using GSNAP (version 2011-03-28.v3) using the following parameters: Mismatches â¤[(read length+2)/12-2]; Mapping score â¥20; Soft-clipping on (-trim-mismatch-score=-3); Known exon-exon junctions (defined by RefSeq (downloaded March 7, 2011) and Gencode (version 3c)) and novel junctions (defined by GSNAP) were accepted. SNP sites in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) were included for SNP-tolerant alignments. Only reads that aligned to one genomic location (uniquely mapped reads) were used in further analyses.,Expression levels of RNA transcripts were analyzed using Cufflinks.,Genome_build: HG18 | RNA were extracted using Qiagen DNeasy blood and tissue kit and RNeasy Mini kit with DNase treatment, respectively (Qiagen). For transcriptome sequencing, total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). RNA-seq libraries were prepared following Illumina TruSeq RNA sample preparation protocol or directional mRNA-Seq sample preparation protocol, respectively. The samples were sequenced using HiSeq 2000 instrument and 100-200 million 100-nt reads per sample were generated. | GSM938891 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX150766,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01001222 | GSM938891 | GSE38233 | 0.01086 | cultured B-cells | Public on Sep 20 2013 | May 29 2012 | 9606 | Sample_GM12750_baseline | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX150766 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01001222 |
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1 | cell type: B-cells,cell line: GM12004,directional rnaseq: Non-directional,experiment: cDNAbaseline,treatment: no | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | We have only FPKM gene expression analysis for 5 samples in current study. For other samples, we generated BAM files and utilized sequence information from the BAM files for studying RNA-editing and other types of single nucleotide differences. We also attached a spreadsheet on the Series record containing the sum of all RDDs determined for the combined analysis from the different individuals in this study.,Low quality bases at the 3' ends of reads defined by Illumina were trimmed, and the resulting reads were aligned to the human reference genome (hg18) using GSNAP (version 2011-03-28.v3) using the following parameters: Mismatches â¤[(read length+2)/12-2]; Mapping score â¥20; Soft-clipping on (-trim-mismatch-score=-3); Known exon-exon junctions (defined by RefSeq (downloaded March 7, 2011) and Gencode (version 3c)) and novel junctions (defined by GSNAP) were accepted. SNP sites in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) were included for SNP-tolerant alignments. Only reads that aligned to one genomic location (uniquely mapped reads) were used in further analyses.,Expression levels of RNA transcripts were analyzed using Cufflinks.,Genome_build: HG18 | RNA were extracted using Qiagen DNeasy blood and tissue kit and RNeasy Mini kit with DNase treatment, respectively (Qiagen). For transcriptome sequencing, total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). RNA-seq libraries were prepared following Illumina TruSeq RNA sample preparation protocol or directional mRNA-Seq sample preparation protocol, respectively. The samples were sequenced using HiSeq 2000 instrument and 100-200 million 100-nt reads per sample were generated. | GSM938892 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX150767,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01001223 | GSM938892 | GSE38233 | 0.074992 | cultured B-cells | Public on Sep 20 2013 | May 29 2012 | 9606 | Sample_GM12004_baseline | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX150767 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01001223 |
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1 | cell type: B-cells,cell line: GM12750,directional rnaseq: Directional,experiment: cDNAdirectional,treatment: no | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | We have only FPKM gene expression analysis for 5 samples in current study. For other samples, we generated BAM files and utilized sequence information from the BAM files for studying RNA-editing and other types of single nucleotide differences. We also attached a spreadsheet on the Series record containing the sum of all RDDs determined for the combined analysis from the different individuals in this study.,Low quality bases at the 3' ends of reads defined by Illumina were trimmed, and the resulting reads were aligned to the human reference genome (hg18) using GSNAP (version 2011-03-28.v3) using the following parameters: Mismatches â¤[(read length+2)/12-2]; Mapping score â¥20; Soft-clipping on (-trim-mismatch-score=-3); Known exon-exon junctions (defined by RefSeq (downloaded March 7, 2011) and Gencode (version 3c)) and novel junctions (defined by GSNAP) were accepted. SNP sites in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) were included for SNP-tolerant alignments. Only reads that aligned to one genomic location (uniquely mapped reads) were used in further analyses.,Expression levels of RNA transcripts were analyzed using Cufflinks.,Genome_build: HG18 | RNA were extracted using Qiagen DNeasy blood and tissue kit and RNeasy Mini kit with DNase treatment, respectively (Qiagen). For transcriptome sequencing, total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). RNA-seq libraries were prepared following Illumina TruSeq RNA sample preparation protocol or directional mRNA-Seq sample preparation protocol, respectively. The samples were sequenced using HiSeq 2000 instrument and 100-200 million 100-nt reads per sample were generated. | GSM938893 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX150768,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01001224 | GSM938893 | GSE38233 | 0.212389 | cultured B-cells | Public on Sep 20 2013 | May 29 2012 | 9606 | Sample_GM12750_Directional | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX150768 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01001224 |
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1 | cell type: B-cells,cell line: GM12004,directional rnaseq: Directional,experiment: cDNAdirectional,treatment: no | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | We have only FPKM gene expression analysis for 5 samples in current study. For other samples, we generated BAM files and utilized sequence information from the BAM files for studying RNA-editing and other types of single nucleotide differences. We also attached a spreadsheet on the Series record containing the sum of all RDDs determined for the combined analysis from the different individuals in this study.,Low quality bases at the 3' ends of reads defined by Illumina were trimmed, and the resulting reads were aligned to the human reference genome (hg18) using GSNAP (version 2011-03-28.v3) using the following parameters: Mismatches â¤[(read length+2)/12-2]; Mapping score â¥20; Soft-clipping on (-trim-mismatch-score=-3); Known exon-exon junctions (defined by RefSeq (downloaded March 7, 2011) and Gencode (version 3c)) and novel junctions (defined by GSNAP) were accepted. SNP sites in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) were included for SNP-tolerant alignments. Only reads that aligned to one genomic location (uniquely mapped reads) were used in further analyses.,Expression levels of RNA transcripts were analyzed using Cufflinks.,Genome_build: HG18 | RNA were extracted using Qiagen DNeasy blood and tissue kit and RNeasy Mini kit with DNase treatment, respectively (Qiagen). For transcriptome sequencing, total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). RNA-seq libraries were prepared following Illumina TruSeq RNA sample preparation protocol or directional mRNA-Seq sample preparation protocol, respectively. The samples were sequenced using HiSeq 2000 instrument and 100-200 million 100-nt reads per sample were generated. | GSM938894 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX150769,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01001225 | GSM938894 | GSE38233 | 0.213455 | cultured B-cells | Public on Sep 20 2013 | May 29 2012 | 9606 | Sample_GM12004_Directional | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX150769 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01001225 |
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1 | cell type: B-cells,cell line: GM12750,directional rnaseq: Non-directional,experiment: cDNA-NTC-siRNA,treatment: non-targeting control siRNA | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | We have only FPKM gene expression analysis for 5 samples in current study. For other samples, we generated BAM files and utilized sequence information from the BAM files for studying RNA-editing and other types of single nucleotide differences. We also attached a spreadsheet on the Series record containing the sum of all RDDs determined for the combined analysis from the different individuals in this study.,Low quality bases at the 3' ends of reads defined by Illumina were trimmed, and the resulting reads were aligned to the human reference genome (hg18) using GSNAP (version 2011-03-28.v3) using the following parameters: Mismatches â¤[(read length+2)/12-2]; Mapping score â¥20; Soft-clipping on (-trim-mismatch-score=-3); Known exon-exon junctions (defined by RefSeq (downloaded March 7, 2011) and Gencode (version 3c)) and novel junctions (defined by GSNAP) were accepted. SNP sites in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) were included for SNP-tolerant alignments. Only reads that aligned to one genomic location (uniquely mapped reads) were used in further analyses.,Expression levels of RNA transcripts were analyzed using Cufflinks.,Genome_build: HG18 | RNA were extracted using Qiagen DNeasy blood and tissue kit and RNeasy Mini kit with DNase treatment, respectively (Qiagen). For transcriptome sequencing, total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). RNA-seq libraries were prepared following Illumina TruSeq RNA sample preparation protocol or directional mRNA-Seq sample preparation protocol, respectively. The samples were sequenced using HiSeq 2000 instrument and 100-200 million 100-nt reads per sample were generated. | GSM938897 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX150772,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01001228 | GSM938897 | GSE38233 | 0 | cultured B-cells | Public on Sep 20 2013 | May 29 2012 | 9606 | Sample_GM12750_NT | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX150772 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01001228 |
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1 | cell type: B-cells,cell line: GM12750,directional rnaseq: Non-directional,experiment: cDNA-ADAR1-siRNA,treatment: siRNA knockdown of ADAR1 | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | We have only FPKM gene expression analysis for 5 samples in current study. For other samples, we generated BAM files and utilized sequence information from the BAM files for studying RNA-editing and other types of single nucleotide differences. We also attached a spreadsheet on the Series record containing the sum of all RDDs determined for the combined analysis from the different individuals in this study.,Low quality bases at the 3' ends of reads defined by Illumina were trimmed, and the resulting reads were aligned to the human reference genome (hg18) using GSNAP (version 2011-03-28.v3) using the following parameters: Mismatches â¤[(read length+2)/12-2]; Mapping score â¥20; Soft-clipping on (-trim-mismatch-score=-3); Known exon-exon junctions (defined by RefSeq (downloaded March 7, 2011) and Gencode (version 3c)) and novel junctions (defined by GSNAP) were accepted. SNP sites in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) were included for SNP-tolerant alignments. Only reads that aligned to one genomic location (uniquely mapped reads) were used in further analyses.,Expression levels of RNA transcripts were analyzed using Cufflinks.,Genome_build: HG18 | RNA were extracted using Qiagen DNeasy blood and tissue kit and RNeasy Mini kit with DNase treatment, respectively (Qiagen). For transcriptome sequencing, total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). RNA-seq libraries were prepared following Illumina TruSeq RNA sample preparation protocol or directional mRNA-Seq sample preparation protocol, respectively. The samples were sequenced using HiSeq 2000 instrument and 100-200 million 100-nt reads per sample were generated. | GSM938898 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX150773,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01001229 | GSM938898 | GSE38233 | 0 | cultured B-cells | Public on Sep 20 2013 | May 29 2012 | 9606 | Sample_GM12750_ADAR_KD | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX150773 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01001229 |
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1 | cell type: B-cells,cell line: GM12004,directional rnaseq: Non-directional,experiment: cDNA-ADAR1-siRNA,treatment: siRNA knockdown of ADAR1 | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | We have only FPKM gene expression analysis for 5 samples in current study. For other samples, we generated BAM files and utilized sequence information from the BAM files for studying RNA-editing and other types of single nucleotide differences. We also attached a spreadsheet on the Series record containing the sum of all RDDs determined for the combined analysis from the different individuals in this study.,Low quality bases at the 3' ends of reads defined by Illumina were trimmed, and the resulting reads were aligned to the human reference genome (hg18) using GSNAP (version 2011-03-28.v3) using the following parameters: Mismatches â¤[(read length+2)/12-2]; Mapping score â¥20; Soft-clipping on (-trim-mismatch-score=-3); Known exon-exon junctions (defined by RefSeq (downloaded March 7, 2011) and Gencode (version 3c)) and novel junctions (defined by GSNAP) were accepted. SNP sites in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) were included for SNP-tolerant alignments. Only reads that aligned to one genomic location (uniquely mapped reads) were used in further analyses.,Expression levels of RNA transcripts were analyzed using Cufflinks.,Genome_build: HG18 | RNA were extracted using Qiagen DNeasy blood and tissue kit and RNeasy Mini kit with DNase treatment, respectively (Qiagen). For transcriptome sequencing, total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). RNA-seq libraries were prepared following Illumina TruSeq RNA sample preparation protocol or directional mRNA-Seq sample preparation protocol, respectively. The samples were sequenced using HiSeq 2000 instrument and 100-200 million 100-nt reads per sample were generated. | GSM938900 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX150775,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01001231 | GSM938900 | GSE38233 | 0.157086 | cultured B-cells | Public on Sep 20 2013 | May 29 2012 | 9606 | Sample_GM12004_ADARkd | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX150775 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01001231 |
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1 | cell type: B-cells,cell line: GM12004,directional rnaseq: Non-directional,experiment: cDNA-ADAR2-siRNA,treatment: siRNA knockdown of ADAR2 | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | We have only FPKM gene expression analysis for 5 samples in current study. For other samples, we generated BAM files and utilized sequence information from the BAM files for studying RNA-editing and other types of single nucleotide differences. We also attached a spreadsheet on the Series record containing the sum of all RDDs determined for the combined analysis from the different individuals in this study.,Low quality bases at the 3' ends of reads defined by Illumina were trimmed, and the resulting reads were aligned to the human reference genome (hg18) using GSNAP (version 2011-03-28.v3) using the following parameters: Mismatches â¤[(read length+2)/12-2]; Mapping score â¥20; Soft-clipping on (-trim-mismatch-score=-3); Known exon-exon junctions (defined by RefSeq (downloaded March 7, 2011) and Gencode (version 3c)) and novel junctions (defined by GSNAP) were accepted. SNP sites in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) were included for SNP-tolerant alignments. Only reads that aligned to one genomic location (uniquely mapped reads) were used in further analyses.,Expression levels of RNA transcripts were analyzed using Cufflinks.,Genome_build: HG18 | RNA were extracted using Qiagen DNeasy blood and tissue kit and RNeasy Mini kit with DNase treatment, respectively (Qiagen). For transcriptome sequencing, total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). RNA-seq libraries were prepared following Illumina TruSeq RNA sample preparation protocol or directional mRNA-Seq sample preparation protocol, respectively. The samples were sequenced using HiSeq 2000 instrument and 100-200 million 100-nt reads per sample were generated. | GSM938901 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX150776,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01001232 | GSM938901 | GSE38233 | 0.060437 | cultured B-cells | Public on Sep 20 2013 | May 29 2012 | 9606 | Sample_GM12004_ADAR2_kd | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX150776 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01001232 |
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1 | cell type: B-cells,cell line: GM12750,directional rnaseq: Non-directional,experiment: Adar1-KD-C-Time72h,treatment: siRNA knockdown of ADAR1, 72 hour time point | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | We have only FPKM gene expression analysis for 5 samples in current study. For other samples, we generated BAM files and utilized sequence information from the BAM files for studying RNA-editing and other types of single nucleotide differences. We also attached a spreadsheet on the Series record containing the sum of all RDDs determined for the combined analysis from the different individuals in this study.,Low quality bases at the 3' ends of reads defined by Illumina were trimmed, and the resulting reads were aligned to the human reference genome (hg18) using GSNAP (version 2011-03-28.v3) using the following parameters: Mismatches â¤[(read length+2)/12-2]; Mapping score â¥20; Soft-clipping on (-trim-mismatch-score=-3); Known exon-exon junctions (defined by RefSeq (downloaded March 7, 2011) and Gencode (version 3c)) and novel junctions (defined by GSNAP) were accepted. SNP sites in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) were included for SNP-tolerant alignments. Only reads that aligned to one genomic location (uniquely mapped reads) were used in further analyses.,Expression levels of RNA transcripts were analyzed using Cufflinks.,Genome_build: HG18 | RNA were extracted using Qiagen DNeasy blood and tissue kit and RNeasy Mini kit with DNase treatment, respectively (Qiagen). For transcriptome sequencing, total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). RNA-seq libraries were prepared following Illumina TruSeq RNA sample preparation protocol or directional mRNA-Seq sample preparation protocol, respectively. The samples were sequenced using HiSeq 2000 instrument and 100-200 million 100-nt reads per sample were generated. | GSM938904 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX150779,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01001235 | GSM938904 | GSE38233 | 0.162819 | cultured B-cells | Public on Sep 20 2013 | May 29 2012 | 9606 | Sample_GM12750_ADARkd_CTime | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX150779 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01001235 |
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1 | cell type: B-cells,cell line: GM12004,directional rnaseq: Non-directional,experiment: RNAIP-ADAR1,treatment: RNA-IP using ADAR1 antibody,antibody vendor/catalog#: Sigma, #HPA003890 | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | We have only FPKM gene expression analysis for 5 samples in current study. For other samples, we generated BAM files and utilized sequence information from the BAM files for studying RNA-editing and other types of single nucleotide differences. We also attached a spreadsheet on the Series record containing the sum of all RDDs determined for the combined analysis from the different individuals in this study.,Low quality bases at the 3' ends of reads defined by Illumina were trimmed, and the resulting reads were aligned to the human reference genome (hg18) using GSNAP (version 2011-03-28.v3) using the following parameters: Mismatches â¤[(read length+2)/12-2]; Mapping score â¥20; Soft-clipping on (-trim-mismatch-score=-3); Known exon-exon junctions (defined by RefSeq (downloaded March 7, 2011) and Gencode (version 3c)) and novel junctions (defined by GSNAP) were accepted. SNP sites in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) were included for SNP-tolerant alignments. Only reads that aligned to one genomic location (uniquely mapped reads) were used in further analyses.,Expression levels of RNA transcripts were analyzed using Cufflinks.,Genome_build: HG18 | RNA were extracted using Qiagen DNeasy blood and tissue kit and RNeasy Mini kit with DNase treatment, respectively (Qiagen). For transcriptome sequencing, total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). RNA-seq libraries were prepared following Illumina TruSeq RNA sample preparation protocol or directional mRNA-Seq sample preparation protocol, respectively. The samples were sequenced using HiSeq 2000 instrument and 100-200 million 100-nt reads per sample were generated. | GSM938907 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX150782,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01001238 | GSM938907 | GSE38233 | 0.016447 | cultured B-cells | Public on Sep 20 2013 | May 29 2012 | 9606 | Sample_RNA-IP_ADAR_GM12004 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX150782 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01001238 |
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1 | cell type: B-cells,cell line: GM12004,directional rnaseq: Non-directional,experiment: RNAIP-IgG,treatment: RNA-IP using control IgG,antibody vendor/catalog#: ABCAM, ab46540 | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | We have only FPKM gene expression analysis for 5 samples in current study. For other samples, we generated BAM files and utilized sequence information from the BAM files for studying RNA-editing and other types of single nucleotide differences. We also attached a spreadsheet on the Series record containing the sum of all RDDs determined for the combined analysis from the different individuals in this study.,Low quality bases at the 3' ends of reads defined by Illumina were trimmed, and the resulting reads were aligned to the human reference genome (hg18) using GSNAP (version 2011-03-28.v3) using the following parameters: Mismatches â¤[(read length+2)/12-2]; Mapping score â¥20; Soft-clipping on (-trim-mismatch-score=-3); Known exon-exon junctions (defined by RefSeq (downloaded March 7, 2011) and Gencode (version 3c)) and novel junctions (defined by GSNAP) were accepted. SNP sites in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) were included for SNP-tolerant alignments. Only reads that aligned to one genomic location (uniquely mapped reads) were used in further analyses.,Expression levels of RNA transcripts were analyzed using Cufflinks.,Genome_build: HG18 | RNA were extracted using Qiagen DNeasy blood and tissue kit and RNeasy Mini kit with DNase treatment, respectively (Qiagen). For transcriptome sequencing, total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). RNA-seq libraries were prepared following Illumina TruSeq RNA sample preparation protocol or directional mRNA-Seq sample preparation protocol, respectively. The samples were sequenced using HiSeq 2000 instrument and 100-200 million 100-nt reads per sample were generated. | GSM938908 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX150783,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01001239 | GSM938908 | GSE38233 | 0.001219 | cultured B-cells | Public on Sep 20 2013 | May 29 2012 | 9606 | Sample_RNA-IP_IgG_GM12004 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX150783 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01001239 |
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1 | cell type: B-cells,cell line: GM12750,directional rnaseq: Non-directional,experiment: RNAIP-ADAR1,treatment: RNA-IP using ADAR1 antibody,antibody vendor/catalog#: Sigma, #HPA003890 | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | We have only FPKM gene expression analysis for 5 samples in current study. For other samples, we generated BAM files and utilized sequence information from the BAM files for studying RNA-editing and other types of single nucleotide differences. We also attached a spreadsheet on the Series record containing the sum of all RDDs determined for the combined analysis from the different individuals in this study.,Low quality bases at the 3' ends of reads defined by Illumina were trimmed, and the resulting reads were aligned to the human reference genome (hg18) using GSNAP (version 2011-03-28.v3) using the following parameters: Mismatches â¤[(read length+2)/12-2]; Mapping score â¥20; Soft-clipping on (-trim-mismatch-score=-3); Known exon-exon junctions (defined by RefSeq (downloaded March 7, 2011) and Gencode (version 3c)) and novel junctions (defined by GSNAP) were accepted. SNP sites in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) were included for SNP-tolerant alignments. Only reads that aligned to one genomic location (uniquely mapped reads) were used in further analyses.,Expression levels of RNA transcripts were analyzed using Cufflinks.,Genome_build: HG18 | RNA were extracted using Qiagen DNeasy blood and tissue kit and RNeasy Mini kit with DNase treatment, respectively (Qiagen). For transcriptome sequencing, total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). RNA-seq libraries were prepared following Illumina TruSeq RNA sample preparation protocol or directional mRNA-Seq sample preparation protocol, respectively. The samples were sequenced using HiSeq 2000 instrument and 100-200 million 100-nt reads per sample were generated. | GSM938909 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX150784,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01001240 | GSM938909 | GSE38233 | 0.020107 | cultured B-cells | Public on Sep 20 2013 | May 29 2012 | 9606 | Sample_RNA-IP_ADAR_GM12750 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX150784 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01001240 |
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1 | treatment: 4SU labeling and UV,purification: oligo(dT) beads | Robert-Rössle-StraÃe 10 | Berlin | Germany | Max-Delbrück-Center for Molecular Medicine | Markus,,Landthaler | We used tophat (version 1.32) (Trapnell et al., 2009) for spliced alignment of single-end reads to the human reference genome sequence (hg18). Prior knowledge on candidate splice junctions was obtained from EnsEMBL (release 54, www.ensembl.org) to increase the sensitivity of the mapping process.,We separated all reads by strand and generated two strand-specific mpileup file with samtools 0.1.18 (Li et al., 2009). These file were subsequently input into custom PERL scripts to produce a separate bedgraph file for each strand (Watson / Crick). Bedgraph files were loaded into our local UCSC hg18 genome browser instance for visualization purposes. Additionally, a single bedgraph file for strand-specific T to C conversions was produced in a similar manner. T to C conversion sites are only included in the final file if at least two conversion events were observed.,Genome_build: hg18,Supplementary_files_format_and_content: bed file reporting consensus profiles | Hafner et al. Methods. 2008 Jan;44(1):3-12 | GSM940575 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX150804,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01001252 | GSM940575 | GSE38157,GSE38355 | 0.077333 | HEK293 cell culture | Public on Jun 01 2012 | May 31 2012 | 9606 | profiling library 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX150804 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01001252 |
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1 | treatment: 4SU labeling and UV,purification: oligo(dT) beads | Robert-Rössle-StraÃe 10 | Berlin | Germany | Max-Delbrück-Center for Molecular Medicine | Markus,,Landthaler | We used tophat (version 1.32) (Trapnell et al., 2009) for spliced alignment of single-end reads to the human reference genome sequence (hg18). Prior knowledge on candidate splice junctions was obtained from EnsEMBL (release 54, www.ensembl.org) to increase the sensitivity of the mapping process.,We separated all reads by strand and generated two strand-specific mpileup file with samtools 0.1.18 (Li et al., 2009). These file were subsequently input into custom PERL scripts to produce a separate bedgraph file for each strand (Watson / Crick). Bedgraph files were loaded into our local UCSC hg18 genome browser instance for visualization purposes. Additionally, a single bedgraph file for strand-specific T to C conversions was produced in a similar manner. T to C conversion sites are only included in the final file if at least two conversion events were observed.,Genome_build: hg18,Supplementary_files_format_and_content: bed file reporting consensus profiles | Hafner et al. Methods. 2008 Jan;44(1):3-12 | GSM940576 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX150805,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01001253 | GSM940576 | GSE38157,GSE38355 | 0.112128 | HEK293 cell culture | Public on Jun 01 2012 | May 31 2012 | 9606 | profiling library 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX150805 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01001253 |
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1 | cell line: LNCaP,cell type: prostate cancer cells,passages: 32-34 | 7703 Floyd Curl Drive | San Antonio | USA | The University of Texas Health Science Center at San Antonio | Zhenqing,,Ye | Sequenced reads were mapped to hg19 by TopHat, and those uniquely mapped reads were used for further analysis.,Differentially expressed genes are retrived by edgeR software with p<0.001.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text file includes differentially expressed gene list from edgeR output | RNA mRNA was isolated with Rneasy Mini kit from Qiagen. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample KitPart # 15008136. Briefly, the polyA containing mRNA was purified, fragmented, and reverse transcribed. This was followed by second strand cDNA synthesis. The cDNA fragments went through end repair, adapter ligation, and PCR amplification processes. The final cDNA library was sequenced by Illumina HiSeq2000 in OSUCCC sequencing core. | GSM941196 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX150913,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01001648 | GSM941196 | GSE38393,GSE38452 | 0.003686 | LNCaP-SiControl | Public on Jun 01 2015 | Jun 01 2012 | 9606 | LNCaP-Sicontrol-rep1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX150913 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01001648 |
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1 | cell line: LNCaP,cell type: prostate cancer cells,passages: 32-34 | 7703 Floyd Curl Drive | San Antonio | USA | The University of Texas Health Science Center at San Antonio | Zhenqing,,Ye | Sequenced reads were mapped to hg19 by TopHat, and those uniquely mapped reads were used for further analysis.,Differentially expressed genes are retrived by edgeR software with p<0.001.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text file includes differentially expressed gene list from edgeR output | RNA mRNA was isolated with Rneasy Mini kit from Qiagen. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample KitPart # 15008136. Briefly, the polyA containing mRNA was purified, fragmented, and reverse transcribed. This was followed by second strand cDNA synthesis. The cDNA fragments went through end repair, adapter ligation, and PCR amplification processes. The final cDNA library was sequenced by Illumina HiSeq2000 in OSUCCC sequencing core. | GSM941198 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX150914,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01001649 | GSM941198 | GSE38393,GSE38452 | 0.003169 | LNCaP-SiControl | Public on Jun 01 2015 | Jun 01 2012 | 9606 | LNCaP-Sicontrol-rep2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX150914 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01001649 |
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1 | cell line: LNCaP,cell type: prostate cancer cells,treated with: siGATA2,passages: 32-34 | 7703 Floyd Curl Drive | San Antonio | USA | The University of Texas Health Science Center at San Antonio | Zhenqing,,Ye | Sequenced reads were mapped to hg19 by TopHat, and those uniquely mapped reads were used for further analysis.,Differentially expressed genes are retrived by edgeR software with p<0.001.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text file includes differentially expressed gene list from edgeR output | RNA mRNA was isolated with Rneasy Mini kit from Qiagen. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample KitPart # 15008136. Briefly, the polyA containing mRNA was purified, fragmented, and reverse transcribed. This was followed by second strand cDNA synthesis. The cDNA fragments went through end repair, adapter ligation, and PCR amplification processes. The final cDNA library was sequenced by Illumina HiSeq2000 in OSUCCC sequencing core. | GSM941211 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX150916,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01001651 | GSM941211 | GSE38393,GSE38452 | 0.002169 | LNCaP-SiGATA2 | Public on Jun 01 2015 | Jun 01 2012 | 9606 | LNCaP-SiGATA2-REP2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX150916 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01001651 |
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1 | cell line: MCF7,passage: 7,sirna: ON-TARGETplus Non-Targeting siRNA Control (Dharmacon, D-001810-01),treatment: control | 212 Biomedical Research Tower,460 West 12th Ave | Columbus | USA | Ohio State University | rui,,wang | Illumina Casava1.7 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat with default parameters,Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol as described in Trapnell et al, Nature Protocols 7, 562â578 (2012). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample | RNA was extracted using Trizol Reagent (Life Technologies) following the suggested protocol; 2ug of each RNA sample was used with the Illumina TruSeq RNA Sample Prep Kit (Cat # RS-122-2001) to make RNA libraries following the Illumina TruSeq RNA Sample preparation Low-Throughput protocol. Briefly, RNA was fragmented, then first-strand cDNA was prepared using the kit supplied 1st Strand Master Mix and user-supplied Superscript III (Life Technologies, cat # 18080-051) followed by second strand cDNA synthesis. The Illumina protocol and reagents were used to complete the library preparation, with 12 cycles of PCR amplification. | GSM942209 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX151408,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01036671 | GSM942209 | GSE38447 | 0.000303 | Human breast adenocarcinoma cell-line MCF7 | Public on Jun 05 2012 | Jun 04 2012 | 9606 | MCF7 siCONTROL | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX151408 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01036671 |
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1 | cell line: MCF7,passage: 7,sirna: ON-TARGETplus Non-Targeting siRNA against GATA3,treatment: GATA3 KD | 212 Biomedical Research Tower,460 West 12th Ave | Columbus | USA | Ohio State University | rui,,wang | Illumina Casava1.7 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat with default parameters,Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol as described in Trapnell et al, Nature Protocols 7, 562â578 (2012). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample | RNA was extracted using Trizol Reagent (Life Technologies) following the suggested protocol; 2ug of each RNA sample was used with the Illumina TruSeq RNA Sample Prep Kit (Cat # RS-122-2001) to make RNA libraries following the Illumina TruSeq RNA Sample preparation Low-Throughput protocol. Briefly, RNA was fragmented, then first-strand cDNA was prepared using the kit supplied 1st Strand Master Mix and user-supplied Superscript III (Life Technologies, cat # 18080-051) followed by second strand cDNA synthesis. The Illumina protocol and reagents were used to complete the library preparation, with 12 cycles of PCR amplification. | GSM942210 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX151409,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01036672 | GSM942210 | GSE38447 | 0 | Human breast adenocarcinoma cell-line MCF7 | Public on Jun 05 2012 | Jun 04 2012 | 9606 | MCF7 siGATA3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX151409 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01036672 |
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1 | cell line: PA-1,cell type: embryonal carcinoma (EC) cells,ploidy: diploid,aso: scrambled | 320 Yue-Yang Road | Shanghai | China | Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences | Ling-Ling,,Chen | Sequencing reads were obtained with Illumina HiSeq 2000.,All reads were uniquely aligned to the human hg19 genome by using Bowtie with up to 2 mismatches.,Genome_build: GRCh37,Supplementary_files_format_and_content: bigWig files were generated from the relevant bedGraph files according to the step-by-step protocol at http://genome.ucsc.edu/goldenPath/help/bigWig.html basically using the bedGraphToBigWig program. The bigWig format is for display of dense, continuous data that will be displayed in the Genome Browser as a graph. The resulting bigWig files are in an indexed binary format. | Total RNAs were prepared using Trizol Reagent. After treatment with DNase I, total RNAs were used for RNA-Seq libraries preparation with Illumina TruSeq RNA Sample Preparation Kits according to the manufacturer's instructions. | GSM945006 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056411,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272036 | GSM945006 | GSE38541 | 0.061369 | embryonal carcinoma PA-1 cells, scrambled ASO | Public on Apr 26 2013 | Jun 06 2012 | 9606 | PA-1 scramble | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272036 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056411 |
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1 | cell line: PA-1,cell type: embryonal carcinoma (EC) cells,ploidy: diploid,aso: specific to PWS-associated sno-lncRNAs | 320 Yue-Yang Road | Shanghai | China | Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences | Ling-Ling,,Chen | Sequencing reads were obtained with Illumina HiSeq 2000.,All reads were uniquely aligned to the human hg19 genome by using Bowtie with up to 2 mismatches.,Genome_build: GRCh37,Supplementary_files_format_and_content: bigWig files were generated from the relevant bedGraph files according to the step-by-step protocol at http://genome.ucsc.edu/goldenPath/help/bigWig.html basically using the bedGraphToBigWig program. The bigWig format is for display of dense, continuous data that will be displayed in the Genome Browser as a graph. The resulting bigWig files are in an indexed binary format. | Total RNAs were prepared using Trizol Reagent. After treatment with DNase I, total RNAs were used for RNA-Seq libraries preparation with Illumina TruSeq RNA Sample Preparation Kits according to the manufacturer's instructions. | GSM945007 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02056412,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX272037 | GSM945007 | GSE38541 | 0.062432 | embryonal carcinoma PA-1 cells, specific ASO | Public on Apr 26 2013 | Jun 06 2012 | 9606 | PA-1 knockdown | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX272037 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02056412 |
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1 | cell line: HeLa,treatment: control,lentiviral construct: SHC002 | 10 Shattuck St | Boston | USA | Harvard Medical School | Peter,J,Park | Paired-end RNA-seq tags were mapped using Tophat software package. Transcript annotations were taken from UCSC RefSeq track.,Tag pairs that had less than 50-bp separation between the mates were filtered out.,RNA-seq coverage was estimated as a number of paired-end fragments spanning over each interrogated genomic position. Coverage was normalized by total number of fragments.,Genome_build: hg18 | For RNA-seq experiments, toRNA from nuclei were depleted of rRNA (Epizyme kit) and libraries were cloned using the truSeq RNAseq kit from Illumina. | GSM949330 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX154876,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01055122 | GSM949330 | GSE38770,GSE38771 | 0.010256 | control | Public on Jul 16 2012 | Jun 18 2012 | 9606 | neg C - KD 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX154876 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01055122 |
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1 | cell line: HeLa,treatment: control,lentiviral construct: SHC002 | 10 Shattuck St | Boston | USA | Harvard Medical School | Peter,J,Park | Paired-end RNA-seq tags were mapped using Tophat software package. Transcript annotations were taken from UCSC RefSeq track.,Tag pairs that had less than 50-bp separation between the mates were filtered out.,RNA-seq coverage was estimated as a number of paired-end fragments spanning over each interrogated genomic position. Coverage was normalized by total number of fragments.,Genome_build: hg18 | For RNA-seq experiments, toRNA from nuclei were depleted of rRNA (Epizyme kit) and libraries were cloned using the truSeq RNAseq kit from Illumina. | GSM949331 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX154877,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01055123 | GSM949331 | GSE38770,GSE38771 | 0.084571 | control | Public on Jul 16 2012 | Jun 18 2012 | 9606 | neg C - KD 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX154877 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01055123 |
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1 | cell type: Hepatocellular Carcinoma,cell line: HCCLM3,organ-tropism: low metastasis ability | Fenglin Rd 180, Xuhui district | Shanghai | China | Fudan University | Wei zhong,,Wu | Illumina Casava1.7 software used for basecalling.,Remove reads with adaptors, remove reads in which unknown bases are more than 10%, Remove low quality reads (the percentage of the low quality bases of quality value ⤠5 is more than 50% in a read) .,Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.,Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample | Medium was removed, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. | GSM952575 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX156169,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01057824 | GSM952575 | GSE38945,GSE39053 | 0.02683 | Human Hepatocellular Carcinoma cell line | Public on Jun 30 2014 | Jun 26 2012 | 9606 | Hepatocellular carcinoma (HCC), parent | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX156169 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01057824 |
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1 | cell type: Hepatocellular Carcinoma,cell line: HCCLM3,organ-tropism: higher metastasis ability specific to lung | Fenglin Rd 180, Xuhui district | Shanghai | China | Fudan University | Wei zhong,,Wu | Illumina Casava1.7 software used for basecalling.,Remove reads with adaptors, remove reads in which unknown bases are more than 10%, Remove low quality reads (the percentage of the low quality bases of quality value ⤠5 is more than 50% in a read) .,Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.,Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample | Medium was removed, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. | GSM952576 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX156170,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01057825 | GSM952576 | GSE38945,GSE39053 | 0.009641 | Human Hepatocellular Carcinoma cell line | Public on Jun 30 2014 | Jun 26 2012 | 9606 | Hepatocellular carcinoma (HCC), subclone1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX156170 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01057825 |
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1 | cell type: Hepatocellular Carcinoma,cell line: HCCLM3,organ-tropism: dual metastasis ability to lung and celiac lymph node | Fenglin Rd 180, Xuhui district | Shanghai | China | Fudan University | Wei zhong,,Wu | Illumina Casava1.7 software used for basecalling.,Remove reads with adaptors, remove reads in which unknown bases are more than 10%, Remove low quality reads (the percentage of the low quality bases of quality value ⤠5 is more than 50% in a read) .,Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.,Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample | Medium was removed, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. | GSM952577 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX156171,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01057826 | GSM952577 | GSE38945,GSE39053 | 0 | Human Hepatocellular Carcinoma cell line | Public on Jun 30 2014 | Jun 26 2012 | 9606 | Hepatocellular carcinoma (HCC), subclone2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX156171 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01057826 |
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1 | cell type: Hepatocellular Carcinomar,cell line: HCCLM3,organ-tropism: low metastasis | Fenglin Rd 180, Xuhui district | Shanghai | China | Fudan University | Wei zhong,,Wu | Basecalls performed using CASAVA version 1.4,The 50nt sequence tags from HiSeq sequencing will go through the data cleaning first, which includes getting rid of the low quality tags and several kinds of contaminants from the 50nt tags,Align small RNA tags to the human miRNA precursor/mature miRNA of corresponding species in miRBase17 using BLAST 2.2.25 ,with the following configurations:blastall -p blastn -F F -e 0.01,Normalize the expression of miRNA in two samples (control and treatment) to get the expression of transcript per million (TPM). Normalization formula: Normalized expression = Actual miRNA count/Total count of clean reads*1000000,Calculate fold-change and P-value from the normalized expression,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample | Medium was removed, and RNA was harvested using Trizol reagent. Illumina TruSeq Small RNA Sample Prep Kit (Cat#RS-200-0012) was used with 1 ug of total RNA for the construction of sequencing libraries. | GSM953599 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX157299,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01085206 | GSM953599 | GSE39003,GSE39053 | 0.261906 | Human Hepatocellular Carcinomar cell line | Public on Jun 30 2014 | Jun 28 2012 | 9606 | Hepatocellular carcinoma (HCC),parent | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX157299 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01085206 |
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1 | cell type: Hepatocellular Carcinomar,cell line: HCCLM3,organ-tropism: higher metastasis ability specific to lung | Fenglin Rd 180, Xuhui district | Shanghai | China | Fudan University | Wei zhong,,Wu | Basecalls performed using CASAVA version 1.4,The 50nt sequence tags from HiSeq sequencing will go through the data cleaning first, which includes getting rid of the low quality tags and several kinds of contaminants from the 50nt tags,Align small RNA tags to the human miRNA precursor/mature miRNA of corresponding species in miRBase17 using BLAST 2.2.25 ,with the following configurations:blastall -p blastn -F F -e 0.01,Normalize the expression of miRNA in two samples (control and treatment) to get the expression of transcript per million (TPM). Normalization formula: Normalized expression = Actual miRNA count/Total count of clean reads*1000000,Calculate fold-change and P-value from the normalized expression,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample | Medium was removed, and RNA was harvested using Trizol reagent. Illumina TruSeq Small RNA Sample Prep Kit (Cat#RS-200-0012) was used with 1 ug of total RNA for the construction of sequencing libraries. | GSM953600 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX157300,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01085207 | GSM953600 | GSE39003,GSE39053 | 0.339039 | Human Hepatocellular Carcinomar cell line | Public on Jun 30 2014 | Jun 28 2012 | 9606 | Hepatocellular carcinoma (HCC),subclone1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX157300 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01085207 |
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1 | cell type: Hepatocellular Carcinomar,cell line: HCCLM3,organ-tropism: dual metastasis ability to lung and celiac lymph node | Fenglin Rd 180, Xuhui district | Shanghai | China | Fudan University | Wei zhong,,Wu | Basecalls performed using CASAVA version 1.4,The 50nt sequence tags from HiSeq sequencing will go through the data cleaning first, which includes getting rid of the low quality tags and several kinds of contaminants from the 50nt tags,Align small RNA tags to the human miRNA precursor/mature miRNA of corresponding species in miRBase17 using BLAST 2.2.25 ,with the following configurations:blastall -p blastn -F F -e 0.01,Normalize the expression of miRNA in two samples (control and treatment) to get the expression of transcript per million (TPM). Normalization formula: Normalized expression = Actual miRNA count/Total count of clean reads*1000000,Calculate fold-change and P-value from the normalized expression,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample | Medium was removed, and RNA was harvested using Trizol reagent. Illumina TruSeq Small RNA Sample Prep Kit (Cat#RS-200-0012) was used with 1 ug of total RNA for the construction of sequencing libraries. | GSM953601 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX157301,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01085208 | GSM953601 | GSE39003,GSE39053 | 0.360515 | Human Hepatocellular Carcinomar cell line | Public on Jun 30 2014 | Jun 28 2012 | 9606 | Hepatocellular carcinoma (HCC),subclone2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX157301 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01085208 |
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1 | cell line: primary thyroid cell line,treatment protocol: no treatment | 1425 Madison Avenue | New York | USA | Mount Sinai School of Medicine | Weijia,,Zhang | Illumina Casava1.7 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human hg18 or mouse mm9 exon and exon junction sequences and contamination datanases using bwa algorithm,After filtering reads mapped to contamination databases, the reads that have one or no mismatch and are uniquely aligned to each exon and splicing-junction sites were extracted and then counted. The read count for each RefSeq transcript was calculated by combining the counts for exons and splicing junctions of corresponding transcript.,Supplementary_files_format_and_content: tab-delimited txt file including count values for RefSeq transcripts,Genome_build: hg18 or mm9 | According to Illumina mRNA Sequencing Sample Preparation Guide. Briefly, 2ug total RNA hybridized to poly dT magnetic beads to capture polyA mRNA molecules. Chemical fragmentation, first strand synthesis with RTase, randomers second strand synthesis. Then end repair, 3' A overhang, multiplex adapter ligation (from Illumina indexing kit), size selection by electrophoresis and cut at 200bp. 18 cycles of PCR with a primer bearing an indexing barcode. | GSM955424 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX157311,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01085217 | GSM955424 | GSE39081 | 0 | primary thyroid cell line | Public on Oct 03 2012 | Jul 03 2012 | 9606 | Human_T0_RNA_seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX157311 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01085217 |
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1 | cell line: primary thyroid cell line,treatment protocol: G28.5 treatment (1 ug, 24 hour) | 1425 Madison Avenue | New York | USA | Mount Sinai School of Medicine | Weijia,,Zhang | Illumina Casava1.7 software used for basecalling.,Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human hg18 or mouse mm9 exon and exon junction sequences and contamination datanases using bwa algorithm,After filtering reads mapped to contamination databases, the reads that have one or no mismatch and are uniquely aligned to each exon and splicing-junction sites were extracted and then counted. The read count for each RefSeq transcript was calculated by combining the counts for exons and splicing junctions of corresponding transcript.,Supplementary_files_format_and_content: tab-delimited txt file including count values for RefSeq transcripts,Genome_build: hg18 or mm9 | According to Illumina mRNA Sequencing Sample Preparation Guide. Briefly, 2ug total RNA hybridized to poly dT magnetic beads to capture polyA mRNA molecules. Chemical fragmentation, first strand synthesis with RTase, randomers second strand synthesis. Then end repair, 3' A overhang, multiplex adapter ligation (from Illumina indexing kit), size selection by electrophoresis and cut at 200bp. 18 cycles of PCR with a primer bearing an indexing barcode. | GSM955425 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX157312,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01085218 | GSM955425 | GSE39081 | 0 | primary thyroid cell line | Public on Oct 03 2012 | Jul 03 2012 | 9606 | Human_T24_RNA-seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX157312 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01085218 |
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1 | cell line: HEK293T,rna associated: endogenous (D8) DGCR8 | Robert-Rössle Str. 10 | Copenhagen | Germany | MDC-Berlin | Mireya,,Plass | Read were processed with MIRO (http://seq.crg.es/main/bin/view/Home/MiroPipeline) to remove reads containing Ns and with a sequence complexity below 0.5. We also removed PCR duplicates.,HITS-CLIP reads were aligned using bowtie v0.11.3 with parameters --best -v2 -a to an index file containg hg18 genome, Ensembl54 transcripts and lincRNA from Ensembl59 mapped to hg18. Initially, all reads are mapped to the index file. After the mapping, all those reads that could not be mapped are trimmed 1 base at the 3â end of the read and mapped again to the index file. This procedure is repeated until the reads have a minimum length of 21nt. For further analyses, only uniquely mapped reads to the genome were used.,Reads mapped to the same strand were clustered according to their position in the reference sequence to generate clusters. To identify significant clusters we applied a modified false discovery rate (mFDR) using Pyicos. Only significant clusters (pval < 0.01) were kept.,Clusters overlapping Genomic and Centromeric Gaps (hg18 Gap Track from UCSC) and Satellites (hg18 repeat masked track from UCSC) were discarded.,Genome_build: hg18,Supplementary_files_format_and_content: bedGraph files. Each of the files contains all the significant clusters identified for a sample in a strand (+ or -). The score given represents the amount of reads in a position. | RNAs (20-100nt long) associated to DGCR8 were phenol extracted and ethanol precipitated. Libraries were prepared from these RNAs using the Illumina Small RNA kit (v1.5) | GSM955512 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX157657,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01085589 | GSM955512 | GSE39086 | 0.214387 | HEK293T | Public on Jul 15 2012 | Jul 03 2012 | 9606 | D8.2 (endogenous DGCR8 IP) | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX157657 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01085589 |
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1 | cell line: HEK293T,rna associated: overexpressed (T7) DGCR8 | Robert-Rössle Str. 10 | Copenhagen | Germany | MDC-Berlin | Mireya,,Plass | Read were processed with MIRO (http://seq.crg.es/main/bin/view/Home/MiroPipeline) to remove reads containing Ns and with a sequence complexity below 0.5. We also removed PCR duplicates.,HITS-CLIP reads were aligned using bowtie v0.11.3 with parameters --best -v2 -a to an index file containg hg18 genome, Ensembl54 transcripts and lincRNA from Ensembl59 mapped to hg18. Initially, all reads are mapped to the index file. After the mapping, all those reads that could not be mapped are trimmed 1 base at the 3â end of the read and mapped again to the index file. This procedure is repeated until the reads have a minimum length of 21nt. For further analyses, only uniquely mapped reads to the genome were used.,Reads mapped to the same strand were clustered according to their position in the reference sequence to generate clusters. To identify significant clusters we applied a modified false discovery rate (mFDR) using Pyicos. Only significant clusters (pval < 0.01) were kept.,Clusters overlapping Genomic and Centromeric Gaps (hg18 Gap Track from UCSC) and Satellites (hg18 repeat masked track from UCSC) were discarded.,Genome_build: hg18,Supplementary_files_format_and_content: bedGraph files. Each of the files contains all the significant clusters identified for a sample in a strand (+ or -). The score given represents the amount of reads in a position. | RNAs (20-100nt long) associated to DGCR8 were phenol extracted and ethanol precipitated. Libraries were prepared from these RNAs using the Illumina Small RNA kit (v1.5) | GSM955513 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX157658,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01085590 | GSM955513 | GSE39086 | 0.060576 | HEK293T | Public on Jul 15 2012 | Jul 03 2012 | 9606 | T7.2 (overexpressed DGCR8 IP) | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX157658 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01085590 |
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1 | cell line: PC9,cell type: human lung Adenocarcinoma,transfected with: lentivirus harboring shRNA of control (Arab1) | 310 Cedar St | New Haven | USA | Yale Shcool of Medicine | Don,,Nguyen | Illumina Casava software used for basecalling.,Sequenced reads were mapped to human transcriptome using tophat 1.4.1 with parameters -p4 --solexa-quals --min-anchor 12 --library-type fr-unstranded -G All_Isoforms_For_ExpressionTable.gtf,Reads per gene was calculated using HtSeq-count in union mode,Reads per gene was nomalized to the library size and differential expressed genes was detected using EdgeR R package.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include normalized count of reads for each gene and each sample. | Illumina TrueSeq RNA Prep, Total RNA from triplicate samples were extracted using RNeasy Mini kit (Qiagen). The quality of RNA samples was first analyzed on Agilent Bioanalyzer. Single-end, barcoded sequence libraries were constructed with TruSeq RNA Sample Prep Kit (Illumina) and sequenced on a HiSeq 2000 instrument according to the manufacturerâs instructions with single-end 50 base pair reads. | GSM956428 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX157744,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01085881 | GSM956428 | GSE39121 | 0 | shCtrl | Public on Jun 10 2013 | Jul 05 2012 | 9606 | shCtrl.1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX157744 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01085881 |
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1 | cell line: PC9,cell type: human lung Adenocarcinoma,transfected with: lentivirus harboring shRNA of control (Arab1) | 310 Cedar St | New Haven | USA | Yale Shcool of Medicine | Don,,Nguyen | Illumina Casava software used for basecalling.,Sequenced reads were mapped to human transcriptome using tophat 1.4.1 with parameters -p4 --solexa-quals --min-anchor 12 --library-type fr-unstranded -G All_Isoforms_For_ExpressionTable.gtf,Reads per gene was calculated using HtSeq-count in union mode,Reads per gene was nomalized to the library size and differential expressed genes was detected using EdgeR R package.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include normalized count of reads for each gene and each sample. | Illumina TrueSeq RNA Prep, Total RNA from triplicate samples were extracted using RNeasy Mini kit (Qiagen). The quality of RNA samples was first analyzed on Agilent Bioanalyzer. Single-end, barcoded sequence libraries were constructed with TruSeq RNA Sample Prep Kit (Illumina) and sequenced on a HiSeq 2000 instrument according to the manufacturerâs instructions with single-end 50 base pair reads. | GSM956429 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX157745,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01085882 | GSM956429 | GSE39121 | 0 | shCtrl | Public on Jun 10 2013 | Jul 05 2012 | 9606 | shCtrl.2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX157745 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01085882 |
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1 | cell line: PC9,cell type: human lung Adenocarcinoma,transfected with: lentivirus harboring shRNA of control (Arab1) | 310 Cedar St | New Haven | USA | Yale Shcool of Medicine | Don,,Nguyen | Illumina Casava software used for basecalling.,Sequenced reads were mapped to human transcriptome using tophat 1.4.1 with parameters -p4 --solexa-quals --min-anchor 12 --library-type fr-unstranded -G All_Isoforms_For_ExpressionTable.gtf,Reads per gene was calculated using HtSeq-count in union mode,Reads per gene was nomalized to the library size and differential expressed genes was detected using EdgeR R package.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include normalized count of reads for each gene and each sample. | Illumina TrueSeq RNA Prep, Total RNA from triplicate samples were extracted using RNeasy Mini kit (Qiagen). The quality of RNA samples was first analyzed on Agilent Bioanalyzer. Single-end, barcoded sequence libraries were constructed with TruSeq RNA Sample Prep Kit (Illumina) and sequenced on a HiSeq 2000 instrument according to the manufacturerâs instructions with single-end 50 base pair reads. | GSM956430 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX157746,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01085883 | GSM956430 | GSE39121 | 0.00117 | shCtrl | Public on Jun 10 2013 | Jul 05 2012 | 9606 | shCtrl.3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX157746 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01085883 |
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1 | cell line: PC9,cell type: human lung Adenocarcinoma,transfected with: lentivirus harboring shRNA of both GATA6 and HOPX | 310 Cedar St | New Haven | USA | Yale Shcool of Medicine | Don,,Nguyen | Illumina Casava software used for basecalling.,Sequenced reads were mapped to human transcriptome using tophat 1.4.1 with parameters -p4 --solexa-quals --min-anchor 12 --library-type fr-unstranded -G All_Isoforms_For_ExpressionTable.gtf,Reads per gene was calculated using HtSeq-count in union mode,Reads per gene was nomalized to the library size and differential expressed genes was detected using EdgeR R package.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include normalized count of reads for each gene and each sample. | Illumina TrueSeq RNA Prep, Total RNA from triplicate samples were extracted using RNeasy Mini kit (Qiagen). The quality of RNA samples was first analyzed on Agilent Bioanalyzer. Single-end, barcoded sequence libraries were constructed with TruSeq RNA Sample Prep Kit (Illumina) and sequenced on a HiSeq 2000 instrument according to the manufacturerâs instructions with single-end 50 base pair reads. | GSM956431 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX157747,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01085884 | GSM956431 | GSE39121 | 0 | shGata6Hopx | Public on Jun 10 2013 | Jul 05 2012 | 9606 | shGata6Hopx.1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX157747 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01085884 |
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1 | cell line: PC9,cell type: human lung Adenocarcinoma,transfected with: lentivirus harboring shRNA of both GATA6 and HOPX | 310 Cedar St | New Haven | USA | Yale Shcool of Medicine | Don,,Nguyen | Illumina Casava software used for basecalling.,Sequenced reads were mapped to human transcriptome using tophat 1.4.1 with parameters -p4 --solexa-quals --min-anchor 12 --library-type fr-unstranded -G All_Isoforms_For_ExpressionTable.gtf,Reads per gene was calculated using HtSeq-count in union mode,Reads per gene was nomalized to the library size and differential expressed genes was detected using EdgeR R package.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include normalized count of reads for each gene and each sample. | Illumina TrueSeq RNA Prep, Total RNA from triplicate samples were extracted using RNeasy Mini kit (Qiagen). The quality of RNA samples was first analyzed on Agilent Bioanalyzer. Single-end, barcoded sequence libraries were constructed with TruSeq RNA Sample Prep Kit (Illumina) and sequenced on a HiSeq 2000 instrument according to the manufacturerâs instructions with single-end 50 base pair reads. | GSM956432 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX157748,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01085885 | GSM956432 | GSE39121 | 0.008925 | shGata6Hopx | Public on Jun 10 2013 | Jul 05 2012 | 9606 | shGata6Hopx.2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX157748 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01085885 |
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1 | cell line: PC9,cell type: human lung Adenocarcinoma,transfected with: lentivirus harboring shRNA of both GATA6 and HOPX | 310 Cedar St | New Haven | USA | Yale Shcool of Medicine | Don,,Nguyen | Illumina Casava software used for basecalling.,Sequenced reads were mapped to human transcriptome using tophat 1.4.1 with parameters -p4 --solexa-quals --min-anchor 12 --library-type fr-unstranded -G All_Isoforms_For_ExpressionTable.gtf,Reads per gene was calculated using HtSeq-count in union mode,Reads per gene was nomalized to the library size and differential expressed genes was detected using EdgeR R package.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include normalized count of reads for each gene and each sample. | Illumina TrueSeq RNA Prep, Total RNA from triplicate samples were extracted using RNeasy Mini kit (Qiagen). The quality of RNA samples was first analyzed on Agilent Bioanalyzer. Single-end, barcoded sequence libraries were constructed with TruSeq RNA Sample Prep Kit (Illumina) and sequenced on a HiSeq 2000 instrument according to the manufacturerâs instructions with single-end 50 base pair reads. | GSM956433 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX157749,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01085886 | GSM956433 | GSE39121 | 0.002188 | shGata6Hopx | Public on Jun 10 2013 | Jul 05 2012 | 9606 | shGata6Hopx.3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX157749 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01085886 |
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1 | sample: GM12004,family: 1420,relation: paternal grandmother,protocol: directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957342 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158796,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086558 | GSM957342 | GSE39167 | 0.645171 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | DiscoverySet_GM12004 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158796 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086558 |
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1 | sample: GM12750,family: 1444,relation: maternal grandfather,protocol: directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957343 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158797,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086559 | GSM957343 | GSE39167 | 0.385278 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | DiscoverySet_GM12750 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158797 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086559 |
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1 | sample: GM07000,family: 1340,relation: paternal grandmother,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957344 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158798,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086560 | GSM957344 | GSE39167 | 0.002714 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | UnrelatedSet1_GM07000 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158798 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086560 |
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1 | sample: GM11992,family: 1362,relation: paternal grandfather,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957346 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158800,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086562 | GSM957346 | GSE39167 | 0.000902 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | UnrelatedSet1_GM11992 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158800 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086562 |
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1 | sample: GM11993,family: 1362,relation: paternal grandmother,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957347 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158801,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086563 | GSM957347 | GSE39167 | 0.003275 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | UnrelatedSet1_GM11993 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158801 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086563 |
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1 | sample: GM11994,family: 1362,relation: maternal grandfather,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957348 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158802,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086564 | GSM957348 | GSE39167 | 0.002758 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | UnrelatedSet1_GM11994 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158802 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086564 |
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1 | sample: GM11995,family: 1362,relation: maternal grandmother,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957349 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158803,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086565 | GSM957349 | GSE39167 | 0.003218 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | UnrelatedSet1_GM11995 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158803 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086565 |
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1 | sample: GM12717,family: 1358,relation: paternal grandmother,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957352 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158806,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086568 | GSM957352 | GSE39167 | 0.000902 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | UnrelatedSet1_GM12717 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158806 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086568 |
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1 | sample: GM12750,family: 1444,relation: maternal grandfather,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957353 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158807,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086569 | GSM957353 | GSE39167 | 0.01086 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | UnrelatedSet1_GM12750 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158807 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086569 |
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1 | sample: GM14382,family: 1700,relation: twin sister,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957398 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158852,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086614 | GSM957398 | GSE39167 | 0.001257 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | TwinSet_GM14382 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158852 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086614 |
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1 | sample: GM14408,family: 1705,relation: proband,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957399 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158853,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086615 | GSM957399 | GSE39167 | 0 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | TwinSet_GM14408 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158853 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086615 |
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1 | sample: GM14409,family: 1705,relation: twin brother,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957400 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158854,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086616 | GSM957400 | GSE39167 | 0.02171 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | TwinSet_GM14409 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158854 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086616 |
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1 | sample: GM14432,family: 1710,relation: proband,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957401 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158855,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086617 | GSM957401 | GSE39167 | 0.001658 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | TwinSet_GM14432 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158855 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086617 |
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1 | sample: GM14447,family: 1715,relation: proband,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957403 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158857,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086619 | GSM957403 | GSE39167 | 0.018793 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | TwinSet_GM14447 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158857 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086619 |
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1 | sample: GM14468,family: 1721,relation: twin sister,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957408 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158862,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086624 | GSM957408 | GSE39167 | 0.020614 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | TwinSet_GM14468 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158862 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086624 |
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1 | sample: GM11982,family: 1362,relation: daughter,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957419 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158873,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086635 | GSM957419 | GSE39167 | 0.019278 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | Family1362Set_GM11982 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158873 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086635 |
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1 | sample: GM11983,family: 1362,relation: daughter,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957420 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158874,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086636 | GSM957420 | GSE39167 | 0.018774 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | Family1362Set_GM11983 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158874 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086636 |
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1 | sample: GM11984,family: 1362,relation: son,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957421 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158875,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086637 | GSM957421 | GSE39167 | 0.020735 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | Family1362Set_GM11984 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158875 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086637 |
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1 | sample: GM11985,family: 1362,relation: daughter,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957422 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158876,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086638 | GSM957422 | GSE39167 | 0.016267 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | Family1362Set_GM11985 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158876 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086638 |
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1 | sample: GM11986,family: 1362,relation: daughter,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957423 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158877,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086639 | GSM957423 | GSE39167 | 0.020218 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | Family1362Set_GM11986 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158877 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086639 |
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1 | sample: GM11989,family: 1362,relation: daughter,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957426 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158880,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086642 | GSM957426 | GSE39167 | 0.00683 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | Family1362Set_GM11989 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158880 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086642 |
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1 | sample: GM11990,family: 1362,relation: son,protocol: non-directional | 210 washtenaw ave | Ann Arbor | USA | HHMI/University of Michigan | Isabel,Xiaorong,Wang | Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.,Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 â 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.,Variants were called with Samtools (v0.1.16),Genome_build: hg18 | RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single âAâ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology. | GSM957427 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX158881,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01086643 | GSM957427 | GSE39167 | 0.00176 | cultured B-cells | Public on Jul 01 2017 | Jul 06 2012 | 9606 | Family1362Set_GM11990 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX158881 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01086643 |