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1 | cell line: MCF7,cell type: breast cancer cells,transfection: siCTCF | 450 Brookline Ave | Boston | USA | Dana-Farber Cancer Institute | Kornelia,,Polyak | Basecalls performed using CASAVA version 1.7 or 1.8.,RNA-Seq raw data was mapped by Tophat to hg19.,Read counting and differential gene expression analysis were done using GFold using significance cutoff = 0.05.,Genome_build: hg19,Supplementary_files_format_and_content: Text file (.cnt) of mapped read counts was generated using Gfold. | Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen) following the manufacturerâs protocol. Then polyA RNA were purified using the MACS mRNA isolation kit (Miltenyi Biotec).,PolyA RNA was fragmented by RNA fragmentation reagent (Ambion), and subjected to first strand synthesis by using SupeScript II (Invitrogen) and random hexamer oligos. The second strand was synthesized, and then subjected to end repair, A-tailing, ligation of Illumia paired end adaptor. Following PCR amplification for 18 cycles, the final library underwent gel purification. | GSM1113300 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX259555,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01997739 | GSM1113300 | GSE45732,GSE46073 | 0.01956 | breast cancer cells | Public on Jun 17 2014 | Apr 03 2013 | 9606 | MCF7_RNAseq_siCTCF | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX259555 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01997739 |
|
1 | cell line: T-47D,cell type: breast cancer cells,transfection: control siRNA | 450 Brookline Ave | Boston | USA | Dana-Farber Cancer Institute | Kornelia,,Polyak | Basecalls performed using CASAVA version 1.7 or 1.8.,RNA-Seq raw data was mapped by Tophat to hg19.,Read counting and differential gene expression analysis were done using GFold using significance cutoff = 0.05.,Genome_build: hg19,Supplementary_files_format_and_content: Text file (.cnt) of mapped read counts was generated using Gfold. | Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen) following the manufacturerâs protocol. Then polyA RNA were purified using the MACS mRNA isolation kit (Miltenyi Biotec).,PolyA RNA was fragmented by RNA fragmentation reagent (Ambion), and subjected to first strand synthesis by using SupeScript II (Invitrogen) and random hexamer oligos. The second strand was synthesized, and then subjected to end repair, A-tailing, ligation of Illumia paired end adaptor. Following PCR amplification for 18 cycles, the final library underwent gel purification. | GSM1113301 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX259556,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01997740 | GSM1113301 | GSE45732,GSE46073 | 0.025298 | breast cancer cells | Public on Jun 17 2014 | Apr 03 2013 | 9606 | T47D_RNAseq_Control | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX259556 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01997740 |
|
1 | cell line: T-47D,cell type: breast cancer cells,transfection: siJARID1B | 450 Brookline Ave | Boston | USA | Dana-Farber Cancer Institute | Kornelia,,Polyak | Basecalls performed using CASAVA version 1.7 or 1.8.,RNA-Seq raw data was mapped by Tophat to hg19.,Read counting and differential gene expression analysis were done using GFold using significance cutoff = 0.05.,Genome_build: hg19,Supplementary_files_format_and_content: Text file (.cnt) of mapped read counts was generated using Gfold. | Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen) following the manufacturerâs protocol. Then polyA RNA were purified using the MACS mRNA isolation kit (Miltenyi Biotec).,PolyA RNA was fragmented by RNA fragmentation reagent (Ambion), and subjected to first strand synthesis by using SupeScript II (Invitrogen) and random hexamer oligos. The second strand was synthesized, and then subjected to end repair, A-tailing, ligation of Illumia paired end adaptor. Following PCR amplification for 18 cycles, the final library underwent gel purification. | GSM1113302 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX259557,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01997741 | GSM1113302 | GSE45732,GSE46073 | 0.025538 | breast cancer cells | Public on Jun 17 2014 | Apr 03 2013 | 9606 | T47D_RNAseq_siJARID1B | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX259557 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01997741 |
|
1 | cell line: SUM185PE,cell type: breast cancer cells,transfection: control siRNA | 450 Brookline Ave | Boston | USA | Dana-Farber Cancer Institute | Kornelia,,Polyak | Basecalls performed using CASAVA version 1.7 or 1.8.,RNA-Seq raw data was mapped by Tophat to hg19.,Read counting and differential gene expression analysis were done using GFold using significance cutoff = 0.05.,Genome_build: hg19,Supplementary_files_format_and_content: Text file (.cnt) of mapped read counts was generated using Gfold. | Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen) following the manufacturerâs protocol. Then polyA RNA were purified using the MACS mRNA isolation kit (Miltenyi Biotec).,PolyA RNA was fragmented by RNA fragmentation reagent (Ambion), and subjected to first strand synthesis by using SupeScript II (Invitrogen) and random hexamer oligos. The second strand was synthesized, and then subjected to end repair, A-tailing, ligation of Illumia paired end adaptor. Following PCR amplification for 18 cycles, the final library underwent gel purification. | GSM1113303 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX259558,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01997742 | GSM1113303 | GSE45732,GSE46073 | 0.002668 | breast cancer cells | Public on Jun 17 2014 | Apr 03 2013 | 9606 | SUM185_RNAseq_Control | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX259558 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01997742 |
|
1 | cell line: SUM185PE,cell type: breast cancer cells,transfection: siCTCF | 450 Brookline Ave | Boston | USA | Dana-Farber Cancer Institute | Kornelia,,Polyak | Basecalls performed using CASAVA version 1.7 or 1.8.,RNA-Seq raw data was mapped by Tophat to hg19.,Read counting and differential gene expression analysis were done using GFold using significance cutoff = 0.05.,Genome_build: hg19,Supplementary_files_format_and_content: Text file (.cnt) of mapped read counts was generated using Gfold. | Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen) following the manufacturerâs protocol. Then polyA RNA were purified using the MACS mRNA isolation kit (Miltenyi Biotec).,PolyA RNA was fragmented by RNA fragmentation reagent (Ambion), and subjected to first strand synthesis by using SupeScript II (Invitrogen) and random hexamer oligos. The second strand was synthesized, and then subjected to end repair, A-tailing, ligation of Illumia paired end adaptor. Following PCR amplification for 18 cycles, the final library underwent gel purification. | GSM1113305 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX259560,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01997744 | GSM1113305 | GSE45732,GSE46073 | 0.023818 | breast cancer cells | Public on Jun 17 2014 | Apr 03 2013 | 9606 | SUM185_RNAseq_siCTCF | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX259560 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01997744 |
|
1 | cell line: SUM159PT,cell type: breast cancer cells,transfection: control siRNA | 450 Brookline Ave | Boston | USA | Dana-Farber Cancer Institute | Kornelia,,Polyak | Basecalls performed using CASAVA version 1.7 or 1.8.,RNA-Seq raw data was mapped by Tophat to hg19.,Read counting and differential gene expression analysis were done using GFold using significance cutoff = 0.05.,Genome_build: hg19,Supplementary_files_format_and_content: Text file (.cnt) of mapped read counts was generated using Gfold. | Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen) following the manufacturerâs protocol. Then polyA RNA were purified using the MACS mRNA isolation kit (Miltenyi Biotec).,PolyA RNA was fragmented by RNA fragmentation reagent (Ambion), and subjected to first strand synthesis by using SupeScript II (Invitrogen) and random hexamer oligos. The second strand was synthesized, and then subjected to end repair, A-tailing, ligation of Illumia paired end adaptor. Following PCR amplification for 18 cycles, the final library underwent gel purification. | GSM1113306 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX259561,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01997745 | GSM1113306 | GSE45732,GSE46073 | 0 | breast cancer cells | Public on Jun 17 2014 | Apr 03 2013 | 9606 | SUM159_RNAseq_Control | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX259561 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01997745 |
|
1 | cell line: SUM159PT,cell type: breast cancer cells,transfection: siJARID1B | 450 Brookline Ave | Boston | USA | Dana-Farber Cancer Institute | Kornelia,,Polyak | Basecalls performed using CASAVA version 1.7 or 1.8.,RNA-Seq raw data was mapped by Tophat to hg19.,Read counting and differential gene expression analysis were done using GFold using significance cutoff = 0.05.,Genome_build: hg19,Supplementary_files_format_and_content: Text file (.cnt) of mapped read counts was generated using Gfold. | Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen) following the manufacturerâs protocol. Then polyA RNA were purified using the MACS mRNA isolation kit (Miltenyi Biotec).,PolyA RNA was fragmented by RNA fragmentation reagent (Ambion), and subjected to first strand synthesis by using SupeScript II (Invitrogen) and random hexamer oligos. The second strand was synthesized, and then subjected to end repair, A-tailing, ligation of Illumia paired end adaptor. Following PCR amplification for 18 cycles, the final library underwent gel purification. | GSM1113307 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX259562,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01997746 | GSM1113307 | GSE45732,GSE46073 | 0.014199 | breast cancer cells | Public on Jun 17 2014 | Apr 03 2013 | 9606 | SUM159_RNAseq_siJARID1B | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX259562 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01997746 |
|
1 | cell line: MDA-MB-231,cell type: breast cancer cells,transfection: control siRNA | 450 Brookline Ave | Boston | USA | Dana-Farber Cancer Institute | Kornelia,,Polyak | Basecalls performed using CASAVA version 1.7 or 1.8.,RNA-Seq raw data was mapped by Tophat to hg19.,Read counting and differential gene expression analysis were done using GFold using significance cutoff = 0.05.,Genome_build: hg19,Supplementary_files_format_and_content: Text file (.cnt) of mapped read counts was generated using Gfold. | Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen) following the manufacturerâs protocol. Then polyA RNA were purified using the MACS mRNA isolation kit (Miltenyi Biotec).,PolyA RNA was fragmented by RNA fragmentation reagent (Ambion), and subjected to first strand synthesis by using SupeScript II (Invitrogen) and random hexamer oligos. The second strand was synthesized, and then subjected to end repair, A-tailing, ligation of Illumia paired end adaptor. Following PCR amplification for 18 cycles, the final library underwent gel purification. | GSM1113308 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX259563,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01997747 | GSM1113308 | GSE45732,GSE46073 | 0.017828 | breast cancer cells | Public on Jun 17 2014 | Apr 03 2013 | 9606 | MDAMB231_RNAseq_Control | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX259563 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01997747 |
|
1 | cell line: HCC2157,cell type: breast cancer cells,transfection: control siRNA | 450 Brookline Ave | Boston | USA | Dana-Farber Cancer Institute | Kornelia,,Polyak | Basecalls performed using CASAVA version 1.7 or 1.8.,RNA-Seq raw data was mapped by Tophat to hg19.,Read counting and differential gene expression analysis were done using GFold using significance cutoff = 0.05.,Genome_build: hg19,Supplementary_files_format_and_content: Text file (.cnt) of mapped read counts was generated using Gfold. | Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen) following the manufacturerâs protocol. Then polyA RNA were purified using the MACS mRNA isolation kit (Miltenyi Biotec).,PolyA RNA was fragmented by RNA fragmentation reagent (Ambion), and subjected to first strand synthesis by using SupeScript II (Invitrogen) and random hexamer oligos. The second strand was synthesized, and then subjected to end repair, A-tailing, ligation of Illumia paired end adaptor. Following PCR amplification for 18 cycles, the final library underwent gel purification. | GSM1113310 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX259565,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01997749 | GSM1113310 | GSE45732,GSE46073 | 0.033628 | breast cancer cells | Public on Jun 17 2014 | Apr 03 2013 | 9606 | HCC2157_RNAseq_Control | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX259565 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01997749 |
|
1 | cell line: HCC2157,cell type: breast cancer cells,transfection: siJARID1B | 450 Brookline Ave | Boston | USA | Dana-Farber Cancer Institute | Kornelia,,Polyak | Basecalls performed using CASAVA version 1.7 or 1.8.,RNA-Seq raw data was mapped by Tophat to hg19.,Read counting and differential gene expression analysis were done using GFold using significance cutoff = 0.05.,Genome_build: hg19,Supplementary_files_format_and_content: Text file (.cnt) of mapped read counts was generated using Gfold. | Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen) following the manufacturerâs protocol. Then polyA RNA were purified using the MACS mRNA isolation kit (Miltenyi Biotec).,PolyA RNA was fragmented by RNA fragmentation reagent (Ambion), and subjected to first strand synthesis by using SupeScript II (Invitrogen) and random hexamer oligos. The second strand was synthesized, and then subjected to end repair, A-tailing, ligation of Illumia paired end adaptor. Following PCR amplification for 18 cycles, the final library underwent gel purification. | GSM1113311 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX259566,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01997750 | GSM1113311 | GSE45732,GSE46073 | 0.023755 | breast cancer cells | Public on Jun 17 2014 | Apr 03 2013 | 9606 | HCC2157_RNAseq_siJARID1B | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX259566 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01997750 |
|
1 | cell line: BJ cells,condition: Control sample | Ramat Aviv | Tel Aviv | Israel | Tel Aviv University | Ran,,Elkon | Reads were aligned to a reference set of human transcripts using Bowtie,Number of reads mapping to each transcript was counted and normalized to FPKMs,Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads | Total RNA was isolated using Trizol Reagent (Invitrogen), following the manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen),Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer's instructions. | GSM1115083 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX260240,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01999137 | GSM1115083 | GSE45785,GSE45833 | 0.005993 | Immortalized primary fibroblasts | Public on Jun 01 2013 | Apr 04 2013 | 9606 | C.rna | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX260240 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01999137 |
|
1 | cell line: BJ cells,condition: Nutlin-3a, 2h | Ramat Aviv | Tel Aviv | Israel | Tel Aviv University | Ran,,Elkon | Reads were aligned to a reference set of human transcripts using Bowtie,Number of reads mapping to each transcript was counted and normalized to FPKMs,Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads | Total RNA was isolated using Trizol Reagent (Invitrogen), following the manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen),Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer's instructions. | GSM1115084 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX260241,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01999138 | GSM1115084 | GSE45785,GSE45833 | 0.003404 | Immortalized primary fibroblasts | Public on Jun 01 2013 | Apr 04 2013 | 9606 | Nutlin.2h.rna | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX260241 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01999138 |
|
1 | cell line: BJ cells,condition: Nutlin-3a, 6h | Ramat Aviv | Tel Aviv | Israel | Tel Aviv University | Ran,,Elkon | Reads were aligned to a reference set of human transcripts using Bowtie,Number of reads mapping to each transcript was counted and normalized to FPKMs,Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads | Total RNA was isolated using Trizol Reagent (Invitrogen), following the manufacturer's instructions. Poly(A) was isolated using the Oligotex mRNA mini kit (Qiagen),Libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer's instructions. | GSM1115086 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX260243,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01999140 | GSM1115086 | GSE45785,GSE45833 | 0.004421 | Immortalized primary fibroblasts | Public on Jun 01 2013 | Apr 04 2013 | 9606 | Nutlin.6h.rna | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX260243 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01999140 |
|
1 | cell line: BJ cells,condition: Control sample | Ramat Aviv | Tel Aviv | Israel | Tel Aviv University | Ran,,Elkon | Reads were aligned to a reference set of human transcripts using Bowtie,Number of reads mapping to each transcript was counted and normalized to FPKMs,Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads | Cells were treated with cycloheximide (100 μg/ml) for 8-10 minutes, washed with ice-cold PBS (cycloheximide, 100 μg/ml), pelleted, and lysed in buffer A (20 mM Tris-HCl, pH7.8, 100mM KCl, 10mM MgCl2, 1% Triton X-100, 2mM DTT, 100 μg/ml cycloheximide, 1x complete protease inhibitor). Lysates were centrifuged at 5000 rpm and the supernatant was treated with 2U/μl of RNase I (Ambion) for 40 minutes at room temperature. Lysates were fractionated on a linear sucrose gradient (7%-47%) using the SW-41Ti rotor at 36,000 rpm for 2hrs. Fractions enriched in monosomes were polled and treated wih proteinase K (Roche) in 1%SDS. Released RNA fragments were purified using trizol and precipitated in the presence of glycogen.,RNA from the pooled monosomes was gel-purified on a denaturing 10% polyacrylamide urea (7M) gel. A section corresponding to 30-33 nucleotides, the region where most of the ribosome-protected fragments are comprised, was excised, eluted, and ethanol precipitated. The resulting fragments were 3â²-dephosphorylated using T4 PNK (NEB) for 6 h at 37 °C in MES buffer (100 mM MES-NaOH, pH 5.5, 10 mM MgCl2, 10 mM β-mercaptoethanol, 300 mM NaCl). 3â² adaptor was added with T4 RNA ligase 1 (NEB) for 2.5h at 37°C. Ligation products were 5â²-phosphorylated with T4 PNK for 30 min at 37°C. 5â² adaptor was added with T4 RNA ligase 1 for 18h at 22°C. | GSM1115204 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX260245,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01999142 | GSM1115204 | GSE45785,GSE45833 | 0.015768 | Immortalized primary fibroblasts | Public on Jun 01 2013 | Apr 04 2013 | 9606 | C.rp | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX260245 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01999142 |
|
1 | cell line: BJ cells,condition: Nutlin-3a, 2h | Ramat Aviv | Tel Aviv | Israel | Tel Aviv University | Ran,,Elkon | Reads were aligned to a reference set of human transcripts using Bowtie,Number of reads mapping to each transcript was counted and normalized to FPKMs,Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads | Cells were treated with cycloheximide (100 μg/ml) for 8-10 minutes, washed with ice-cold PBS (cycloheximide, 100 μg/ml), pelleted, and lysed in buffer A (20 mM Tris-HCl, pH7.8, 100mM KCl, 10mM MgCl2, 1% Triton X-100, 2mM DTT, 100 μg/ml cycloheximide, 1x complete protease inhibitor). Lysates were centrifuged at 5000 rpm and the supernatant was treated with 2U/μl of RNase I (Ambion) for 40 minutes at room temperature. Lysates were fractionated on a linear sucrose gradient (7%-47%) using the SW-41Ti rotor at 36,000 rpm for 2hrs. Fractions enriched in monosomes were polled and treated wih proteinase K (Roche) in 1%SDS. Released RNA fragments were purified using trizol and precipitated in the presence of glycogen.,RNA from the pooled monosomes was gel-purified on a denaturing 10% polyacrylamide urea (7M) gel. A section corresponding to 30-33 nucleotides, the region where most of the ribosome-protected fragments are comprised, was excised, eluted, and ethanol precipitated. The resulting fragments were 3â²-dephosphorylated using T4 PNK (NEB) for 6 h at 37 °C in MES buffer (100 mM MES-NaOH, pH 5.5, 10 mM MgCl2, 10 mM β-mercaptoethanol, 300 mM NaCl). 3â² adaptor was added with T4 RNA ligase 1 (NEB) for 2.5h at 37°C. Ligation products were 5â²-phosphorylated with T4 PNK for 30 min at 37°C. 5â² adaptor was added with T4 RNA ligase 1 for 18h at 22°C. | GSM1115207 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX260246,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01999143 | GSM1115207 | GSE45785,GSE45833 | 0.016184 | Immortalized primary fibroblasts | Public on Jun 01 2013 | Apr 04 2013 | 9606 | Nutlin.2h.rp | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX260246 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01999143 |
|
1 | cell line: BJ cells,condition: Nutlin-3a, 4h | Ramat Aviv | Tel Aviv | Israel | Tel Aviv University | Ran,,Elkon | Reads were aligned to a reference set of human transcripts using Bowtie,Number of reads mapping to each transcript was counted and normalized to FPKMs,Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads | Cells were treated with cycloheximide (100 μg/ml) for 8-10 minutes, washed with ice-cold PBS (cycloheximide, 100 μg/ml), pelleted, and lysed in buffer A (20 mM Tris-HCl, pH7.8, 100mM KCl, 10mM MgCl2, 1% Triton X-100, 2mM DTT, 100 μg/ml cycloheximide, 1x complete protease inhibitor). Lysates were centrifuged at 5000 rpm and the supernatant was treated with 2U/μl of RNase I (Ambion) for 40 minutes at room temperature. Lysates were fractionated on a linear sucrose gradient (7%-47%) using the SW-41Ti rotor at 36,000 rpm for 2hrs. Fractions enriched in monosomes were polled and treated wih proteinase K (Roche) in 1%SDS. Released RNA fragments were purified using trizol and precipitated in the presence of glycogen.,RNA from the pooled monosomes was gel-purified on a denaturing 10% polyacrylamide urea (7M) gel. A section corresponding to 30-33 nucleotides, the region where most of the ribosome-protected fragments are comprised, was excised, eluted, and ethanol precipitated. The resulting fragments were 3â²-dephosphorylated using T4 PNK (NEB) for 6 h at 37 °C in MES buffer (100 mM MES-NaOH, pH 5.5, 10 mM MgCl2, 10 mM β-mercaptoethanol, 300 mM NaCl). 3â² adaptor was added with T4 RNA ligase 1 (NEB) for 2.5h at 37°C. Ligation products were 5â²-phosphorylated with T4 PNK for 30 min at 37°C. 5â² adaptor was added with T4 RNA ligase 1 for 18h at 22°C. | GSM1115210 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX260247,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01999144 | GSM1115210 | GSE45785,GSE45833 | 0.030553 | Immortalized primary fibroblasts | Public on Jun 01 2013 | Apr 04 2013 | 9606 | Nutlin.4h.rp | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX260247 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01999144 |
|
1 | cell line: BJ cells,condition: Nutlin-3a, 6h | Ramat Aviv | Tel Aviv | Israel | Tel Aviv University | Ran,,Elkon | Reads were aligned to a reference set of human transcripts using Bowtie,Number of reads mapping to each transcript was counted and normalized to FPKMs,Supplementary_files_format_and_content: wig files represent read coverage at each genomic location (hg19), normalized to 10M reads | Cells were treated with cycloheximide (100 μg/ml) for 8-10 minutes, washed with ice-cold PBS (cycloheximide, 100 μg/ml), pelleted, and lysed in buffer A (20 mM Tris-HCl, pH7.8, 100mM KCl, 10mM MgCl2, 1% Triton X-100, 2mM DTT, 100 μg/ml cycloheximide, 1x complete protease inhibitor). Lysates were centrifuged at 5000 rpm and the supernatant was treated with 2U/μl of RNase I (Ambion) for 40 minutes at room temperature. Lysates were fractionated on a linear sucrose gradient (7%-47%) using the SW-41Ti rotor at 36,000 rpm for 2hrs. Fractions enriched in monosomes were polled and treated wih proteinase K (Roche) in 1%SDS. Released RNA fragments were purified using trizol and precipitated in the presence of glycogen.,RNA from the pooled monosomes was gel-purified on a denaturing 10% polyacrylamide urea (7M) gel. A section corresponding to 30-33 nucleotides, the region where most of the ribosome-protected fragments are comprised, was excised, eluted, and ethanol precipitated. The resulting fragments were 3â²-dephosphorylated using T4 PNK (NEB) for 6 h at 37 °C in MES buffer (100 mM MES-NaOH, pH 5.5, 10 mM MgCl2, 10 mM β-mercaptoethanol, 300 mM NaCl). 3â² adaptor was added with T4 RNA ligase 1 (NEB) for 2.5h at 37°C. Ligation products were 5â²-phosphorylated with T4 PNK for 30 min at 37°C. 5â² adaptor was added with T4 RNA ligase 1 for 18h at 22°C. | GSM1115213 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX260248,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01999145 | GSM1115213 | GSE45785,GSE45833 | 0 | Immortalized primary fibroblasts | Public on Jun 01 2013 | Apr 04 2013 | 9606 | Nutlin.6h.rp | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX260248 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01999145 |
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1 | cell line: MCF7,treatment: 1hr treatment with 100nM E2 | 9500 Gilman Dr, | San Diego | USA | UCSD | Qi,,Ma | Basecalls performed using CASAVA version 1.4,Gro-seq reads were aligned to the hg18 genome assembly using Bowtie version 2.0.1.,The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.,Genome_build: hg18 | MCF7 cells were subjected to nuclear run-on for 5minutes at 30 degree with BrU labeling. The run-on RNAs were pull down by BrU beads and subjected to library preparation for deep sequencing.,We followed a previous published protocol (Ingolia et al., 2009 Science; Wang et al., 2011 Nature). Briefly, the run-on RNA were first added with a polyA tracts by RNA polyA polymerase. This polyA tail enables the run-on RNA to be reverse transcribed into single strand cDNA by Reverse Transcriptase. The cDNA was circularized by CircLigase (Epicentre) and re-linearized by Ape1, subsequently subjected to PCR amplification and deep sequencing. | GSM1115995 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX261278,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01999645,Named Annotation: NA000028217.1 (GSM1115995_Groseq-MCF7-E2-rep1.minusstrand.bigWig),Named Annotation: NA000028218.1 (GSM1115995_Groseq-MCF7-E2-rep1.plusstrand.bigWig) | GSM1115995 | GSE45822 | 0 | MCF7 | Public on Jun 04 2013 | Apr 05 2013 | 9606 | GROSeq_E2_repeat1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX261278 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01999645 |
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1 | cell line: MCF7,treatment: 1hr treatment with 100nM E2 | 9500 Gilman Dr, | San Diego | USA | UCSD | Qi,,Ma | Basecalls performed using CASAVA version 1.4,Gro-seq reads were aligned to the hg18 genome assembly using Bowtie version 2.0.1.,The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.,Genome_build: hg18 | MCF7 cells were subjected to nuclear run-on for 5minutes at 30 degree with BrU labeling. The run-on RNAs were pull down by BrU beads and subjected to library preparation for deep sequencing.,We followed a previous published protocol (Ingolia et al., 2009 Science; Wang et al., 2011 Nature). Briefly, the run-on RNA were first added with a polyA tracts by RNA polyA polymerase. This polyA tail enables the run-on RNA to be reverse transcribed into single strand cDNA by Reverse Transcriptase. The cDNA was circularized by CircLigase (Epicentre) and re-linearized by Ape1, subsequently subjected to PCR amplification and deep sequencing. | GSM1115996 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX261279,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01999646,Named Annotation: NA000028219.1 (GSM1115996_Groseq-MCF7-E2-rep2.minusstrand.bigWig),Named Annotation: NA000028220.1 (GSM1115996_Groseq-MCF7-E2-rep2.plusstrand.bigWig) | GSM1115996 | GSE45822 | 0.078555 | MCF7 | Public on Jun 04 2013 | Apr 05 2013 | 9606 | GROSeq_E2_repeat2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX261279 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01999646 |
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1 | cell line: MCF7,treatment: 1hr treatment with ethanol | 9500 Gilman Dr, | San Diego | USA | UCSD | Qi,,Ma | Basecalls performed using CASAVA version 1.4,Gro-seq reads were aligned to the hg18 genome assembly using Bowtie version 2.0.1.,The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.,Genome_build: hg18 | MCF7 cells were subjected to nuclear run-on for 5minutes at 30 degree with BrU labeling. The run-on RNAs were pull down by BrU beads and subjected to library preparation for deep sequencing.,We followed a previous published protocol (Ingolia et al., 2009 Science; Wang et al., 2011 Nature). Briefly, the run-on RNA were first added with a polyA tracts by RNA polyA polymerase. This polyA tail enables the run-on RNA to be reverse transcribed into single strand cDNA by Reverse Transcriptase. The cDNA was circularized by CircLigase (Epicentre) and re-linearized by Ape1, subsequently subjected to PCR amplification and deep sequencing. | GSM1115997 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX261280,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01999647,Named Annotation: NA000028221.1 (GSM1115997_Groseq-MCF7-EtoH-rep1.minusstrand.bigWig),Named Annotation: NA000028222.1 (GSM1115997_Groseq-MCF7-EtoH-rep1.plusstrand.bigWig) | GSM1115997 | GSE45822 | 0.012597 | MCF7 | Public on Jun 04 2013 | Apr 05 2013 | 9606 | GROSeq_EtOH_repeat1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX261280 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01999647 |
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1 | cell type: leukemic cell line,cell line: U937CM,treatment: 3 days Tet free medium | Geert Grooteplein 28 | Nijmegen | Netherlands | Radboud University | Joost,,Martens | Basecalls performed using CASAVA,Reads were aligned to the hg18 or hg19 genome assembly (see characteristics) using ELAND/BWA,Peaks were called using MACS 1.3.3 on settings:mfold =8, tsize=32, p value = e-6,Genome_build: hg19,Supplementary_files_format_and_content: wig or bedgraph files were generated (extended to 300bps) with regions having more than 1 read in a window of 10 bps | RNA was extracted using qiagen RNeasy kit according to manufacturer instructions and total RNA was treated using Ribo-zero to remove rRNA according to manufacturer instructions.,Libraries were prepared according to Illumina's standard protocol. | GSM1122324 | Illumina HiSeq 2000 | Nov 11 2021 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX265240,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02045674 | GSM1122324 | GSE46044 | 0.009137 | U937CM cell line (leukemic) | Public on Sep 09 2013 | Apr 15 2013 | 9606 | U937CM_induced RNA-Seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX265240 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02045674 |
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1 | cell type: leukemic cell line,cell line: ME-1,treatment: 3 days Dox (1 mM) | Geert Grooteplein 28 | Nijmegen | Netherlands | Radboud University | Joost,,Martens | Basecalls performed using CASAVA,Reads were aligned to the hg18 or hg19 genome assembly (see characteristics) using ELAND/BWA,Peaks were called using MACS 1.3.3 on settings:mfold =8, tsize=32, p value = e-6,Genome_build: hg19,Supplementary_files_format_and_content: wig or bedgraph files were generated (extended to 300bps) with regions having more than 1 read in a window of 10 bps | RNA was extracted using qiagen RNeasy kit according to manufacturer instructions and total RNA was treated using Ribo-zero to remove rRNA according to manufacturer instructions.,Libraries were prepared according to Illumina's standard protocol. | GSM1122326 | Illumina HiSeq 2000 | Nov 11 2021 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX265242,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02045676 | GSM1122326 | GSE46044 | 0 | ME-1 (leukemic) | Public on Sep 09 2013 | Apr 15 2013 | 9606 | ME-1_scrambled RNA-Seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX265242 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02045676 |
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1 | cell type: leukemic cell line,cell line: ME-1,treatment: 3 days Dox (1 mM) | Geert Grooteplein 28 | Nijmegen | Netherlands | Radboud University | Joost,,Martens | Basecalls performed using CASAVA,Reads were aligned to the hg18 or hg19 genome assembly (see characteristics) using ELAND/BWA,Peaks were called using MACS 1.3.3 on settings:mfold =8, tsize=32, p value = e-6,Genome_build: hg19,Supplementary_files_format_and_content: wig or bedgraph files were generated (extended to 300bps) with regions having more than 1 read in a window of 10 bps | RNA was extracted using qiagen RNeasy kit according to manufacturer instructions and total RNA was treated using Ribo-zero to remove rRNA according to manufacturer instructions.,Libraries were prepared according to Illumina's standard protocol. | GSM1122327 | Illumina HiSeq 2000 | Nov 11 2021 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX265243,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02045677 | GSM1122327 | GSE46044 | 0.03558 | ME-1 (leukemic) | Public on Sep 09 2013 | Apr 15 2013 | 9606 | ME-1_Knockdown RNA-Seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX265243 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02045677 |
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1 | cell type: leukemic cell line,cell line: ME-1,treatment: none | Geert Grooteplein 28 | Nijmegen | Netherlands | Radboud University | Joost,,Martens | Basecalls performed using CASAVA,Reads were aligned to the hg18 or hg19 genome assembly (see characteristics) using ELAND/BWA,Peaks were called using MACS 1.3.3 on settings:mfold =8, tsize=32, p value = e-6,Genome_build: hg18,Supplementary_files_format_and_content: wig or bedgraph files were generated (extended to 300bps) with regions having more than 1 read in a window of 10 bps | RNA was extracted using qiagen RNeasy kit according to manufacturer instructions and total RNA was treated using Ribo-zero to remove rRNA according to manufacturer instructions.,Libraries were prepared according to Illumina's standard protocol. | GSM1122328 | Illumina HiSeq 2000 | Nov 11 2021 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX265244,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02045678 | GSM1122328 | GSE46044 | 0.047501 | ME-1 (leukemic) | Public on Sep 09 2013 | Apr 15 2013 | 9606 | ME-1 RNA-Seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX265244 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02045678 |
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1 | cell type: primary CD34+ cell,genotype/variation: control | 1275 York Ave. | New York | USA | Memorial SLoan-Kettering Cancer Center | Bic,,MSKCC | Basecalls performed using CASAVA version 1.8,Reads were aligned using Tophat 1.4.0 with Bowtie 1,Normalized gene counts were calculated using the DESeq Bioconductor package version 1.10.1 with detault settings,Genome_build: hg19,Supplementary_files_format_and_content: counts_scaled_DESeq.txt is a tab-delimited file containing normalized gene counts for each sample. | Total RNA was extracted using Qiagen RNeasy Plus® mini kit (QIAGEN, Germany).,Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# RS-122-2001). Briefly, mRNA was purified and fragmented, then synthesized cDNA strand, end-repaired following Illumina standard RNA sample preparation protocols. Libraries were sequenced on Hiseq 2000 following the manufacturer's protocols. | GSM1122673 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02045840,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX265379 | GSM1122673 | GSE46056 | 0.00812 | cord blood | Public on Dec 19 2013 | Apr 15 2013 | 9606 | control-1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX265379 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02045840 |
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1 | cell type: primary CD34+ cell,genotype/variation: control | 1275 York Ave. | New York | USA | Memorial SLoan-Kettering Cancer Center | Bic,,MSKCC | Basecalls performed using CASAVA version 1.8,Reads were aligned using Tophat 1.4.0 with Bowtie 1,Normalized gene counts were calculated using the DESeq Bioconductor package version 1.10.1 with detault settings,Genome_build: hg19,Supplementary_files_format_and_content: counts_scaled_DESeq.txt is a tab-delimited file containing normalized gene counts for each sample. | Total RNA was extracted using Qiagen RNeasy Plus® mini kit (QIAGEN, Germany).,Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# RS-122-2001). Briefly, mRNA was purified and fragmented, then synthesized cDNA strand, end-repaired following Illumina standard RNA sample preparation protocols. Libraries were sequenced on Hiseq 2000 following the manufacturer's protocols. | GSM1122674 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX265380,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02045876 | GSM1122674 | GSE46056 | 0.005807 | cord blood | Public on Dec 19 2013 | Apr 15 2013 | 9606 | control-2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX265380 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02045876 |
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1 | cell type: primary CD34+ cell,genotype/variation: control | 1275 York Ave. | New York | USA | Memorial SLoan-Kettering Cancer Center | Bic,,MSKCC | Basecalls performed using CASAVA version 1.8,Reads were aligned using Tophat 1.4.0 with Bowtie 1,Normalized gene counts were calculated using the DESeq Bioconductor package version 1.10.1 with detault settings,Genome_build: hg19,Supplementary_files_format_and_content: counts_scaled_DESeq.txt is a tab-delimited file containing normalized gene counts for each sample. | Total RNA was extracted using Qiagen RNeasy Plus® mini kit (QIAGEN, Germany).,Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# RS-122-2001). Briefly, mRNA was purified and fragmented, then synthesized cDNA strand, end-repaired following Illumina standard RNA sample preparation protocols. Libraries were sequenced on Hiseq 2000 following the manufacturer's protocols. | GSM1122675 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX265381,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02045877 | GSM1122675 | GSE46056 | 0.00814 | cord blood | Public on Dec 19 2013 | Apr 15 2013 | 9606 | control-3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX265381 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02045877 |
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1 | cell type: primary CD34+ cell,genotype/variation: PRMT4-KD | 1275 York Ave. | New York | USA | Memorial SLoan-Kettering Cancer Center | Bic,,MSKCC | Basecalls performed using CASAVA version 1.8,Reads were aligned using Tophat 1.4.0 with Bowtie 1,Normalized gene counts were calculated using the DESeq Bioconductor package version 1.10.1 with detault settings,Genome_build: hg19,Supplementary_files_format_and_content: counts_scaled_DESeq.txt is a tab-delimited file containing normalized gene counts for each sample. | Total RNA was extracted using Qiagen RNeasy Plus® mini kit (QIAGEN, Germany).,Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# RS-122-2001). Briefly, mRNA was purified and fragmented, then synthesized cDNA strand, end-repaired following Illumina standard RNA sample preparation protocols. Libraries were sequenced on Hiseq 2000 following the manufacturer's protocols. | GSM1122676 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX265382,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02045878 | GSM1122676 | GSE46056 | 0.048278 | cord blood | Public on Dec 19 2013 | Apr 15 2013 | 9606 | PRMT4-KD1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX265382 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02045878 |
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1 | cell type: primary CD34+ cell,genotype/variation: PRMT4-KD | 1275 York Ave. | New York | USA | Memorial SLoan-Kettering Cancer Center | Bic,,MSKCC | Basecalls performed using CASAVA version 1.8,Reads were aligned using Tophat 1.4.0 with Bowtie 1,Normalized gene counts were calculated using the DESeq Bioconductor package version 1.10.1 with detault settings,Genome_build: hg19,Supplementary_files_format_and_content: counts_scaled_DESeq.txt is a tab-delimited file containing normalized gene counts for each sample. | Total RNA was extracted using Qiagen RNeasy Plus® mini kit (QIAGEN, Germany).,Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# RS-122-2001). Briefly, mRNA was purified and fragmented, then synthesized cDNA strand, end-repaired following Illumina standard RNA sample preparation protocols. Libraries were sequenced on Hiseq 2000 following the manufacturer's protocols. | GSM1122677 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX265383,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02045879 | GSM1122677 | GSE46056 | 0.014083 | cord blood | Public on Dec 19 2013 | Apr 15 2013 | 9606 | PRMT4-KD2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX265383 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02045879 |
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1 | cell type: primary CD34+ cell,genotype/variation: PRMT4-KD | 1275 York Ave. | New York | USA | Memorial SLoan-Kettering Cancer Center | Bic,,MSKCC | Basecalls performed using CASAVA version 1.8,Reads were aligned using Tophat 1.4.0 with Bowtie 1,Normalized gene counts were calculated using the DESeq Bioconductor package version 1.10.1 with detault settings,Genome_build: hg19,Supplementary_files_format_and_content: counts_scaled_DESeq.txt is a tab-delimited file containing normalized gene counts for each sample. | Total RNA was extracted using Qiagen RNeasy Plus® mini kit (QIAGEN, Germany).,Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# RS-122-2001). Briefly, mRNA was purified and fragmented, then synthesized cDNA strand, end-repaired following Illumina standard RNA sample preparation protocols. Libraries were sequenced on Hiseq 2000 following the manufacturer's protocols. | GSM1122678 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX265384,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02045880 | GSM1122678 | GSE46056 | 0.017714 | cord blood | Public on Dec 19 2013 | Apr 15 2013 | 9606 | PRMT4-KD3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX265384 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02045880 |
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1 | cell type: HUES64 derived hepatoblast,chip antibody: NA | Kraepelinstrasse 2-10 | Munich | Germany | Max Planck Institute of Psychiatry | Michael,Johannes,Ziller | BiSeq: raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010).,RNA-Seq: raw sequence reads were aligned using Tophat v2.0.6 and Bowtie version 0.12.7.,RNA-Seq: Reads were mapped to the human genome (hg19) using TopHat v2.0.6 (Trapnell et al., 2009)(http://tophat.cbcb.umd.edu) with the following options: ââlibrary-type firststrandâ and ââtranscriptome-indexâ with a TopHat transcript index built from RefSeq. Transcript expression was estimated with an improved version of Cuffdiff 2 (Trapnell et al., 2013) (http://cufflinks.cbcb.umd.edu). Cuffdiff was run with the following options: ââmin-reps-for-js-test 2 âdispersion-method per-conditionâ against the UCSC iGenomes GTF file from Illumina (available at http://cufflinks.cbcb.umd.edu/igenomes.html). The workflow used to analyze the data is described in detail in (Trapnell et al., 2012) (alternate protocol B).,ChIP-Seq data was aligned to the hg19/GRCh37 reference genome using bwa version 0.5.7 (Li et al., 2009) with default parameter settings. Subsequently, an improved version of Cuffdiff 2 was used to conduct de novo transcript assembly and RNA expression quantification. Following assembly, transcripts were annotated using known RefSeq genes,For OCT4, SOX2, NANOG and FOXA2 aligned read files were processed with macs version 1.4 (Zhang et al., 2008) using the following parameters: -g 2.7e9 --tsize=36 --pvalue=1e-5 --keep-dup=1. HUES64 WCE (GSM772807) was used as input control.,Genome_build: hg19,Supplementary_files_format_and_content: Hepatoblast_genes_fpkm_tracking.gtf file contains transcript coordinates, FPKM counts and detection p-values. | Cells collected by FACS were crosslinked in 1% formaldehyde for 15 minutes at room temperature, with constant agitation, followed by quenching with 125mM Glycine for 5 minutes at room temperature with constant agitation. Nuclei were isolated and chromatin was sheared using Branson sonifier until the majority of DNA was in the range of 200-700 base pairs. Chromatin was incubated with antibody overnight at 4°C, with constant agitation. Co-immunoprecipitation of antibody-protein complexes was completed using Protein A or Protein G Dynabeads for 1 hour 4°C, with constant agitation. ChIPs were completed using previously reported methods (Mikkelsen et al., 2010),ChIP-Bisulfite Sequencing (adapted from Brinkman et al, 2012) DNA was first subjected to end-repair in a 30-μl reaction containing 6 units T4 DNA polymerase, 2.5 units DNA Polymerase I (Large Klenow Fragment), 20 units T4 Polynucleotide Kinase (all New England Biolabs), dATP, dCTP, dGTP, and dTTP (0.125 mM each), and 1à T4 Ligase buffer with ATP for 30 min at 20°C. DNA was then adenylated in a 20-μl reaction containing 10 units Klenow Fragment (3â²â5â² exo-) (New England Biolabs), 0.5 mM dATP and 1à NEB buffer 2 for 30 min at 37°C. DNA was then ligated to preannealed Illumina genomic DNA adapters containing 5-methylcytosine instead of cytosine (ATDBio) using T4 DNA ligase (New England Biolabs). Adapter-ligated DNA fragments were subsequently purified by phenol extraction and ethanol precipitation and size-selected on gel. 50 ng sheared and dephosphorylated Escherichia coli K12 genomic DNA was added to adapter-ligated DNA as carrier during size-selection and bisulfite conversion. DNA was run on 2.5% Nusieve 3:1 Agarose (Lonza) gels. Lanes containing marker (50 bp ladder; New England Biolabs) were stained with SYBR Green (Invitrogen), and size regions to be excised were marked with toothpicks and adapter-ligated DNA fragments from 200â400 and 400â550 bp were excised. DNA was isolated from gel using the MinElute Gel Extraction kit (QIAGEN). The low and high libraries were kept separate in subsequent steps. Adapter-ligated and size-selected DNA was subjected to two subsequent 5-h bisulfite treatments using the EpiTect Bisulfite kit (QIAGEN) following the manufacturer's protocol for DNA isolated from FFPE tissue samples. PCR amplification was done with 1.25 units Pfu Turbo Cx Hotstart DNA Polymerase (Stratagene), primer LPX 1.1 and 2.1 (0.3 μM each), dNTPs (0.25 mM each), 1à Turbo Cx buffer. Amplified libraries were purified with the MinElute PCR Purification kit (QIAGEN) and subsequently purified from gel essentially as described above; whole gels were stained with SYBR Green, and no carrier DNA was added. Final libraries were analyzed on analytical 4%â20% TBE Criterion precast gels (BioRad), and measured by Quant-iT dsDNA HS Assays (Invitrogen). CHIP:Cells collected by FACS were crosslinked in 1% formaldehyde for 15 minutes at room temperature, with constant agitation, followed by quenching with 125mM Glycine for 5 minutes at room temperature with constant agitation. Nuclei were isolated and chromatin was sheared using Branson sonifier until the majority of DNA was in the range of 200-700 base pairs. Chromatin was incubated with antibody overnight at 4°C, with constant agitation. Co-immunoprecipitation of antibody-protein complexes was completed using Protein A or Protein G Dynabeads for 1 hour 4°C, with constant agitation. ChIPs were completed using previously reported methods (Mikkelsen et al., 2010). Sequencing library production details can be found in the Supplemental Experimental Procedures. Sequencing libraries were submitted for sequencing on the Illumina Hiseq 2000. Immunoprecipitated DNA was end repaired using the End-It DNA End-Repair Kit (Epicentre), extended using a Klenow fragment (3â-5â exo)(NEB), and ligated to sequencing adapter oligos (Illumina). Each library was then PCR-amplified using PFU Ultra II Hotstart Master Mix (Agilent), and a size range of 300-600 was selected for sequencing. RNA-Seq: Strand specific libraries were constructed as described in the main text using a strand specific method (Levin et al., 2010). Polyadenylated RNA was isolated using Oligo dT beads (Invitrogen) and fragmented to 200-600 base pairs, and then ligated to RNA adaptors using T4 RNA Ligase, (NEB), preserving strand of origin information. A primer that anneals to the RNA adaptor was used to facilitate cDNA synthesis, which was then followed by RNA degradation. The cDNA library was then ligated to a DNA adaptor, which was used for PCR enrichment of the library, with index sequences included in the primers used for amplification. | GSM1124072 | Illumina HiSeq 2500 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL16791 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02046822,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX266864 | GSM1124072 | GSE46130 | 0.139817 | in vitro derived hepatoblast | Public on May 01 2013 | Apr 17 2013 | 9606 | Hepatoblast derived from HUES64 RNA-Seq reps1and2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX266864 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02046822 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-failing,lvad support: nil | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126613 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053684,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268709 | GSM1126613 | GSE46224 | 0.005648 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NF2_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268709 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053684 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-failing,lvad support: nil | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126614 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053685,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268710 | GSM1126614 | GSE46224 | 0.008488 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NF3_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268710 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053685 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-failing,lvad support: nil | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126615 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053686,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268711 | GSM1126615 | GSE46224 | 0.009248 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NF4_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268711 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053686 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-failing,lvad support: nil | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126616 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053687,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268712 | GSM1126616 | GSE46224 | 0.007057 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NF5_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268712 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053687 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-failing,lvad support: nil | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126617 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053688,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268713 | GSM1126617 | GSE46224 | 0.011221 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NF6_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268713 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053688 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-failing,lvad support: nil | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126618 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053689,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268714 | GSM1126618 | GSE46224 | 0.005325 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NF7_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268714 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053689 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-failing,lvad support: nil | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126619 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053690,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268715 | GSM1126619 | GSE46224 | 0.003554 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NF8_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268715 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053690 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126620 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053691,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268716 | GSM1126620 | GSE46224 | 0.007186 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM1_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268716 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053691 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126621 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053692,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268717 | GSM1126621 | GSE46224 | 0.006745 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM2_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268717 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053692 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126622 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053693,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268718 | GSM1126622 | GSE46224 | 0.007021 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM3_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268718 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053693 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126623 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053694,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268719 | GSM1126623 | GSE46224 | 0.0028 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM4_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268719 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053694 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126624 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053695,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268720 | GSM1126624 | GSE46224 | 0.008416 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM5_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268720 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053695 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126625 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053696,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268721 | GSM1126625 | GSE46224 | 0.008 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM6_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268721 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053696 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126626 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053697,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268722 | GSM1126626 | GSE46224 | 0.002578 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM7_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268722 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053697 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126627 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053698,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268723 | GSM1126627 | GSE46224 | 0.003549 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM8_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268723 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053698 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126628 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053699,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268724 | GSM1126628 | GSE46224 | 0.016221 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM1_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268724 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053699 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126629 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053700,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268725 | GSM1126629 | GSE46224 | 0.011171 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM2_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268725 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053700 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126630 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053701,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268726 | GSM1126630 | GSE46224 | 0.010695 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM3_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268726 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053701 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126631 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053702,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268727 | GSM1126631 | GSE46224 | 0.003077 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM4_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268727 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053702 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126632 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053703,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268728 | GSM1126632 | GSE46224 | 0.00459 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM5_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268728 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053703 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126633 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053704,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268729 | GSM1126633 | GSE46224 | 0.005765 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM6_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268729 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053704 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126634 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053705,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268730 | GSM1126634 | GSE46224 | 0.005177 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM7_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268730 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053705 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126637 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053708,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268733 | GSM1126637 | GSE46224 | 0.015419 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM+LVAD2_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268733 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053708 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126638 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053709,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268734 | GSM1126638 | GSE46224 | 0.004011 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM+LVAD3_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268734 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053709 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126639 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053710,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268735 | GSM1126639 | GSE46224 | 0.008 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM+LVAD4_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268735 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053710 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126640 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053711,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268736 | GSM1126640 | GSE46224 | 0.009097 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM+LVAD5_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268736 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053711 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126641 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053720,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268737 | GSM1126641 | GSE46224 | 0.00258 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM+LVAD6_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268737 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053720 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126642 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053721,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268738 | GSM1126642 | GSE46224 | 0.002579 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM+LVAD7_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268738 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053721 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126643 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053722,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268739 | GSM1126643 | GSE46224 | 0.006915 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM+LVAD8_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268739 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053722 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126644 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053723,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268740 | GSM1126644 | GSE46224 | 0.005677 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM+LVAD1_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268740 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053723 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126646 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053725,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268742 | GSM1126646 | GSE46224 | 0.010876 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM+LVAD3_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268742 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053725 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126647 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053726,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268743 | GSM1126647 | GSE46224 | 0.007848 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM+LVAD4_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268743 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053726 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126648 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053717,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268744 | GSM1126648 | GSE46224 | 0.00716 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM+LVAD5_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268744 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053717 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126649 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053714,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268745 | GSM1126649 | GSE46224 | 0.00373 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM+LVAD6_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268745 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053714 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126650 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053715,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268746 | GSM1126650 | GSE46224 | 0.002126 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM+LVAD7_RNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268746 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053715 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-failing,lvad support: nil | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126652 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053727,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268748 | GSM1126652 | GSE46224 | 0.274848 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NF1_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268748 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053727 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-failing,lvad support: nil | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126653 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053719,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268749 | GSM1126653 | GSE46224 | 0.270109 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NF2_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268749 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053719 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-failing,lvad support: nil | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126654 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053712,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268750 | GSM1126654 | GSE46224 | 0.18431 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NF3_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268750 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053712 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-failing,lvad support: nil | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126655 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053713,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268751 | GSM1126655 | GSE46224 | 0.22586 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NF4_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268751 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053713 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-failing,lvad support: nil | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126656 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053718,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268752 | GSM1126656 | GSE46224 | 0.21909 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NF5_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268752 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053718 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-failing,lvad support: nil | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126657 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053655,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268753 | GSM1126657 | GSE46224 | 0.184449 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NF6_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268753 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053655 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-failing,lvad support: nil | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126658 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053656,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268754 | GSM1126658 | GSE46224 | 0.233563 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NF7_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268754 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053656 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-failing,lvad support: nil | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126659 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053657,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268755 | GSM1126659 | GSE46224 | 0.112467 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NF8_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268755 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053657 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126660 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053658,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268756 | GSM1126660 | GSE46224 | 0.214093 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM1_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268756 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053658 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126661 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053659,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268757 | GSM1126661 | GSE46224 | 0.102403 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM2_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268757 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053659 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126662 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053660,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268758 | GSM1126662 | GSE46224 | 0.005234 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM3_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268758 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053660 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126663 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053661,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268759 | GSM1126663 | GSE46224 | 0.008367 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM4_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268759 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053661 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126664 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053662,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268760 | GSM1126664 | GSE46224 | 0.245489 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM5_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268760 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053662 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126665 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053663,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268761 | GSM1126665 | GSE46224 | 0.169054 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM6_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268761 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053663 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126666 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053664,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268762 | GSM1126666 | GSE46224 | 0.258336 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM7_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268762 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053664 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126667 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053665,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268763 | GSM1126667 | GSE46224 | 0.117222 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM8_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268763 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053665 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126668 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053666,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268764 | GSM1126668 | GSE46224 | 0.154175 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM1_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268764 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053666 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126669 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053667,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268765 | GSM1126669 | GSE46224 | 0.115748 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM2_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268765 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053667 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126670 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053668,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268766 | GSM1126670 | GSE46224 | 0.386197 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM3_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268766 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053668 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126671 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053669,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268767 | GSM1126671 | GSE46224 | 0.004958 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM4_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268767 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053669 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126672 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053670,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268768 | GSM1126672 | GSE46224 | 0.136394 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM5_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268768 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053670 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126673 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053671,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268769 | GSM1126673 | GSE46224 | 0.160409 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM6_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268769 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053671 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126674 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053672,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268770 | GSM1126674 | GSE46224 | 0.15022 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM7_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268770 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053672 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: pre-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126675 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053673,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268771 | GSM1126675 | GSE46224 | 0.207154 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM8_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268771 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053673 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126676 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053674,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268772 | GSM1126676 | GSE46224 | 0.07579 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM+LVAD1_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268772 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053674 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126677 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053675,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268773 | GSM1126677 | GSE46224 | 0.065508 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM+LVAD2_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268773 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053675 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126678 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053676,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268774 | GSM1126678 | GSE46224 | 0.090278 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM+LVAD3_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268774 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053676 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126679 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053682,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268775 | GSM1126679 | GSE46224 | 0 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM+LVAD4_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268775 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053682 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126680 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053648,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268776 | GSM1126680 | GSE46224 | 0.191887 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM+LVAD5_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268776 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053648 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126681 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053649,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268777 | GSM1126681 | GSE46224 | 0.259846 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM+LVAD6_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268777 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053649 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126682 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053677,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268778 | GSM1126682 | GSE46224 | 0.187096 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM+LVAD7_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268778 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053677 |
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1 | tissue: left ventricle apex tissue,diagnosis: ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126683 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053678,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268779 | GSM1126683 | GSE46224 | 0.178958 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | ICM+LVAD8_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268779 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053678 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126684 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053679,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268780 | GSM1126684 | GSE46224 | 0.183668 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM+LVAD1_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268780 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053679 |
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1 | tissue: left ventricle apex tissue,diagnosis: non-ischemic cardiomyopathy,lvad support: Post-LVAD | 660 South Euclid Avenue Box 8103 | St Louis | USA | Washington University in St Louis | Kai-Chien,,Yang | Demultiplexing and basecalling performed using CASAVA version 1.6,(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.,(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.,Genome_build: hg9,Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file | LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80â; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8),RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits | GSM1126685 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02053680,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX268781 | GSM1126685 | GSE46224 | 0.11323 | human left ventricle apex tissue | Public on Feb 10 2014 | Apr 19 2013 | 9606 | NICM+LVAD2_miRNASeq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX268781 | https://www.ncbi.nlm.nih.gov/biosample/SAMN02053680 |