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Sample GSM2184038 Query DataSets for GSM2184038
Status Public on Nov 28, 2018
Title HEY2CL7
Sample type SRA
Source name fibroblasts
Organism Homo sapiens
Characteristics cell type: hiPSCs-CMs (HEY2 CRISPR edited)
Stage: day 30
replicate: 1
Treatment protocol no treatment
Growth protocol hiPSCs and hESCs were grown in E8 media on Matrigel
Extracted molecule total RNA
Extraction protocol RNA-seq: mRNA was extracted using the miRNEASY kit from Qiagen. ChIP-seq: Cells were crosslinked with formalin.
Bulk RNA-seq: Ovation® RNA-Seq System V2 kit (NuGEN) and NEBNext DNA Library Prep Master Mix Set for Illumina. Single-cell RNA-seq: SMARTer Ultra Low RNA Kit for the Fluidigm C1 Nextera XT DNA Sample Preparation Kit. Gene edited lines RNA-seq: Ion AmpliSeq™ Transcriptome Human Gene Expression Kit, the Ion PI™ Hi-Q™ Sequencing 200 Kit. ChIP-seq: NEBNext DNA Library Prep Master Mix Set for Illumina or NEBNext® Ultra™ DNA Library Prep.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Description Processed data file: Gene_edited_lines.txt
Gene edited lines RNA-seq
Data processing RNA-seq: reads were deduplicated using prinseq, mapped to reference Ensembl GRCh38 genome using Tophat and RPKM values were obtained using AltAnalyze
ChIP-seq: reads were deduplicated using prinseq, mapped to reference Ensembl GRCh38 genome using Bowtie, Bedtools 2.19.1 was used to generate bigwig files
AltAnalyze was used to generated a table of RPKM values
Genome_build: Ensembl GRCh38, UCSC hg19
Supplementary_files_format_and_content: RNA-Seq: RPKM files
Supplementary_files_format_and_content: ChIP-Seq: bw files
Submission date Jun 01, 2016
Last update date May 15, 2019
Contact name Jared Churko
Organization name Stanford
Department Radiology
Street address 265 Campus Dr G1105 SIM1
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platform ID GPL17303
Series (1)
GSE81585 Transcriptome signatures of human induced pluripotent stem cell-derived cardiomyocytes classify cardiomyocyte subtype populations
BioSample SAMN05195151
SRA SRX1815063

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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