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Sample GSM3227588 Query DataSets for GSM3227588
Status Public on Oct 26, 2021
Title WT_CM rep 1
Sample type SRA
 
Source name cardiac myocytes
Organism Mus musculus
Characteristics genotype: BRG1-3XFLAG
cell type: ES cell derived cardiac myocyte
passage: 4-8
Growth protocol ES cells differentiated to cardiac myocytes
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from 2 mill cells using TRizol Reagent and Qiagen microRNAeasy kit
Libraries were prepared according to NuGEN Ultralow V2 kit and paired-end 100bp sequenced on an Illumina HiSeq 2500 instrument.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Reads were trimmed using the fastq-mcf program (Aronesty, 2011), and then aligned to the mm9 mouse genome assembly using tophat2 (RNA-seq) (Kim et al., 2013). For each gene, reads were counted, and counts-per-million (CPM) calculated using featureCounts (Liao et al., 2014). Finally, edgeR was used to perform differential expression analyses (Robinson et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig
 
Submission date Jun 26, 2018
Last update date Oct 26, 2021
Contact name Benoit Bruneau
E-mail(s) benoit.bruneau@gladstone.ucsf.edu
Organization name Gladstone Institute of Cardiovascular Disease
Street address 1650 Owens Street
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
 
Platform ID GPL21103
Series (2)
GSE116292 Chromatin remodeler Brahma safeguards canalization in cardiac mesoderm differentiation [RNA-seq]
GSE150186 Brahma safeguards canalization of cardiac mesoderm differentiation
Relations
BioSample SAMN09491514

Supplementary file Size Download File type/resource
GSM3227588_WT_CM_Rep1.bw 219.2 Mb (ftp)(http) BW
Raw data are available in SRA
Processed data provided as supplementary file

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