|
Status |
Public on Oct 26, 2021 |
Title |
BRMKO_CM rep 1 |
Sample type |
SRA |
|
|
Source name |
cardiac myocytes
|
Organism |
Mus musculus |
Characteristics |
genotype: BRG1-3XFLAG; BRM KO 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.
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|
|
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
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|
|
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 |
SAMN09491499 |