|
| Status |
Public on Feb 28, 2019 |
| Title |
BAF60cKO_CP Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Cardiac progenitors
|
| Organism |
Mus musculus |
| Characteristics |
genotype: BRG1-3XFLAG; BAF60c KO
cell type: ES cell derived Cardiac progenitors
passage: 4-8
strain: W4/129S6
|
| 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 2500 |
| |
|
| 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 |
Feb 28, 2019 |
| 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 |
GPL17021 |
| Series (2) |
| GSE116279 |
Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis [RNA-Seq III] |
| GSE116296 |
Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis |
|
| Relations |
| BioSample |
SAMN09491317 |
