|
| Status |
Public on Oct 26, 2021 |
| Title |
WT_D4_highBMP4_Rep3_ATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
WT_D4_highBMP4
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse ES cell derived cardiac mesoderm
genotype: Brg1-3xFLAG
timepoint: Day 4
|
| Treatment protocol |
ES cells were differentiated to cardiac precursor or cardiomyocytes before harvested for ATACseq
|
| Growth protocol |
Es cell were differentiated following Katman et al., 2011 and Wamstad et al., 2012 papers
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We followed Corces et al., 2017 paper to perform ATACSeq
Lysed nuclei were tagmented at 37C for 45 mins for D4, and D6 samples and 3hrs for D10 samples, before purified and PCR amplified with Ad1 and Ad2 primers (corces et al., 2017)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Libraries were sequenced on Nextseq 500
Raw sequencing reads were converted to FASTQ files using bcl2fastq
Reads were aligned to mm9 using the bowtie
Genome_build: mm9
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
May 09, 2020 |
| Last update date |
Oct 26, 2021 |
| Contact name |
Benoit Bruneau |
| E-mail(s) |
[email protected]
|
| 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 |
GPL19057 |
| Series (2) |
| GSE150180 |
ATACseq of WT and BRM KO cells at D4, D6 and D10 of cardiac differentiation |
| GSE150186 |
Brahma safeguards canalization of cardiac mesoderm differentiation |
|
| Relations |
| BioSample |
SAMN14860232 |
| SRA |
SRX8297696 |
