|
| Status |
Public on Oct 26, 2021 |
| Title |
D6_WT_REST_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
mouse ES cell derived cardiac precursors
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Brm-3xFLAG
timepoint: Day 6
antibody: REST
|
| Treatment protocol |
mouse ESC lines were differentiated to cardiac mesoderma dn cardiac precursors using the Kattman et al 2011 Cardiomyocyte Differentiation protocol.
|
| Growth protocol |
mouse ESCs were maintained in DMEM media supplemented with LIF and serum
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed, lysates were clarified and incubated with REST antibody(Sigma, 17-10456) for O/N, captured with IgG coated magnetic beads, washed, and ChIPed DNA eluted. Protein-DNA complexes were reverse crosslinked, proteinase digested and ampure bead purified
To prepare libraries DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3 to 5 exo minus) and dATP and ligated of Illumina adapters. Adapter ligated DNA was PCR amplified with Illumina primers for 14 cycles and library fragments of 200 - 500bp bp were band isolated from an agarose e-gel (invitrogen). The purified libraries were quantified, and libraries were pooled before sequencing on Illumina NextSeq 500 system
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Libraries were sequenced on Nextseq 500 using V75 high poutput kit
Raw sequencing reads were converted to FASTQ files using bcl2fastq
Reads were aligned to mm9 using Bowtie2
Genome_build: mm9
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Jun 12, 2021 |
| 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) |
| GSE150186 |
Brahma safeguards canalization of cardiac mesoderm differentiation |
| GSE177481 |
Chromatin remodeler Brahma safeguards canalization in cardiac mesoderm differentiation [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN19679073 |
| SRA |
SRX11127141 |
