|
| Status |
Public on Oct 31, 2023 |
| Title |
ChIP-Seq CardiacProgenitor_WT_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
PGP1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PGP1
cell type: iPSC-derived Cardiac Progenitor
genotype: wild type
treatment: H2Bub1
|
| Treatment protocol |
N/A
|
| Growth protocol |
iPSCs were maintained in feeder-free conditions on matrigel coated plates and fed mTESR. Cardiomyocytes were made according to Lian et al., 2012.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
frozen tissue were ground, DNA was sonicated on Bioruptor Pico sonicator, and precipitated with H2Bub1 antibody
Illumina protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CardiacProgenitor_WT_rep1
|
| Data processing |
trimmed reads using FASTX-Toolkit
aligned using BWA Mem algorithm
peaks identified using Model-based Analysis of ChIP-seq (MACS) (version 2.1.1.20160309) using the BAMPE option, the nomodel option, and the broad option (with a cutoff of 0.2)
differentially bound sites were obtained using the "DiffBind" package in R, with a maximum q value of 0.05 and a minimum absolute fold change of 1.5
nearest genes to the differentially bound sites were obtained using the "ChIPseeker" package in R
Assembly: hg38
Supplementary files format and content: bigwig files were generated using fold enrichments as scores
|
| |
|
| Submission date |
Oct 27, 2023 |
| Last update date |
Oct 31, 2023 |
| Contact name |
Syndi Barish |
| Organization name |
Harvard Medical School
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE246410 |
The H2Bub1-deposition complex is required for human and mouse cardiogenesis (ChIP-Seq) |
| GSE246413 |
The H2Bub1-deposition complex is required for human and mouse cardiogenesis |
|
| Relations |
| BioSample |
SAMN38022207 |
| SRA |
SRX22253732 |
