|
| Status |
Public on Oct 19, 2023 |
| Title |
HA_parental_H4K91Q_Input |
| Sample type |
SRA |
| |
|
| Source name |
mESCs
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cells
genotype: Stably expressing PiggyBAC_H4K91Q_3HA
chip antibody: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% paraformaldehyde for 5 minutes with gentle rotation and then quenched with 125 mM glycine for 5 minutes. After cell lysis, chromatin was sonicated using a Covaris E220. Genomic DNA was isolated after the immunoprecipitation of sonicated chromatin.
Libraries were generated using NEBNext Ultra II kits.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
ChIP-seq reads were aligned using Rsubread’s align method and predicted fragment lengths were calculated by the ChIPQC R Bioconductor package. Normalized, fragment extended signal bigWigs were created using the rtracklayer R Bioconductor package. Peak calls were made using the MACS2 software.
Assembly: mm10
Supplementary files format and content: bigwig files normalized to read depth
Supplementary files format and content: narrowPeak files generated by MACS2
|
| |
|
| Submission date |
May 03, 2023 |
| Last update date |
Oct 19, 2023 |
| Contact name |
Douglas Barrows |
| E-mail(s) |
dbarrows@rockefeller.edu
|
| Phone |
7749940981
|
| Organization name |
Rockefeller University
|
| Street address |
1230 York Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE231566 |
Altered chromatin occupancy of patient-associated H4 mutants misregulate neuronal differentiation [ChIP-seq] |
| GSE231567 |
Altered chromatin occupancy of patient-associated H4 mutants misregulate neuronal differentiation |
|
| Relations |
| BioSample |
SAMN34568132 |
| SRA |
SRX20209094 |
