|
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 |