|
| Status |
Public on Apr 06, 2024 |
| Title |
WT_MEFs_IRF9_ChIP_Seq |
| Sample type |
SRA |
| |
|
| Source name |
MEFs
|
| Organism |
Mus musculus |
| Characteristics |
cell line: MEFs
cell type: Mouse embryonic fibroblasts
chip antibody: IRF9 (Millipore, #MABS1920)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA library prep kit following the manufacturer's protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5). In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
HOMER (v4.8) (http://homer.salk.edu/homer/) was used to process alignment files to generate normalized bedGraphs for the UCSC Genome Browser. ChIP-seq peaks for STAT1, STAT2, and IRF9 were found by using the findPeaks program in HOMER with the default parameters for option "-style factor" using the appropriate ChIP input experiments as background.
Differential peaks were called using getDifferentialPeaksReplicates.pl (Homer) comparing WT and Arid1a -/- groups for each ChIP.
Assembly: mm10
Supplementary files format and content: bedgraph, narrowPeak (except for Input sample)
|
| |
|
| Submission date |
Nov 11, 2022 |
| Last update date |
May 17, 2024 |
| Contact name |
Diana C. Hargreaves |
| E-mail(s) |
dhargreaves@salk.edu
|
| Organization name |
The Salk Institute for Biological Studies
|
| Street address |
10010 North Torrey Pines Road
|
| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (2) |
| GSE217805 |
ARID1A suppresses R-loop mediated STING-Type I Interferon pathway activation of anti-tumor immunity (ChIP-Seq) |
| GSE217807 |
ARID1A suppresses R-loop mediated STING-Type I Interferon pathway activation of anti-tumor immunity |
|
| Relations |
| BioSample |
SAMN31695052 |
| SRA |
SRX18239628 |
