|
| Status |
Public on May 15, 2020 |
| Title |
ChIP_SEQ_PECs_p50ko_UT |
| Sample type |
SRA |
| |
|
| Source name |
Peritoneal Exudate Macrophages (PEC)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C56Bl6/J
genotype: p50ko
cell type: Peritoneal Exudate Macrophages (PEC)
treatment: Untreated
chip antibody: anti-STAT1 (Santa Cruz, sc-592)
|
| Treatment protocol |
50 million PECs were plated in RPMI1640 containing 10% FBS and left untreated or stimulated with 200U/ml interferon gamma for 4 hours.
|
| Growth protocol |
PEC were harvested from mice injected with 500 L of 3% (wt/vol) thioglycollate medium (Difco) 4 days before isolation
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-Seq library preparation was performed as described in Ostuni et al., Cell 2013
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
PECs_p50ko_UT_vs_INPUT_peaks.bed
|
| Data processing |
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome using Bowtie 4.1.2 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS 1.4 (PMID 18798982) with default parameters and bw=100. Each IP was compared to input DNA derived from BMDM (GSM487453).
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *_peaks.bed, list of the peaks called by MACS
|
| |
|
| Submission date |
Jan 16, 2019 |
| Last update date |
May 15, 2020 |
| Contact name |
Viviana Piccolo |
| E-mail(s) |
[email protected]
|
| Organization name |
European Institute of Oncology (IEO)
|
| Department |
Department of Experimental Oncology
|
| Lab |
Gioacchino Natoli Lab
|
| Street address |
Via Adamello 16
|
| City |
Milano |
| State/province |
Milano |
| ZIP/Postal code |
20139 |
| Country |
Italy |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE84468 |
Tumor-derived prostaglandin E2 promotes p50 NF-κB-dependent differentiation of monocytic MDSC. |
|
| Relations |
| BioSample |
SAMN10756484 |
| SRA |
SRX5255297 |
