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Sample GSM3565022 Query DataSets for GSM3565022
Status Public on May 15, 2020
Title ChIP_SEQ_PECs_p50ko_IFNg
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: Interferon-treated
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_IFNg_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
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.
BioSample SAMN10756483
SRA SRX5255298

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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