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Sample GSM3565019 Query DataSets for GSM3565019
Status Public on May 15, 2020
Title ChIP_SEQ_PECs_WT
Sample type SRA
 
Source name Peritoneal Exudate Macrophages (PEC)
Organism Mus musculus
Characteristics strain: C56Bl6/J
genotype: wild type
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_WT_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) viviana.piccolo@ieo.it
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 SAMN10756485
SRA SRX5255295

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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