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Sample GSM873427 Query DataSets for GSM873427
Status Public on Apr 11, 2013
Title Atf4-/ Tm ChIP-seq
Sample type SRA
 
Source name Mouse embronic fibroblast
Organism Mus musculus
Characteristics cell type: Mouse embryonic fibroblast
developmental stage: 11.5-12.5 days
strain: C57BL/6
antibody: anti-ATF4
genotype/variation: Atf4-/-
treatment: Tunicamycin
Treatment protocol MEFs were treated with tunicamycin for 10hr. After treatment, chromatin immunoprecipitation or RNA isolation were performed.
Growth protocol Mouse embryonic fibroblast cells were rountinely subcultured in high-glucose DMEM supplemented with 10% FBS, Pen/Strep, NEAA (all invitorgen) on cell culture dishes.
Extracted molecule genomic DNA
Extraction protocol unknown
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description ATF4 KO ChIP-Seq Replicates
Data processing ERANGE was used to create .rds database files and then bedgraph files with -raw option turned on.
ChIP-Seq peaks were identified using ERANG with default settings
Genome Build:
run48_s_2.bedgraph: mm9
run58_s_5.bedgraph: mm9
run58_s_7.bedgraph: mm9
 
Submission date Feb 09, 2012
Last update date May 15, 2019
Contact name Maureen A Sartor
E-mail(s) sartorma@med.umich.edu
Organization name University of Michigan
Department Department of Computational Medicine and Bioinformatics
Lab Sartor
Street address 2017 Palmer Commons Bldg., 100 Washtenaw Ave
City Ann Arbor
State/province MI
ZIP/Postal code 48109-2218
Country USA
 
Platform ID GPL9185
Series (1)
GSE35681 ChIP-seq and mRNA-seq experiment to find the direct target genes of ATF4 and CHOP
Relations
Reanalyzed by GSE80791
SRA SRX119353
BioSample SAMN00787458

Supplementary file Size Download File type/resource
GSM873427_run48_s_2.bedgraph.gz 150.7 Mb (ftp)(http) BEDGRAPH
GSM873427_run58_s_5.bedgraph.gz 80.3 Mb (ftp)(http) BEDGRAPH
GSM873427_run58_s_7.bedgraph.gz 69.4 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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