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Series GSE35681 Query DataSets for GSE35681
Status Public on Apr 11, 2013
Title ChIP-seq and mRNA-seq experiment to find the direct target genes of ATF4 and CHOP
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary We report the direct target genes of ATF4 and CHOP in response to endoplasim reticulum stress through next generation sequencing. By obtaining genowide sequence from chromatin immunoprecipitated DNA with anti-CHOP and anit-ATF4, we identified direct binding sites of ATF4 and CHOP in promoter regions of their target genes in mouse embrynic fibroblasts (MEFs) in response to ER stress. In addition, we obtained list of genes which are differentially regulated in Atf4 or Chop-deficient MEFs compared to the wild-type MEFs in response to ER stress. We found that genes related with unfolded protein response and protein synthesis were directly regulated by ATF4 and CHOP. Through this observation, we conclude that main role of ATF4 and CHOP as transcription factors is to enhance mRNA translation in respone to ER stress. This sutdy provide new insight of genetic network of ATF4 and CHOP in response to ER stress.
Overall design For ChIP-seq, Chop+/+ and Chop-/- MEFs were treated with Tunicamycin, N-glycosylation inhibitor, to induce ER stress for 8hr. Atf4+/+ and Atf4-/- MEFs were also treated same condition for ChIP-Seq. For mRNA-seq, wild-type, Atf4-/-, and Chop-/- MEFs were treated with tunicamycin for 8hr for experiments.
Contributor(s) Kaufman RJ, Han J, Sartor MA
Citation(s) 23624402, 24894502, 29615789
Submission date Feb 09, 2012
Last update date May 15, 2019
Contact name Maureen A Sartor
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
Platforms (1)
GPL9185 Illumina Genome Analyzer (Mus musculus)
Samples (10)
GSM873424 Chop+/+ Tm ChIP-seq
GSM873425 Chop -/- Tm ChIP-seq
GSM873426 Atf4+/+ Tm ChIP-seq
SRA SRP010861
BioProject PRJNA152405

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Supplementary file Size Download File type/resource
GSE35681_RAW.tar 768.0 Mb (http)(custom) TAR (of BEDGRAPH, RPKM)
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Raw data are available in SRA
Processed data provided as supplementary file

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