|
Status |
Public on Apr 11, 2013 |
Title |
Chop-/- Tm-RNA-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 genotype/variation: Chop-/- 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 |
total RNA |
Extraction protocol |
unknown
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina Genome Analyzer |
|
|
Description |
CHOP KO Treatment
|
Data processing |
ERANGE was used to create .rds database files and then wig files with -raw option turned on. ChIP-Seq peaks were identified using ERANG with default settings rpkm files: mm9
|
|
|
Submission date |
Feb 09, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Maureen A Sartor |
E-mail(s) |
sartorma@med.umich.edu, sartorma@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 |
SRA |
SRX119357 |
BioSample |
SAMN00787462 |