|
| 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 |
