|
| Status |
Public on Jun 30, 2014 |
| Title |
HNF4A ChIPSeq DSS |
| Sample type |
SRA |
| |
|
| Source name |
colonic epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
antibody: HNF4A (ab41898, Abcam, lot # GR4841-13)
treatment: 3% DSS
|
| Treatment protocol |
3% DSS for 6 days or water only controls
|
| Growth protocol |
Adult mice, 2-4 months old
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Colonic epithelial scraping
Tru-seq Illumina Kit according to manufacturer's instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina CASAVA 1.8.2 for basecalling
ELAND mapping
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using MACS1.0, HNF4A ChIP-seq bed files generated using MACS2, H3K27ac Bed files were generated using NPS and BINOCh. The top 1000 scoring regions (indicating most dynamic chromatin between conditions) for each condition used for data analysis were retained in the bed file.
|
| |
|
| Submission date |
Nov 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael P Verzi |
| Organization name |
Rutgers, the State University of New Jersey
|
| Department |
Genetics
|
| Lab |
Verzi
|
| Street address |
145 Bevier Road
|
| City |
Piscataway |
| State/province |
NJ |
| ZIP/Postal code |
08854 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE52426 |
H3K27ac profiling in control and DSS-treated colonic epithelium |
|
| Relations |
| BioSample |
SAMN02404460 |
| SRA |
SRX378046 |
