|
| Status |
Public on Aug 01, 2013 |
| Title |
H3K9me3_ChIPSeq_Prox |
| Sample type |
SRA |
| |
|
| Source name |
proximal colon crypts, H3K9me3 ChIP
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain/background: Sprague Dawley
age: 14 weeks
tissue: proximal colon crypts
chip antibody: H3K9me3 (Abcam, ab8898)
|
| Growth protocol |
Samples from 7 rats, 14 weeks old, were pooled together for each sequencing run.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Colonic crypts were isolated from distal and proximal regions of the colon. Lysate from nuclei of colonic crypt cells were ChIPed for histone modifications and RNA Polymerase II.
ChIP libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava software used for basecalling.
ChIP-Seq reads were aligned to the Baylor 3.4/rn4 genome assembly. Sequence read numbers were summed into 200 bp non-overlapping windows with read position shifted 75 bp to represent the DNA fragment center. Genomic regions with histone modification marks were identified using SICER. The nearest gene to each island, i.e., within 2 kb of the island, was identified using closestBed from the BEDTools software suite and the refGene table downloaded from the UCSC Genome Browser for the Baylor 3.4/rn4 assembly.
Genome_build: RGSC_v3.4
Supplementary_files_format_and_content: ChIP-Seq wig files were generated using SICER, scores represent peak intensity.
|
| |
|
| Submission date |
Jul 31, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Karen Triff |
| E-mail(s) |
ktriff@tamu.edu
|
| Phone |
979 845 0448
|
| Organization name |
Texas A&M University
|
| Street address |
321 Kleberg Center, 5523 TAMU
|
| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77840 |
| Country |
USA |
| |
|
| Platform ID |
GPL14844 |
| Series (1) |
| GSE49389 |
Genome-wide analysis of the rat colon reveals site-specific differences in histone modifications and proto-oncogene expression |
|
| Relations |
| BioSample |
SAMN02298417 |
| SRA |
SRX330076 |
