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Sample GSM1198705 Query DataSets for GSM1198705
Status Public on Aug 01, 2013
Title H3K4me3_ChIPSeq_Prox
Sample type SRA
 
Source name proximal colon crypts, H3K4me3 ChIP
Organism Rattus norvegicus
Characteristics strain/background: Sprague Dawley
age: 14 weeks
tissue: proximal colon crypts
chip antibody: H3K4me3 (Abcam, ab1012)
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 SAMN02298420
SRA SRX330074

Supplementary file Size Download File type/resource
GSM1198705_Prox_H3K4me3_islands-min-score-100.bedgraph.gz 110.9 Kb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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