Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Digestive tract
Cell type
Colon
NA
NA

Attributes by original data submitter

Sample

source_name
male_WT_HF.input
strain background
C57BL/6
genotype/variation
wild type
gender
male
cell type
colon epithelial cells
treatment
high-fat diet
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Colonic epithelial cells were isolated as previously described (Roediger et al, 1979, Gut, 20: 484-488). Cells were treated with 1% formaldehyde in PBS for 10 min at room temperature. Cross-linking was terminated by addition of glycine. The cells were spun down and rinsed with ice-cold PBS two times. The cell lysates were sonicated using a Bioruptor (Diagenode) to generate 150–350 bp fragments for immunoprecipitation. h3k27ac antibody (Active Motif, cat no. 39133) was used for ChIP. Libraries were prepared using TruSeq™ RNA Sample Preparation kit (Illumina) following the manufacturer’s instructions. Illumina TruSeq RNA Sample Preparation Kit v1 was used for library preparation.

Sequencing Platform

instrument_model
Illumina MiSeq

mm10

Number of total reads
20602700
Reads aligned (%)
98.6
Duplicates removed (%)
12.7
Number of peaks
408 (qval < 1E-05)

mm9

Number of total reads
20602700
Reads aligned (%)
98.3
Duplicates removed (%)
12.8
Number of peaks
455 (qval < 1E-05)

Base call quality data from DBCLS SRA