Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Digestive tract
Cell type
Intestinal epithelial cells
NA
NA

Attributes by original data submitter

Sample

source_name
Ileal endoscopic biopsy
cell type
Intestinal epithelial cells
diagnosis
Newly-diagnosed Crohn's Disease
age
12-18 years
chip antibody
Histone H3 lysine 4 trimethylation

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Fresh formaldehyde was added to each IEC sample for a final concentration of 1% and mixed end over end at room temperature for 10min to crosslink proteins to DNA. Cells were lysed with a Triton X-100 and Igepal buffer (0.25% Triton C-100, 0.5% Igepal, 10% glycerol, 1mM EDTA, 140mM NaCl, 50mM Hepes). Nuclei were then washed and chromatin sheared in a 0.1%SDS in TE buffer using a S220 Covaris Sonicator to 150-500 bp size. Immunoprecipitation was carried out with a SX-8G IP-STAR robot and an antibody optimized for histone H3 lysine 4 trimethylation (H3K4me3) as described previously. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Sequencing was performed using Illumina HiSeq 2500.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
9511137
Reads aligned (%)
86.1
Duplicates removed (%)
50.0
Number of peaks
6804 (qval < 1E-05)

hg19

Number of total reads
9511137
Reads aligned (%)
85.6
Duplicates removed (%)
50.5
Number of peaks
6710 (qval < 1E-05)

Base call quality data from DBCLS SRA