Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

Cell type Class
Digestive tract
Cell type
Gastric primary sample
NA
NA

Attributes by original data submitter

Sample

source_name
Gastric Primary Sample
tissue
Gastric Primary Sample
chip antibody
H3K4Me1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Fresh-frozen cancer and normal tissues were dissected using a razor blade in liquid nitrogen to obtain ~5mg sized piece for each ChIP. Tissue pieces were fixed in 1% formaldehyde/PBS buffer for 10 min at room temperature. Fixation was stopped by addition of glycine to a final concentration of 125 mM. Tissue pieces were washed 3 times with TBSE buffer, and wrapped tightly with foil. Foil wrapped tissue was snap frozen in liquid nitrogen for about 10 sec. The frozen tissue was immediately pulverized. Pelleted cells and pulverized tissues were lysed in 100 µl 1% SDS lysis buffer and sonicated to 300-500bp using a Bioruptor (Diagenode). ChIPs were performed using the following antibodies: H3K4me3 (07-473, Millipore); H3K4me1 (ab8895, Abcam); H3K27ac (ab4729, Abcam) using same chromatin preparation. Pelleted cells and pulverized tissues were lysed in 100 µl 1% SDS lysis buffer and sonicated to 300-500bp using a Bioruptor (Diagenode). ChIPs were performed using the following antibodies: H3K4me3 (07-473, Millipore); H3K4me1 (ab8895, Abcam); H3K27ac (ab4729, Abcam); H3K36me3 (ab9050, Abcam); H3K27me3 (07-449, Millipore), using same chromatin preparation.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
49813057
Reads aligned (%)
81.6
Duplicates removed (%)
18.1
Number of peaks
5268 (qval < 1E-05)

hg19

Number of total reads
49813057
Reads aligned (%)
81.2
Duplicates removed (%)
18.3
Number of peaks
4424 (qval < 1E-05)

Base call quality data from DBCLS SRA