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
tissuetype
Normal
chip antibody
H3K4me1
reads length
101

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 pieces (~ 5 ml by apparent volume). Tissue pieces were fixed in 1% formaldehyde/TBSE buffer for 10 minutes (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 transferred into Lysonator cartridges (SG Microlab Devices, Singapore). Tissues were dissociated following the manufacturer’s guidelines (4K Hz for 3 min), and taken directly to the lysis step in the Nano ChIP assay. Dissociated tissues were lysed in 200 ml of lysis buffer and divided into two 1.5 ml tubes for sonication (6 min) using a Bioruptor (Diagenode). 5 CHiPs were performed on individual chromatin preparations using the following antibodies: H3K4me3 (07-473, Millipore); H3K4me1 (ab8895, Abcam); H3K27ac (ab4729, Abcam); H3K36me3 (ab9050, Abcam); H3K27me3 (07-449, Millipore). Amplified DNA was digested with BpmI (New EngliandBiolabs), ligated to a 2ndBpmI adaptor and digested again to trim the WGA primer regions and semi-random priming ends. 15 ng of amplified DNA was used for each Illumina sequencing library using the ChIPseq kit (Illumina). Each library was sequenced on one lane of HiSeq2000 to obtain either 36- or 101-base single reads.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
112190461
Reads aligned (%)
84.1
Duplicates removed (%)
37.3
Number of peaks
115443 (qval < 1E-05)

hg19

Number of total reads
112190461
Reads aligned (%)
83.8
Duplicates removed (%)
37.6
Number of peaks
114842 (qval < 1E-05)

Base call quality data from DBCLS SRA