Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Digestive tract
Cell type
GIST48
NA
NA

Attributes by original data submitter

Sample

source_name
GIST48 Cells
chip antibody
H3K4me3, Abcam, ab8580
tissue
GIST cell line
cell line
GIST48

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
GIST48 cells were crosslinked for 15-minutes in 1% parformaldehyde. Cells were lysed and chromatin sheared using bioruptor. Sheared chromatin was incubated with anti-rabbit IgG dynabeads pre-conjugated with antibody, washed, eluted, reverse cross-linked, and purified. Purified ChIP DNA was blunt-ended, ligated to Solexa adaptors, amplified with 18-cycles of PCR, and sequenced on Solexa Genome Analyzer.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg38

Number of total reads
52630997
Reads aligned (%)
71.2
Duplicates removed (%)
29.3
Number of peaks
36300 (qval < 1E-05)

hg19

Number of total reads
52630997
Reads aligned (%)
70.8
Duplicates removed (%)
30.1
Number of peaks
37318 (qval < 1E-05)

Base call quality data from DBCLS SRA