Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H2A.XS139ph

Cell type

Cell type Class
Blood
Cell type
GM09027A
NA
NA

Attributes by original data submitter

Sample

source_name
Lymphoblastoid
biomaterial_provider
CC
cell line
GM09027A
cell
Human B-lyphocytes
treatment
untreated
chip antibody
g-H2AX (Active Motif, 39118)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde for 15 min, and crosslinking was stopped with glycine. Cells were then lysed and whole cell lysates were sonicated to obtain DNA fragment sizes <500bp. gamma-H2AX antibody was then used to isolate DNA bound to gamma-H2AX. Libraries were prepared according to Illumina's TruSeq® ChIP Sample Preparation Guide (Part# 15023092 Rev. B) . Briefly, ChIP-enriched DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation, DNA fragments with sizes of 250-300 bp were selected on 2% agarose gels and were PCR amplified with Illumina primers for 18 cycles. The libraries were captured on an Illumina flow cell for cluster generation and sequenced on HiSeq 2500 following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
90592837
Reads aligned (%)
97.9
Duplicates removed (%)
8.3
Number of peaks
2571 (qval < 1E-05)

hg19

Number of total reads
90592837
Reads aligned (%)
93.6
Duplicates removed (%)
8.5
Number of peaks
927 (qval < 1E-05)

Base call quality data from DBCLS SRA