Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H2A.X

Cell type

Cell type Class
Bone
Cell type
U2OS
Tissue
bone
Lineage
mesoderm
Description
osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590)

Attributes by original data submitter

Sample

source_name
ChIP-Seq of γH2AX in WT cells
cell line
U2OS
genotype/variation
WT
treatment
untreated
antibody
Abgent ; AJ1351a

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were lysed in the sonication buffer (50mM Hepes pH8, 140mM NaCl, 1mM EDTA, 1% Triton, 0,1% sodium deoxycholate, 0.5% SDS). Chromatin was treated with protease K followed by Phenol/chloroform extraction and ethanol precipitation. NeoPrep Illumina system for automatic NGS library preparation using TruSeq Nano DNA Library Prep Kit for NeoPrep (Illumina)_Sequencer:HiSeq 4000 (1x51 nt).

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
18918996
Reads aligned (%)
92.7
Duplicates removed (%)
3.3
Number of peaks
527 (qval < 1E-05)

hg19

Number of total reads
18918996
Reads aligned (%)
92.3
Duplicates removed (%)
3.8
Number of peaks
502 (qval < 1E-05)

Base call quality data from DBCLS SRA