Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H2A.XS139ph

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
U2OS osteosarcoma cells
cell line
U2OS
cell type
Osteosarcoma cells
genotype/variation
RB1+/-
chip antibody
gammaH2AX (clone JBW301, EMD Millipore)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was conducted according to protocols adapted from Cecchini et al., 2014. Briefly, asynchronously cycling cells were fixed in 2mM ethylene glycol bis(succinimidyl succinate) (EGS) in 1X PBS followed by 1% formaldehyde. Fixing reactions were neutralized with 0.125M glycine. Cross-linked chromatin was sonicated so most chromatin was ≤400 bp. Sheared chromatin was then normalized between experimental groups and pre-cleared with protein G Dynabeads and IgG. Pre-cleared chromatin was then incubated with protein G Dynabeads and ChIP antibodies to immunoprecipitate proteins. DNA was isolated for library preparation, and 20 replicates per genotype for γH2AX ChIP-Seq were pooled to achieve DNA yield required for library preparation. Libraries were constructed according to the NEBNext Ultra II DNA library prep kit.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
77510139
Reads aligned (%)
76.5
Duplicates removed (%)
8.3
Number of peaks
1583 (qval < 1E-05)

hg19

Number of total reads
77510139
Reads aligned (%)
75.8
Duplicates removed (%)
10.2
Number of peaks
1394 (qval < 1E-05)

Base call quality data from DBCLS SRA