Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

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

ENA first public
2014-10-10
ENA last update
2018-03-08
ENA-CHECKLIST
ERC000011
External Id
SAMEA2228011
INSDC center alias
University of California, Riverside
INSDC center name
University of California, Riverside
INSDC first public
2014-10-10T17:01:08Z
INSDC last update
2018-03-08T16:52:15Z
INSDC status
public
Submitter Id
E-MTAB-1988:cell_culture_UV_8hr_IN
broker name
ArrayExpress
cell line
U2OS
common name
human
sample name
E-MTAB-1988:cell_culture_UV_8hr_IN

Sequenced DNA Library

library_name
Extract_UV8hr_IN
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
U2OS cells were maintained in McCoys 5A media (Invitrogen) 20 J/m2 UVC irradiation treatment for 0, 8 or 16 hr Formaldehyde Cross-linking and chromatin immunoprecipitation assays for this experiment were performed as described by Boyd and Farnham (MCB 29:8389-8299) and Y. Shang et al. (Cell 103:843-852) with some modifications. Formaldehyde concentration used was 1% for 10 minutes. Antibody used for immunoprecipitation was Rabbit p53 (Santa Cruz FL-393) Purified ChIP DNA was used to prepare Illumina multiplexed sequencing libraries. Libraries for Illumina sequencing were prepared following the Illumina-compatible NEXTflex ChIP-Seq Kit (Bioo Scientific).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
25966683
Reads aligned (%)
99.1
Duplicates removed (%)
16.4
Number of peaks
921 (qval < 1E-05)

hg19

Number of total reads
25966683
Reads aligned (%)
98.2
Duplicates removed (%)
18.2
Number of peaks
988 (qval < 1E-05)

Base call quality data from DBCLS SRA