Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
XRCC4

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

Alias
E-MTAB-1241:XRCC4_2 ChIP
Broker name
ArrayExpress
CellLine
AsiSI-ER-U20S
Compound
4-hydroxytamoxifen
Description
Protocols: U20S AsiSI-ER cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with antibiotics and 10% FCS (Invitrogen) at 37 C under a humidified atmosphere with 5% CO2. Cells were treated with 300 nM 4OHT for 4 hours ChIP assays were carried out according the protocol described in (Iacovoni et al, 2010). Briefly, 200 ug of chromatin was subjected to immunoprecipitation using 2 ug of a gammaH2AX antibody (Epitomics 2212-1), XRCC4 (Abcam), or Rad51 (Santa Cruz). For ChIP against PolII-S2P (Abcam) 50 ug of chromatin was used, instead of 200 ug. After the washes the beads/chromatin complexes were re-suspended in 200 uL of TE buffer (Tris 10mM pH8, EDTA 0,5mM pH8) and were directly subjected to crosslink reversal in presence of 0,5% SDS overnight at 70 C. Following crosslink reversion, all immunoprecipitated DNA and input DNA were purified by phenol/chloroform, followed by DNA precipitation. DNA amount was quantified using the Quant-iTTM kit from Invitrogen. 10ng of DNA was next used for sequencing.
Dose
300 nanomolar
INSDC center alias
1 Universite de Toulouse ; UPS ; LBCMCP ; 118 route de Narbonne, 31062, Toulouse, France
INSDC center name
1 Universite de Toulouse ; UPS ; LBCMCP ; 118 route de Narbonne, 31062, Toulouse, France
INSDC first public
2014-03-22T17:00:38Z
INSDC last update
2018-03-08T16:09:24Z
INSDC status
public
SRA accession
ERS195674
Sample Name
ERS195674
Title
XRCC4_2 ChIP

Sequenced DNA Library

library_name
XRCC4_2 ChIP
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP assays were carried out according the protocol described in (Iacovoni et al, 2010). Briefly, 200 ug of chromatin was subjected to immunoprecipitation using 2 ug of a gammaH2AX antibody (Epitomics 2212-1), XRCC4 (Abcam), or Rad51 (Santa Cruz). For ChIP against PolII-S2P (Abcam) 50 ug of chromatin was used, instead of 200 ug. After the washes the beads/chromatin complexes were re-suspended in 200 uL of TE buffer (Tris 10mM pH8, EDTA 0,5mM pH8) and were directly subjected to crosslink reversal in presence of 0,5% SDS overnight at 70 C. Following crosslink reversion, all immunoprecipitated DNA and input DNA were purified by phenol/chloroform, followed by DNA precipitation. DNA amount was quantified using the Quant-iTTM kit from Invitrogen. 10ng of DNA was next used for sequencing.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
32349481
Reads aligned (%)
26.4
Duplicates removed (%)
12.2
Number of peaks
6929 (qval < 1E-05)

hg38

Number of total reads
32349481
Reads aligned (%)
26.7
Duplicates removed (%)
11.5
Number of peaks
6674 (qval < 1E-05)

Base call quality data from DBCLS SRA