Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

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-5352:U2OS_dex_CTCF_ChIPseq
Broker name
ArrayExpress
Description
Protocols: Cells were cultured to confluency and treated for 90 min with 1μM dexamethasone. Chromatin was fixed at room temperature for 3 min with 1% formaldehyde. After quenching with 200mM glycine, the cells were sonicated using a Bioruptur (Diagenode). ChIP-assays targeting CTCF were essentially done as previously described (Meijsing, S.H., et al., Science, 2009. 324(5925): p. 407-10.) using a polyclonal CTCF-antibody (Active Motif, Cat. No. 61311) except that a modified RIPA wash buffer (50 mM HEPES-KOH, 1 mM EDTA, 1% NP40, 0.7% Na-deoxycholat, 500 mM LiCl, pH 7.5) was used.
ENA checklist
ERC000011
INSDC center alias
Abt Vingron Max Planck Institute for Molecular Genetics
INSDC center name
Abt Vingron Max Planck Institute for Molecular Genetics
INSDC first public
2018-04-12T17:02:49Z
INSDC last update
2016-12-20T11:53:31Z
INSDC status
public
SRA accession
ERS1482085
Sample Name
ERS1482085
Title
U2OS_dex_CTCF_ChIPseq
cell_line
U2OS
genotype
wild type genotype
organism
Homo sapiens
stimulus
dexamethasone

Sequenced DNA Library

library_name
U2OS_dex_CTCF_ChIPseq_p
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cultured to confluency and treated for 90 min with 1μM dexamethasone. Chromatin was fixed at room temperature for 3 min with 1% formaldehyde. After quenching with 200mM glycine, the cells were sonicated using a Bioruptur (Diagenode). ChIP-assays targeting CTCF were essentially done as previously described (Meijsing, S.H., et al., Science, 2009. 324(5925): p. 407-10.) using a polyclonal CTCF-antibody (Active Motif, Cat. No. 61311) except that a modified RIPA wash buffer (50 mM HEPES-KOH, 1 mM EDTA, 1% NP40, 0.7% Na-deoxycholat, 500 mM LiCl, pH 7.5) was used.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
38157304
Reads aligned (%)
97.8
Duplicates removed (%)
42.1
Number of peaks
37358 (qval < 1E-05)

hg38

Number of total reads
38157304
Reads aligned (%)
98.4
Duplicates removed (%)
41.4
Number of peaks
37932 (qval < 1E-05)

Base call quality data from DBCLS SRA