Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Lung
Cell type
A549
Primary Tissue
Lung
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

ENA first public
2018-04-12
ENA last update
2016-12-20
ENA-CHECKLIST
ERC000011
External Id
SAMEA32977168
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
Submitter Id
E-MTAB-5352:A549_dex_input
broker name
ArrayExpress
cell line
A549
common name
human
genotype
wild type genotype
sample name
E-MTAB-5352:A549_dex_input
stimulus
dexamethasone

Sequenced DNA Library

library_name
A549_dex_input_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

hg38

Number of total reads
48360185
Reads aligned (%)
99.4
Duplicates removed (%)
26.5
Number of peaks
745 (qval < 1E-05)

hg19

Number of total reads
48360185
Reads aligned (%)
98.8
Duplicates removed (%)
26.9
Number of peaks
440 (qval < 1E-05)

Base call quality data from DBCLS SRA