Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Breast
Cell type
ZR-75-1
Primary Tissue
Breast
Tissue Diagnosis
Adenocarcinoma Ductal

Attributes by original data submitter

Sample

ENA first public
2011-12-16
ENA last update
2018-03-08
External Id
SAMEA1032048
INSDC center alias
CRUK-CRI
INSDC center name
CRUK-CRI
INSDC first public
2011-12-16T16:59:35Z
INSDC last update
2018-03-08T15:27:48Z
INSDC status
public
Submitter Id
E-MTAB-740:ZR-75-1_jc431
broker name
ArrayExpress
cell line
ZR-75-1
cell type
epithelial
common name
human
organism part
breast
sample name
E-MTAB-740:ZR-75-1_jc431
sex
female

Sequenced DNA Library

library_name
jc431
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
MCF-7 cells were grown in DMEM containing 10% heat-inactivated FBS, 2 mM L glutamine, 50 U/ml penicillin and 50 _g/ml streptomycin and ZR75-1 cells were grown in RPMI containing 10% heat-inactivated FBS, 2 mM L glutamine, 50 U/ml penicillin and 50 _g/ml streptomycin. MCF10A cells were maintained in Mammary Epithelium Cell Growth Medium bullet kit (Clonetics, Lonza, MD, USA), containing mammary epithelium basal medium supplemented with bovine pituitary extract, human epidermal growth factor, hydrocortisone and GA-1000 (Gentamicin Sulfate and Amphotericin-B). To hormone deprive the cells, cells were grown in steroid-depleted medium for three days and then treated with vehicle (ethanol), 100 nM estrogen or 1 uM tamoxifen for 45 minutes or three hours. The antibodies used were anti-ER (sc-543) from Santa Cruz Biotechnologies and anti-CTCF (07-729) from Millipore. At least four 15 cm dishes of cells were used per chromatin immunoprecipitation (ChIP) and samples were processed according to standard ChIP procedures. The CTCF ChIP samples were performed as described in Carroll, 2005, Cell and the ER ChIP samples were performed as described in Schmidt, 2009, Methods. The immunoprecipitated DNA was subsequently amplified as previously described for Illumina sequencing Schmidt, 2009, Methods.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
27750131
Reads aligned (%)
99.1
Duplicates removed (%)
15.2
Number of peaks
56990 (qval < 1E-05)

hg19

Number of total reads
27750131
Reads aligned (%)
98.6
Duplicates removed (%)
15.9
Number of peaks
56950 (qval < 1E-05)

Base call quality data from DBCLS SRA