Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

ENA first public
2012-11-20
ENA last update
2018-03-08
External Id
SAMEA1573843
INSDC center alias
Cancer Research UK
INSDC center name
Cancer Research UK
INSDC first public
2012-11-20T17:02:01Z
INSDC last update
2018-03-08T16:09:00Z
INSDC status
public
Submitter Id
E-MTAB-1368:Jc11_2
bio source type
frozen
biosourceprovider
ATCC
broker name
ArrayExpress
cell line
MCF-7
cell type
breast epithelial
common name
human
sample name
E-MTAB-1368:Jc11_2
sex
female

Sequenced DNA Library

library_name
Jc11_2
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The antibodies used were anti-ER (sc-543) from Santa Cruz Biotechnologies, RNA Pol II (ab5131) and FoxA1 (ab5089) from Abcam. At least four 15 cm dishes of cells were used per chromatin immunoprecipitation (ChIP) and samples were processed according to standard ChIP procedures. 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 II

hg38

Number of total reads
16754938
Reads aligned (%)
38.1
Duplicates removed (%)
31.6
Number of peaks
2679 (qval < 1E-05)

hg19

Number of total reads
16754938
Reads aligned (%)
37.7
Duplicates removed (%)
32.5
Number of peaks
2694 (qval < 1E-05)

Base call quality data from DBCLS SRA