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
2014-02-10
ENA last update
2018-03-08
ENA-CHECKLIST
ERC000011
External Id
SAMEA2242754
INSDC center alias
The Nuffield Department of Medicine, University of Oxford, Oxford, UK
INSDC center name
The Nuffield Department of Medicine, University of Oxford, Oxford, UK
INSDC first public
2014-02-10T17:00:48Z
INSDC last update
2018-03-08T16:52:56Z
INSDC status
public
Submitter Id
E-MTAB-1995:cell_culture_Hypoxia_RNA-Pol2
broker name
ArrayExpress
cell line
MCF-7
common name
human
sample name
E-MTAB-1995:cell_culture_Hypoxia_RNA-Pol2

Sequenced DNA Library

library_name
cell_culture_Hypoxia_RNA-Pol2
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
MCF-7 cells were cultured in Dulbeccos modified Eagle's medium 'DMEM' (Invitrogen). Media were supplemented with and 10% Fetal Bovine Serum (FBS) (Sigma-Aldrich). Cells were incubated for 24 hours in an In vivo2 Hypoxia Work Station (Ruskin Technologies) in an atmosphere of either normoxia (21% oxygen) or hypoxia (0.5% oxygen). Chromatin immunoprecipitation was performed as described in the paper. Libraries were prepared using the Illumina ChIP-Seq kit.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg38

Number of total reads
32545838
Reads aligned (%)
99.0
Duplicates removed (%)
40.5
Number of peaks
19058 (qval < 1E-05)

hg19

Number of total reads
32545838
Reads aligned (%)
98.5
Duplicates removed (%)
41.2
Number of peaks
19037 (qval < 1E-05)

Base call quality data from DBCLS SRA