Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

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

source_name
Breast Cancer Cell Line
cell line
MCF-7
treatment
Hypoxia
repeat
2
chip antibody
CTCF (#07-729, Millipore)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq: Cells were fixed with 1% formaldehyde and quenched with glycine (125mM). After washing, cells were lysed (0.5%SDS, 10mM EDTA, 50mM Tris-HCl pH 8.1) and sonicated (Diagenode Biorupter, Belgium). Chromatin was immunoprecipitated using antibodies indicated. Eluted chromatin was heated to reverse cross-linking, treated with proteinase-K, RNaseA and purified on a qiagen PCR pufircation column. Libraries were prepared using PrepX Complete ILMN DNA library kit (#400076, Wafergen) by the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics, Oxford, UK.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
22721971
Reads aligned (%)
88.2
Duplicates removed (%)
10.5
Number of peaks
45929 (qval < 1E-05)

hg38

Number of total reads
22721971
Reads aligned (%)
89.8
Duplicates removed (%)
9.4
Number of peaks
46195 (qval < 1E-05)

Base call quality data from DBCLS SRA