Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

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
MCF-7 cells
cell type
MCF-7 cells
method
enriched with normal IgG

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, the FOXA1-complex components and their associated DNA were extracted from the sonicated nuclei and isolated with antibody. For ChIP-seq, 10 ng of ChIP DNA was end polished with T4 DNA polymerase and kinase. An 'A' base was added to the polished DNA fragments, followed by the Qiaquick column clean up. Solexa adaptors were ligated to the ChIP DNA fragments and enriched by 15 cycles of PCR amplification. 200-300 bp size fractions were selectively isolated from the 1% agarose gel and eluted by the Qiagen gel extraction kit. The extracted DNA was quantified by picogreen assay and subjected to HiSeq2000 sequencing according to the manufacturer’s instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
25932864
Reads aligned (%)
97.1
Duplicates removed (%)
5.4
Number of peaks
714 (qval < 1E-05)

hg19

Number of total reads
25932864
Reads aligned (%)
96.4
Duplicates removed (%)
6.9
Number of peaks
858 (qval < 1E-05)

Base call quality data from DBCLS SRA