Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FOXA1

Cell type

Cell type Class
Breast
Cell type
T-47D
Primary Tissue
Breast
Tissue Diagnosis
Adenocarcinoma Ductal

Attributes by original data submitter

Sample

source_name
Breast Cancer Cell
cell line
T47D
passages
5 to 10
chip-antibody
FOXA1 (ab5089) Abcam

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were lysed and sonicated leading to a DNA average size of 200bp. Protein G dynabeads were pre-incubated with 5μg of ER alpha (sc-543) or FOXA1 (ab5089) with pre cleared chromatin. The complexes were reverse cross-linked and DNA was purified. ChIP-seq libraries were prepared using 10 ng of DNA and Illumina's TruSeq ChIP sample prep.Libraries were validated using the Agient Technologies 2100 Bioanalyzer and Qubit high sensitivity assay.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
42188952
Reads aligned (%)
94.1
Duplicates removed (%)
7.4
Number of peaks
66203 (qval < 1E-05)

hg19

Number of total reads
42188952
Reads aligned (%)
93.5
Duplicates removed (%)
8.4
Number of peaks
66048 (qval < 1E-05)

Base call quality data from DBCLS SRA