Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
FOXA1

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
Sample_DMSO_ET_KO_FOXA1
cell line
MCF-7
cell line
Breast Cancer Cells
genotype
ARID1A KO
sgguide
sgARID1A-2
chip-antibody
FOXA1 (Abcam, ab23738)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The fixed cells were lysed in SDS buffer and the chromatin was sheared by Covaris sonication. The sheared chromatin was incubated with the aforementioned antibodies and protein G-Dynabeads. The samples underwent decrosslinking, RNase and proteinase K treatment. DNA fragments were eluted using AMP Pure beads, library was prepared and samples were subjected to high-throughput sequencing using HiSeq 2000 platform (Illumina). 

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
24753316
Reads aligned (%)
98.3
Duplicates removed (%)
5.0
Number of peaks
2627 (qval < 1E-05)

hg19

Number of total reads
24753316
Reads aligned (%)
97.5
Duplicates removed (%)
6.1
Number of peaks
2814 (qval < 1E-05)

Base call quality data from DBCLS SRA