SRX3923512
GSM3092501: JC4235 MCF-7 estrogen rep2 FOXA1; Homo sapiens; ChIP-Seq

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
MCF-7_estrogen_rep2_FOXA1
cell line
MCF7
cell type
breast cancer cell line
chip antibody
anti-FOXA1 (ab5089) Abcam
treatment
hormone-deprived cells treated with estrogen

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIPseq, Schmidt et al, 2009. PMID: 19275943 phenol chloroform isoamyl DNA extraction ChIPseq, Schmidt et al, 2009. PMID: 19275939

Sequencing Platform

instrument_model
Illumina HiSeq 4000

Where can I get the processing logs?

Read processing pipeline log

hg38

Number of total reads
43935747
Reads aligned (%)
99.3
Duplicates removed (%)
21.3
Number of peaks
22613 (qval < 1E-05)

hg19

Number of total reads
43935747
Reads aligned (%)
98.5
Duplicates removed (%)
22.3
Number of peaks
22507 (qval < 1E-05)

Base call quality data from DBCLS SRA