Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
POU2F1

Cell type

Cell type Class
Breast
Cell type
Mammary gland ductal carcinoma
NA
NA

Attributes by original data submitter

Sample

source_name
mammary gland ductal carcinoma
parental cell line
T-47D
esr1 genotype
WT
treatment
None
chip antibody
Anti-OCT1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Fixation was performed by treating cells with 1% formaldehyde for 10 minutes at room temperature. The cross-linking reaction was stopped with the addition of glycine to a final concentration of 125 mM. Cells were then washed with cold PBS and harvested via cell scraping in Farnham lysis buffer supplemented with protease inhibitors. Chromatin immunoprecipitation was performed as previously described (Reddy et al. Genome Research 2009) with either Anti-FLAG (Sigma-Aldrich M2) antibody that recognizes a FLAG tag on ESR1, Anti-CTCF (sc-5916, Santa Cruz Biotechnology), or Anti-OCT1 (A301-716A and A301-717A, Bethyl Laboratories Inc.) antibodies.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
40927748
Reads aligned (%)
93.6
Duplicates removed (%)
4.0
Number of peaks
20723 (qval < 1E-05)

hg38

Number of total reads
40927748
Reads aligned (%)
94.4
Duplicates removed (%)
3.6
Number of peaks
20790 (qval < 1E-05)

Base call quality data from DBCLS SRA