Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ESR1

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
Mcf7_ER ChIP
cell line
Mcf7
chip antibody
Santa Cruz HC-20 and the monoclonal ER Ab10 antibodies

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP extraction done 1% SDS lysis buffer followed by Immunoprecipitation in a low detergent buffer (dilution 1/10 of original lysis buffer) using lab protocol on a sciclone ngs liquid handler with lab developed protocols with Santa Cruz HC-20 and the monoclonal ER Ab10 antibodies libraries generated using standard protocol, end repair, AT overhang, oligo ligation, pippin prep size selection, PCR amplification, pippin prep size selection, Ethanol salt precipitation

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
80975256
Reads aligned (%)
25.6
Duplicates removed (%)
61.8
Number of peaks
77526 (qval < 1E-05)

hg38

Number of total reads
80975256
Reads aligned (%)
25.7
Duplicates removed (%)
61.7
Number of peaks
77625 (qval < 1E-05)

Base call quality data from DBCLS SRA