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
Human breast cancer cell line
cell line
MCF-7
condition
control
procedure
ChIP-seq
antibody
anti-ERa (SC-543; Santa Cruz)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin Immunoprecipitation was performed as described (Zwart W et al. EMBO J. 2011, 30:4764-76) : 10ug of antibody was used, with 100ml of Protein A magnetic beads. Antibody used was raised to detect Estrogen Receptor alpha (HC-20, SC-543; Santa Cruz). DNA was amplified as described (Ross-Innes CS et al. Nature 2012;481(7381):389-93). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
28573711
Reads aligned (%)
87.0
Duplicates removed (%)
7.6
Number of peaks
29360 (qval < 1E-05)

hg38

Number of total reads
28573711
Reads aligned (%)
88.8
Duplicates removed (%)
6.2
Number of peaks
29494 (qval < 1E-05)

Base call quality data from DBCLS SRA