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
MCF-7
cell line
MCF-7
treatment
100nM estradiol 40 mins
antibody
ER (Santa Cruz, sc-542)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
To achieve high temporal resolution, ChIP crosslinking concentration of formaldehyde was 2% and crosslinking was quenched after 1 minute with 250mM glycine. The ER antibody we used for IP was Santa Cruz: sc-542. The ends of the ChIP DNA were blunted and phosphorylated in 1X END Repair Buffer (Epicentre Biotechnologies, #ER0720), 250nM dNTPs, 1mM ATP, and 1X END-IT enzyme mix (Epicentre Biotechnologies, #ER0720) for 45 minutes. An A overhang was achieved in 1xNEB2 buffer, 200nM dATP (Invitrogen), 3units of Klenow (3¢-5¢ exo-) 5U/ml (from New England BioLabs), in 50ul volume for 30 minutes. 10nM of adapter was ligated to the DNA in 1X ligation buffer, 5ml (3000units) of UltraPure Ligase from enzymatics (Enzymatics T4 DNA Ligase #L603-HC-L) in a total volume of 50ul. Thirteen cycles of PCR with Phusion polymerase were performed to acquire the final library.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
26130460
Reads aligned (%)
15.8
Duplicates removed (%)
48.6
Number of peaks
4573 (qval < 1E-05)

hg38

Number of total reads
26130460
Reads aligned (%)
16.2
Duplicates removed (%)
47.6
Number of peaks
4501 (qval < 1E-05)

Base call quality data from DBCLS SRA