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 breast cancer cells
cell type
Human breast adenocarcinoma
cell line
MCF7
passages
20-30
chip-seq antibody
ERα HC-20 (sc543 from Santa Cruz, 1 µg used)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% Formaldehyde for 10 or 20 minutes and quenched with 125 mM Glycine. The nuclear pellets were sonicated to the fragment range of 200-400 bp. Sonicated extracts were incubated with specific antibodies at 4˚C overnight and ChIP-immune complexes were pulled down using Protein A sepharose. Library preparations were done using NEBnext Ultra DNA library preparation kit according to the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
14674808
Reads aligned (%)
29.1
Duplicates removed (%)
3.3
Number of peaks
682 (qval < 1E-05)

hg38

Number of total reads
14674808
Reads aligned (%)
29.7
Duplicates removed (%)
2.2
Number of peaks
655 (qval < 1E-05)

Base call quality data from DBCLS SRA