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
mammary gland, adenocarcinoma
cell line
MCF-7
chip antibody
ERα (Santa Cruz Biotechnology; sc-534X, sc-7207X)
transfection
siERα

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked by adding 1% formaldehyde, immunoprecipitation was performed as described using antibodies against ERα. DNA purification was achieved with Phenol:Chloroform:IAA (25:24:1) according to the manufacturer's instructions. ChIP-Seq was performed using 10ng of immunoprecipitated DNA obtained from 240 μg of chromatin for each sample, followed by library amplification and Illumina sequencing.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg19

Number of total reads
49388965
Reads aligned (%)
67.1
Duplicates removed (%)
23.0
Number of peaks
1597 (qval < 1E-05)

hg38

Number of total reads
49388965
Reads aligned (%)
69.6
Duplicates removed (%)
20.9
Number of peaks
1632 (qval < 1E-05)

Base call quality data from DBCLS SRA