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
ER alpha ChIP-seq on MCF7 cell stimulated with Estrogen + 1,6-Hexanediol
biomaterial_provider
ATCC
cell line
MCF7
chip antibody
Santacruz biotechnology (HC-20)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, samples were fixed for 8 minutes with 1% formaldehyde. Fixation was stopped by adding Glycine (0.125M). Chromatin DNA was sheared to 200–500 bp size by sonication. Soluble sheared chromatin was immunoprecipitated with specific antibodies overnight at 4°C. Next day, lysates were incubated in prewashed protein G dynabeads (Invitrogen). After washing and elution, the protein–DNA complex was decross-linked by heating at 65°C for 4 hours. Immunoprecipitated DNA was purified by using QIAquick PCR purificaion kit. The libraries were constructed following Illumina's Chip-Seq Sample prep kit.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
20456619
Reads aligned (%)
94.2
Duplicates removed (%)
3.6
Number of peaks
5142 (qval < 1E-05)

hg38

Number of total reads
20456619
Reads aligned (%)
96.3
Duplicates removed (%)
2.5
Number of peaks
5220 (qval < 1E-05)

Base call quality data from DBCLS SRA