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
cell line
MCF7
chip antibody
Estrogen Receptor alpha (Santa Cruz, sc-543, lot F1716)
cell type
breast cancer cell line
treatment
Rad1901

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were formaldehyde fixed for 15 minutes (1% formaldehyde, 100 mM NaCl, 0.1 mM EDTA pH8.0, 5 mM Hepes pH 7.9). Fixation was stopped with 2.5M glycine and cells were washed 2X in PBS/0.5% Igepal CA-630. Cell pellets were snap frozen and chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina's NextSeq 500 (75 nt reads, single end).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
31834192
Reads aligned (%)
77.3
Duplicates removed (%)
18.7
Number of peaks
10155 (qval < 1E-05)

hg38

Number of total reads
31834192
Reads aligned (%)
79.0
Duplicates removed (%)
17.5
Number of peaks
10338 (qval < 1E-05)

Base call quality data from DBCLS SRA