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 type
Breast cancer
passages
25
chip antibody
ab3575 (abcam)/06-935 (Millipore)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 2mM DSG for 20 min followed by crosslinking in 1% formaldehyde for 10 min and then quenched in 100mM glycine. Nuclear enrichment was performed followed by sonication for 15 minutes (Bioruptor plus, Diagenode). Chromatin was immunoprecipitated over night using specific antibodies. Beads were washed six times in RIPA buffer and eluted from beads using SDS buffer. After RNase and proteinase K treatment, DNA was purified by phenol/chloroform extraction. Libraries were prepared using the Thruplex kit (Illumina) according to the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg19

Number of total reads
43787732
Reads aligned (%)
84.0
Duplicates removed (%)
15.1
Number of peaks
36720 (qval < 1E-05)

hg38

Number of total reads
43787732
Reads aligned (%)
85.0
Duplicates removed (%)
14.4
Number of peaks
36751 (qval < 1E-05)

Base call quality data from DBCLS SRA