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
cell type
Breast cancer cell line
passages
P29
chip antibody
anti-ERalpha (Santa Cruz, sc-543)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked in 1% formaldehyde for 10 min and then quenched in 100mM glycine. Nuclear enrichment was performed followed by sonication (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

hg38

Number of total reads
39078005
Reads aligned (%)
99.2
Duplicates removed (%)
16.3
Number of peaks
4020 (qval < 1E-05)

hg19

Number of total reads
39078005
Reads aligned (%)
98.5
Duplicates removed (%)
17.3
Number of peaks
4036 (qval < 1E-05)

Base call quality data from DBCLS SRA