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_plusDOX_E2_ER-ChIP
cell type
Luminal breast carcinoma epithelial MCF-7 cells
cell subtype
Doxycycline inducible NF1 knockdown model
cell line
MCF7
condition
Hormone-deprived media + E2
chip antibody
ER (Santa Cruz, sc-8002, clone F-10)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were grown in hormone-deprived media for 48 hrs before treatment for 45 min. Dox was added when seeding. Crosslinking was then performed followed by chromatin extraction, sonication, and ChIP. Crosslink reversal and chromatin isolation was performed before sequencing. Rubicon ThruPlex DNA-Seq library preparation system (publication number R400523, protocol QAM-108-002)

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
62221791
Reads aligned (%)
51.9
Duplicates removed (%)
46.5
Number of peaks
43874 (qval < 1E-05)

hg38

Number of total reads
62221791
Reads aligned (%)
53.1
Duplicates removed (%)
45.5
Number of peaks
44150 (qval < 1E-05)

Base call quality data from DBCLS SRA