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
breast cancer cell line
tissue
breast cancer cell line
biomaterial provider
ATCC
cell line
MCF7
estrogen
No, LTED (long term estrogen deprived) ESR1 mutant
antibody
ESR1 (Santa-Cruz sc543)
esr1 mutation
Y537C

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked in 1% formaldehyde at room temperature for 10 minutes and then quenched with 125 mmol/L glycine. Samples were then lysed, sonicated, and chromatin was immunoprecipitated by overnight incubation at 4C with ER antibodies prebound with Protein G magnetic dynabeads (Invitrogen). Samples were then washed vigorously with RIPA buffer and reversed crosslinked by an overnight incubation in elution buffer at 65C. DNA was digested with RNase and Proteinase K, purify precipitated with phenol chloroform and eluted in Tris-HCl pH 8.0.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
46231355
Reads aligned (%)
157.2
Duplicates removed (%)
19.5
Number of peaks
10754 (qval < 1E-05)

hg38

Number of total reads
46231355
Reads aligned (%)
158.6
Duplicates removed (%)
19.2
Number of peaks
11022 (qval < 1E-05)

Base call quality data from DBCLS SRA