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
ER_LET-R_Veh
cell line
Let-R
cell type
Letrozole-resistant breast cancer cells
treated with
10% ethanol (vehicle control) for 45min
chip antibody
anti-ER
chip antibody vendor
Santa Cruz Biotechnologies

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were treated and harvested for ChIP-seq as described previously (Schmidt et al, 2009, http://www.ncbi.nlm.nih.gov/pubmed/19275939). The anti-ER (sc-543) from Santa Cruz Biotechnologies was used as the antibody. Chromatin was extracted from the cells and the protein of interest, along with the DNA attached, was immunoprecipitated using the antibody attached to Dynal beads (Dynabeads® Protein A 10001D, Life Technologies). The proteins were then removed from the DNA by reverse crosslinking overnight and the DNA purified and amplified before being sequenced. DNA libraries were generated from ChIP output DNA by adaptor ligation, gel purification, and cycles of PCR as described by Illumina.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
28030814
Reads aligned (%)
93.1
Duplicates removed (%)
4.3
Number of peaks
1121 (qval < 1E-05)

hg38

Number of total reads
28030814
Reads aligned (%)
95.7
Duplicates removed (%)
2.6
Number of peaks
786 (qval < 1E-05)

Base call quality data from DBCLS SRA