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
Vehicle E2, ER ChIP
cell line
MCF7-tet-on-shCtr9
cell type
ER{alpha}-positive breast cancer cells
culture conditions
Vehicle
treatment
E2
chip antibody
Anti-ERα (Santa Cruz, sc-543, clone HC-20)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. ChIPed DNA was purified using a Qiagen PCR Purification Kit according to the manufacturer’s protocol Prior to ChIP-seq library preparation, ChIPed DNA samples were submitted to the Sequencing Facility at University of Wisconsin Madison Biotechnology Center for determining DNA concentration and size distribution, using Qubit Fluorometer (Thermo Fisher Scientific) and Agilent High Sensitivity DNA Kit (Agilent Technologies), respectively. 10 ng of ChIPed DNA from each condition was used to generate ChIP-seq library using the Ovation Ultralow System V2 1-16 Kit (NuGEN Technologies), according to the manufacturer’s protocol. Briefly, the DNA was end-repaired and subsequently ligated to Illumina sequencing adaptors. The ligated DNA was purified using the Agencourt RNAClean XP bead (Beckman Coulter). A subsequent PCR amplification step (15 cycles) added additional linker sequence to the purified fragments to prepare them for annealing to the Genome Analyzer flow-cell. Following PCR amplification, the library was size selected to a narrow range of fragment sizes by separation on a 2% agarose gel (120 V, 1.5 hours) and a band between 300-500 bp was excised. The library was purified from the excised agarose using the Qiagen MiniElute PCR Purification Kit, according to the manufacturer’s protocol. Purified libraries were then submitted to the Sequencing Facility at University of Wisconsin Madison Biotechnology Center for quality control to determine the size, purity, and concentration of the final ChIP-seq libraries. Qualified libraries were submitted to New York Genome Center (NYGC) for deep sequencing using an Illumina HiSeq 2000 per the manufacturer’s instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
36284283
Reads aligned (%)
92.2
Duplicates removed (%)
3.9
Number of peaks
3987 (qval < 1E-05)

hg38

Number of total reads
36284283
Reads aligned (%)
94.1
Duplicates removed (%)
2.7
Number of peaks
3861 (qval < 1E-05)

Base call quality data from DBCLS SRA