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
ChIP-seq_ER_siFOXA1_E2+TNF
cell line
MCF-7
cell type
ER Positive Breast Cancer Cells
treatment
E2+TNFa
chip antibody
ER alpha (rabbit polyclonal generated in the Kraus Lab)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq libraries were generated from two biological replicates for each condition. The immunoprecipitated DNA was purified using a MiniElute PCR Purification Kit from Qiagen. After purification, 50 ng of ChIPed DNA for each condition was used to generate libraries for deep sequencing, as previously described (Quail et al., 2008), with some modifications. Briefly, the DNA was end-repaired and a single “A”-base overhang was added using the Klenow fragment of E. coli DNA polymerase. The A-modified DNA was ligated to Illumina sequencing adaptors using the Illumina TruSeq DNA Sample Prep Kit. The ligated DNA (250-300 bp) was size-selected by agarose gel electrophoresis and purified using a Qiagen Gel Extraction Kit. The size-selected fragments were amplified using Illumina TruSeq P5 and P7 PCR primers, and purified using AMPure beads (Beckman Coulter). Quality control was performed to determine the size, purity, and concentration of the final libraries, which were sequenced using an Illumina HiSeq 2000 per the manufacturer’s instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
26991740
Reads aligned (%)
58.5
Duplicates removed (%)
39.8
Number of peaks
12400 (qval < 1E-05)

hg38

Number of total reads
26991740
Reads aligned (%)
60.6
Duplicates removed (%)
38.1
Number of peaks
12474 (qval < 1E-05)

Base call quality data from DBCLS SRA