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-shCTRL-ER_ChIPSeq
cell line
MCF-7
cell type
breast cancer cell line
genotype/variation
shCTRL
chip antibody
ERa (santa cruze, sc-543x,Lot # E3014 )

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified form sonicated nuclei and protein-DNA complexes were isolated with antibody. The Chromatin immunoprecipitated DNA fragments (approx.10 ng in 30 µl water) are end repaired by using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase in the presence of dNTPs. And an 'A' base is added to the 3'end of the blunt phosphorylated DNA fragments, using the polymerase activity of Klenow fragment. Then, adaptors (Adaptor oligo mix, Illumina) are ligated to the ends of the DNA fragments. The resulting DNA fragments are purified by MinElute column (QIAGEN). 300 ~ 500 bp DNA fragments are purified by using E-Gel SizeSelect agarose Gels (Invitrogen) according to manufacturer's instruction. Size selected adaptor-modified DNA fragments are amplifiedand the resulting PCR products are purified by MinElute column (QIAGEN). The size and amount of DNA fragments (libraries) are validated by Bioanalyzer (Agilent)

Sequencing Platform

instrument_model
Illumina HiSeq X Ten

hg19

Number of total reads
33572923
Reads aligned (%)
166.5
Duplicates removed (%)
9.3
Number of peaks
6623 (qval < 1E-05)

hg38

Number of total reads
33572923
Reads aligned (%)
168.1
Duplicates removed (%)
9.1
Number of peaks
7241 (qval < 1E-05)

Base call quality data from DBCLS SRA