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
cell line
MCF-7
chip-antibody
ER
genotype
Control
sgguide
sgNT-1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cell samples were crosslinked with 1% formaldehyde for 10 min, and quenched by glycine to a 125nM final concentration. The fixed cells were lysed in SDS buffer and the chromatin was sheared by Covaris sonication. The sheared chromatin was incubated with the indicated antibodies and protein G-Dynabeads. The samples underwent decrosslinking, RNase and proteinase K treatment. DNA fragments were eluted using AMP Pure beads ChIP-seq libraries were prepared using 10 ng of DNA and Illumina's TruSeq ChIP sample prep.Libraries were validated using the Agient Technologies 2100 Bioanalyzer and Qubit high sensitivity assay.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
33754131
Reads aligned (%)
173.3
Duplicates removed (%)
11.5
Number of peaks
397 (qval < 1E-05)

hg38

Number of total reads
33754131
Reads aligned (%)
175.4
Duplicates removed (%)
11.3
Number of peaks
579 (qval < 1E-05)

Base call quality data from DBCLS SRA