Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PRKDC

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
cell line
MCF7
cell description
beast cancer cell line
chip antibody or biotin-streptavidin pulldown of blrp-tagged proteins
Bethyl, A300-517A
treatment
shRARs, 1hr treatment with 100nM E2

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 or by streptavidin magnet beads pull-down. The extracted ChIP DNA was ligated to specific adaptors of Truseq system from Illumina, according to the manufacturer’s instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
12160019
Reads aligned (%)
47.1
Duplicates removed (%)
50.7
Number of peaks
195 (qval < 1E-05)

hg38

Number of total reads
12160019
Reads aligned (%)
48.9
Duplicates removed (%)
49.1
Number of peaks
114 (qval < 1E-05)

Base call quality data from DBCLS SRA