Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PARP1

Cell type

Cell type Class
Breast
Cell type
MDA-MB-231
Primary Tissue
Breast
Site of Extraction
Effusion, Pleural
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MDA-MB-231
chip antibody
PARP1 (Cell Signaling Technology)
cell line
MDA-MB-231
geo_loc_name
missing
collection_date
missing

Sequenced DNA Library

library_name
GSM6443233
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
10 ng of ChIP DNA was end polished with T4 DNA polymerase and kinase. An 'A' base was added to the polished DNA fragments, followed by the Qiaquick column clean up. Solexa adaptors were ligated to the ChIP DNA fragments and enriched by 15 cycles of PCR amplification. 200-300 bp size fractions were selectively isolated from the 1% agarose gel and eluted by the Qiagen gel extraction kit. The extracted DNA was quantified by picogreen assay and subjected to HiSeq2000 sequencing according to the manufacturer's instructions. DNA libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
18355862
Reads aligned (%)
33.5
Duplicates removed (%)
36.3
Number of peaks
1165 (qval < 1E-05)

hg19

Number of total reads
18355862
Reads aligned (%)
33.3
Duplicates removed (%)
37.1
Number of peaks
1153 (qval < 1E-05)

Base call quality data from DBCLS SRA