Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GABPA

Cell type

Cell type Class
Prostate
Cell type
DU 145
Primary Tissue
Prostate
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
DU145 Prostate cancer cell line
antibody
GABPA (Santa Cruz, sc-13442, lot #B2009)
cell line
DU145

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP DNA was isolated as described in Hollenhorst et. al., Genes and Development, 2011 Sequencing libraries were generated using a modified Illumina Truseq sample preparation protocol. ChIP DNA's were sheared to ~150 nucleotides using a Diagenode BioRuptor and the size was confirmed by DNA gel electrophoresis. DNA end repair of the cDNA was performed using Klenow DNA polymerase (New England BioLabs), T4 DNA polymerase (New England BioLabs), and T4 DNA ligase (New England BioLabs) before the sample was subjected to QIAquick PCR purification (Qiagen). Adapters were ligated to DNA fragments using the T4 DNA ligase (New England BioLabs). The product was run on a 2% agarose gel and size selected between 200 and 300 nucleotides to then be purified by a Gel Extraction kit (Qiagen). Universal and indexing adapters were taken from the TruSeq sample preparation kit (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
24862122
Reads aligned (%)
82.3
Duplicates removed (%)
4.3
Number of peaks
3177 (qval < 1E-05)

hg38

Number of total reads
24862122
Reads aligned (%)
84.2
Duplicates removed (%)
2.9
Number of peaks
3075 (qval < 1E-05)

Base call quality data from DBCLS SRA