Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SOX9

Cell type

Cell type Class
Prostate
Cell type
VCaP
Primary Tissue
Prostate
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
VCaP Prostate Cancer Cell line
cell line
VCaP
chip antibody
SOX9: Millipore AB5535

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cell was fixed by 1% formaldehyde for 10min and then lysed. Lysates were sonicated and Input DNA were set aside. Lysates were then clarified from sonicated nuclei and SOX9-DNA complexes were isolated with SOX9 antibody. Cross-linking of the DNA were reversed by heating for both Input and immunoprecipitated DNA. All DNA were purified by Qiagen PCR purification kit before library construction. Libraries were prepared according to Illumina's instructions accompanying the ChIP Sample Prep Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
31068832
Reads aligned (%)
73.3
Duplicates removed (%)
17.3
Number of peaks
984 (qval < 1E-05)

hg38

Number of total reads
93516866
Reads aligned (%)
43.2
Duplicates removed (%)
16.9
Number of peaks
2743 (qval < 1E-05)

Base call quality data from DBCLS SRA