Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HOXC5

Cell type

Cell type Class
Prostate
Cell type
PC-3
Primary Tissue
Prostate
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
Prostate cancer line
cell line
Prostate cancer line PC-3
genotype/variation
Hoxc5 overexpression
chip antibody
Hoxc5 (HPA026794, Sigma, lot# R28092)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 1% formaldehyde for 10mins at room temperature, and stopped by adding glycine to a final concentration of 0.2M. Cells were washed with ice cold TBSE(20mM Tris-HCl, 150mM NaCl, 1mM EDTA) for three times. Chromatin were then extracted and sonicated to ~500bp. Input DNA was precleared with protein G Dynabeads (Life technologies), and followed by chromatin immunoprecipitation with Hoxc5 (HPA026794, Sigma) and PBX4 (HPA049859, Sigma) at 4°C overnight. ChIP beads were washed six times at room temperature. At least 10ng ChIP DNA were used to prepare libraries with NEBNext ChIP-Seq library prep reagent set (New England Biolabs), and multiplexed (New England Biolabs).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
32786371
Reads aligned (%)
72.7
Duplicates removed (%)
25.9
Number of peaks
39610 (qval < 1E-05)

hg38

Number of total reads
32786371
Reads aligned (%)
74.3
Duplicates removed (%)
24.8
Number of peaks
39939 (qval < 1E-05)

Base call quality data from DBCLS SRA