Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
DAXX

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
cell line
PC3
source tissue
Prostate
genotype
wild type
antibody
anti-DAXX (sc-7001)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed using the Active Motif’s ChIP-IT High Sensitivity kit (cat # 53040), starting with PC3 and DAXX K/D PC3 cells. The manufacturer’s protocol was followed. The following goat polyclonal antibodies from Santa Cruz Biotechnology Inc. were used for ChIP: anti-DAXX (sc-7001) and anti-DNMT1 (sc-10219). A two-step cross-linking procedure (protein-protein & DNA-protein) preceded ChIP using disuccinimidyl glutarate (DSG) for protein-protein cross-linking (Thermo Scientific, cat # 20593). For ChIP, anti-DAXX or anti-DNMT1 antibodies were used to collect chromatin bound to the respective antibody, and was followed by deep sequencing (ChIP-Seq) using an Illumina HiSeq 2500 system. Non-immunoprecipitated (input) chromatin, subjected to the same treatment, served as a control. Illumina HiSeq 2500 system and associated protocol was used.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
17831501
Reads aligned (%)
88.2
Duplicates removed (%)
5.8
Number of peaks
45557 (qval < 1E-05)

hg38

Number of total reads
17831501
Reads aligned (%)
89.8
Duplicates removed (%)
4.7
Number of peaks
45602 (qval < 1E-05)

Base call quality data from DBCLS SRA