GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1678030 Query DataSets for GSM1678030
Status Public on Jun 24, 2015
Sample type SRA
Source name Prostate
Organism Homo sapiens
Characteristics cell line: PC3
source tissue: Prostate
genotype: DAXX knock-down
antibody: anti-DAXX (sc-7001)
Growth protocol The human prostate cancer cell line PC3 and its DAXX knock-down counterpart were maintained in Roswell Park Memorial Institute-1640 (RPMI-1640) medium, containing 10% fetal bovine serum, FBS (HyClone), and 1% penicillin/streptomycin plus L-glutamine. For the DAXX K/D PC3 cells, the RPMI medium was supplemented with puromycin (Sigma, Cat # P9620; 2 μg/ml).
Extracted molecule genomic DNA
Extraction 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.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Description ChIP-Seq: PC3 DAXX K/D - DAXX IP
Data processing Basecalls performed using CASAVA version 1.8.2
ChIP-Seq reads were aligned to the human genome (hg19) using bowtie2 (v2.1.0), keeping only reads that mapped to a unique genomic location (MAPQ > 10).
HOMER (v4.6) was used to process alignment files to generate normalized bedGraphs and bigwigs for the UCSC Genome Browser and identify peaks. Peaks for WT and DAXX K/D conditions were found relative to the condition specific input experiments. HOMER's findPeaks program was run in "factor" mode for DAXX and DNMT1 peak finding and "histone" mode for DMHH3 (H3K4me2) peak finding.
Genome_build: hg19
Supplementary_files_format_and_content: bed format (peak regions)
Submission date May 07, 2015
Last update date May 15, 2019
Contact name Christopher Benner
Organization name University of California, San Diego (UCSD)
Department Medicine
Street address 9500 Gilman Dr. MC 0640
City La Jolla
State/province California
ZIP/Postal code 92093-0640
Country USA
Platform ID GPL16791
Series (2)
GSE68647 The DAXX co-repressor is directly recruited to active regulatory elements genome-wide to regulate autophagy programs in a model of human prostate cancer (ChIP-seq)
GSE68656 The DAXX co-repressor is directly recruited to active regulatory elements genome-wide to regulate autophagy programs in a model of human prostate cancer
BioSample SAMN03612215
SRA SRX1021631

Supplementary file Size Download File type/resource
GSM1678030_Sample2.PC3-DAXXKD-DAXXIP.peaks.bed.gz 524.4 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap