|
| Status |
Public on Jun 24, 2015 |
| Title |
PC3 DAXX K/D - DNMT1 IP |
| Sample type |
SRA |
| |
|
| Source name |
Prostate
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PC3
source tissue: Prostate
genotype: DAXX knock-down
antibody: anti-DNMT1 (sc-10219)
|
| 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 - DNMT1 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 |
| E-mail(s) |
cbenner@ucsd.edu
|
| 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 |
|
| Relations |
| BioSample |
SAMN03612217 |
| SRA |
SRX1021633 |
