|
| Status |
Public on Oct 02, 2012 |
| Title |
C42B H3K4ME3 treated |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: C4-2B
chip antibody: H3K4Me3
chip antibody manufacturer: Millipore
chip antibody lot #: DAM1661080
chip antibody catalog #: 07-473
treatment: DHT treated (4h)
|
| Treatment protocol |
Cells were cultured in phenol red-free RPMI 1640 supplemented with 5% charcoal/dextran-stripped FBS (CSS) for 3 days. Cells were then treated with EtOH vehicle or 10nM DHT for additional 4 hr or 16 hr. For siRNA experiments cells were grown in phenol red-free RPMI 1640 containing 5% CSS for 2 days, and then transfected with siRNA duplexes as indicated at a final concentration of 15nM using Lipofectamine RNAiMAX Transfection Reagent according to the manufacturer’s instructions. After transfection, cells were grown in phenol red-free RPMI 1640 containing 5% CSS for 48 hr and then treated with 10nM DHT or vehicle for additional 16 hr.
|
| Growth protocol |
Cells were maintained in RPMI 1640 medium with 5% fetal bovine serum (FBS).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The ChIP-seq library was prepared according to the Illumina Protocol (www. illumina.com). Briefly, 10ng of ChIP DNA was end-repaired, ligated to barcoded adaptors, size selected on agrose gel (300-500 bp) and PCR amplified for 16 cycles using Phusion polymerase (Finnzymes). Ligation of 4 base adapters resulted in fragments consisting of the 4 base barcode followed by the sequence. The libraries were sequenced in the Illumina HiSeq2000 or Genome Analyzer IIx system according to the manufacturer’s instruction.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
genomic DNA
|
| Data processing |
bedgraph file: Samples were split according to barcode and barcodes were removed from fastq files. ChIP-seq reads were mapped to the human genome (hg18) using Bowtie v. 0.12.1. Reads that did not map uniquely were eliminated
Genome Build:
CHIPSEQ.C42B_H3K4ME3_TREATED.384.s_1.TCAT.bedGraph: hg18
|
| |
|
| Submission date |
Aug 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Keith F Decker |
| E-mail(s) |
kfd1@cec.wustl.edu
|
| URL |
http://pharmacogenomics.dom.wustl.edu/
|
| Organization name |
Washington University School of Medicine
|
| Department |
Internal Medicine
|
| Lab |
Li Jia
|
| Street address |
660 S. Euclid Ave, Campus Box 8220
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE40050 |
Persistent androgen receptor-mediated transcription in castration-resistant prostate cancer under androgen-deprived conditions |
|
| Relations |
| SRA |
SRX176066 |
| BioSample |
SAMN01112622 |
