|
| Status |
Public on Oct 02, 2012 |
| Title |
C42B treated 1 |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: C4-2B
chip antibody: none
chip antibody manufacturer: none
chip antibody lot #: none
chip antibody catalog #: none
treatment: DHT treated (16h)
|
| 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 |
total RNA |
| Extraction protocol |
For RNA-seq, 10 ug of total RNA was oligo(dT) selected using the Dynabeads mRNA purification kit (Invitrogen) or depleted of ribosomal RNA (rRNA) using the RiboMinus kit (Invitrogen), and subsequently fragmented using RNA Fragmentation Reagents (Ambion). The fragmented RNA was randomly primed with hexamers and reverse-transcribed using the Just cDNA Double-stranded cDNA Synthesis kit (Stratagene). After second-strand synthesis, the cDNA was end-repaired, ligated to barcoded adaptors, size selected on agrose gel (150-300 bp) and PCR amplified for 14 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 Genome Analyzer IIx system according to the manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
polyA RNA
|
| Data processing |
bedGraph file: wigples were split according to barcode and barcodes were removed from fastq files. RNA-seq reads were mapped to the human genome (hg18) using Tophat v. 1.0.14. Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA).
gene expression count table: Aligned reads were filtered to eliminate reads that mapped to rRNA and RNA repeats (snRNA, scRNA, srpRNA, tRNA and RNA). Htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html) was used to obtain raw read counts based on Ensembl gene annotations (hg18 v54) using the union method.
Genome Build:
RNASEQ.C42B_TREATED_1.0293.s_5.CAGT.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 |
SRX176038 |
| BioSample |
SAMN01112594 |
