|
| Status |
Public on Sep 30, 2018 |
| Title |
PC3-AR_12hr_R1881, rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
prostate
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PC3
|
| Treatment protocol |
Cells were plated in phenol-free medium supplemented with charcoal-stripped FBS serum for 48-72 hours prior to treatment. Cells were treated for the indicated timepoint with 2 nM R1881.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy kit according to the manufacturer’s instructions.
Indexed libraries were made by Hudson Alpha using the standard polyA method.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Aligned with STAR aligner (version 2.5.3a) using GRCh38.d1.vd1.fa.tar.gz
Generated raw counts using HTSeq (version 0.10.0) with parameters --mode=union --stranded=no --type=exon --idattr=gene_id --format=bam --order=pos. Using Homo_sapiens.GRCh38.89.chrchr.gtf as the annotation file.
Genome_build: hg38
Supplementary_files_format_and_content: text file of raw read counts
|
| |
|
| Submission date |
Sep 29, 2018 |
| Last update date |
Oct 01, 2018 |
| Contact name |
Aakrosh Ratan |
| Organization name |
University of Virginia
|
| Department |
Center for Public Health Genomics
|
| Street address |
1335 Lee Street, West Complex
|
| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22903 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE120660 |
Genomic Analysis of DNA Repair Genes and Androgen Signaling in Prostate Cancer |
|
| Relations |
| BioSample |
SAMN10146785 |
| SRA |
SRX4778114 |
