|
| Status |
Public on Sep 09, 2020 |
| Title |
PC-3_control_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
prostate
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: prostate cancer
cell line: PC-3
treatment: control
passages: 20-30
|
| Treatment protocol |
PC-3-GDC-R cells were maintained by continuous treatment of GDC-0068. Control cells PC-3-control were generated in parallel by treating cells with vehicle (DMSO).
|
| Growth protocol |
Cells were maintained at 37°C and 5% CO2 in RPMI 1640 containing 10% fetal bovine serum (FBS) and 1% antibiotic/antimycotic (Thermo Fisher Scientific).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted using RNeasy Mini Kit.
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Reads aligned to human reference genome (hg19) using Tophat (v2.0.6) with default parameters
Raw count and RPKM were calcualted using RSeQC (v2.3.6) on hg19.refseq.bed12
Genome_build: hg19
Supplementary_files_format_and_content: xls file for raw count and FPKM
|
| |
|
| Submission date |
Sep 10, 2019 |
| Last update date |
Sep 09, 2020 |
| Contact name |
Zhenqing Ye |
| E-mail(s) |
iamyezhenqing@gmail.com
|
| Organization name |
UT Health San Antonio
|
| Department |
6Department of Population Health Sciences
|
| Street address |
8403 Floyd Curl Dr
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE137200 |
Pattern occupation of HDACs on chromatin determines PI3K/AKT inhibitor resistance in cancers [RNA-seq] |
| GSE137209 |
Bromodomain and HDAC inhibitors equivalently suppress PI3K/AKT inhibition resistance in cancers |
|
| Relations |
| BioSample |
SAMN12723126 |
| SRA |
SRX6827656 |
