|
| Status |
Public on Nov 08, 2016 |
| Title |
PC-3 + rtTA2 + TTP-tdTom + Dox #1 |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PC-3
tissue: prostate; derived from metastatic site: bone
cell type: epithelial
disease: adenocarcinoma
disease stage: grade IV
|
| Treatment protocol |
300 ng/ml doxycycline (Dox) for 4h prior to collection
|
| Growth protocol |
RPMI + 10% FBS, 1x glutamine, 1% penicillin/streptomycin at 37°C, 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cells using the Macherey-Nagel NucleoSpin RNA kit (Ref # 740955).
RNA-Seq was performed using the NuGen Ovation Encore Complete kit. Briefly, 100 ng of RNA was used to generate cDNA and a strand-specific library following the manufacturer’s protocol (NuGEN Technologies, Inc., San Carlos, CA). ). Quality control steps including analysis on the BioAnalyzer RNA chip and quantitative RT-PCR for library quantification were performed. The libraries were then sequenced on the Illumina NextSeq 500 sequencer with a 75-base paired-end run in order to generate 40-50 million read pairs per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
infected with a pRetroX-Tet-On-Advanced retrovirus, then a second pRetroX-Tight-TTP-pPGK-tdTomato retrovirus
|
| Data processing |
BASECALLING was performed by Illumina BaseSpace Sequence Hub
READ TRIMMING & CLEANUP were performed by Illumina BaseSpace Sequence Hub
Read alignment using TopHat v2.0.13
Abundance (Reads Per Kilobase of exon per Megabase of library size --RPKM) calculation using cufflinks v2.2.1
Differential expression calculation using cufflinks.
Genome_build: hs375d
Supplementary_files_format_and_content: cufflinks output
|
| |
|
| Submission date |
Sep 30, 2016 |
| Last update date |
Oct 19, 2022 |
| Contact name |
Chia-Ho Cheng |
| E-mail(s) |
chia-ho.cheng@moffitt.org
|
| Organization name |
Moffitt Cancer Center
|
| Street address |
12902 USF Magnolia Drive
|
| City |
Tampa |
| ZIP/Postal code |
33647 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE87532 |
Tristetraprolin disables prostate cancer maintenance by impairing proliferation and metabolic function |
|
| Relations |
| BioSample |
SAMN05856099 |
| SRA |
SRX2203321 |
