|
| Status |
Public on Apr 10, 2015 |
| Title |
WT1 |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: none
cell line: PC3
tissue: prostate
cell type: cancer cell
|
| Treatment protocol |
PC-3 cells were incubated in the presence or absence of GPNA or BenSer for 48 h
|
| Growth protocol |
PC-3 cells were cultured in RPMI 1640 medium containing 10% (v/v) fetal bovine serum (FBS), penicillin-streptomycin solution and 1 mM sodium pyruvate. Cells were maintained at 37°C in an atmosphere containing 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells harvested and total RNA was extracted from cells using Trizol. RNA quality was confirmed (RIN values 9.8-10) using RNA 6000 Nano Chips on an Agilent 2100 Bioanalyzer (Agilent Technologies).
Libraries were prepared using TruSeq Stranded Total RNA kit (Illumina, San Diego) and paired end sequencing was performed on an Illumina HiSeq 2500 at The Kinghorn Cancer Centre (Sydney).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
cmp_ben.txt
cmp_gpna.txt
|
| Data processing |
Paired-end RNA-sequencing reads were trimmed and mapped to annotated human genome (hg19/GRCh37.p13) using Tophat2 with default settings.
For each gene, the number of reads were counted and normalized to the library size.
The threshold for expression was set at 5 reads in at least one experimental group. Exact tests were applied to compare differences in the means of read-counts from 4 replicates between the treated and untreated group.
The gene expression levels were estimated in CPM (count-per-million-read).
The sequencing reads were mapped to hg19 using the bowtie2 default setting. Htseq 0.6.2p2 was applied to count number of reads within each gene. Differential expression was measured by DESeq package of R
Genome_build: hg19
Supplementary_files_format_and_content: Normalized abundance measurements. Differential expression of each gene.
|
| |
|
| Submission date |
Jan 20, 2015 |
| Last update date |
Mar 12, 2020 |
| Contact name |
Jeff Holst |
| E-mail(s) |
J.Holst@centenary.org.au
|
| Organization name |
Centenary Institute
|
| Street address |
Building 93, Royal Prince Alfred Hospital, Missenden Rd
|
| City |
Camperdown |
| State/province |
NSW |
| ZIP/Postal code |
2022 |
| Country |
Australia |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE65112 |
Genome-wide effect of inhibition of glutamine transporter ASCT2 in PC-3 cells by BenSer or GPNA |
|
| Relations |
| BioSample |
SAMN03288250 |
| SRA |
SRX848657 |
