|
| Status |
Public on Jul 09, 2024 |
| Title |
VCaP, Vehicle_CFS, 0, 24 hours, RNA, Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Prostate
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Prostate
cell line: VCaP
cell type: epithelial
compound: Vehicle
dose: 0 nM
time: 24 hours
|
| Treatment protocol |
LNCaP and VCaP cells were tretaed with vehicle, increasing concentrations of low-dose (0.01, 0.03, 0.06, 0.1 nM R1881) or High-Dose (10nM R1881) androgens for 24 hours
|
| Growth protocol |
LNCaP cells (130,000 cells/well) were seeded in 6-well plates in RPMI 1640 supllemented with 8% charcoal dextran treated FBS(CFS). For VCaP cell line (300,000 cells/well), cells were seeded in 6-well plates in DMEM (8% CFS). 48 hrs later, cells were treated with R1881 for an additional 24 hrs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were isolated using the Aurum™ Total RNA Mini-Kit according to the manufacturer’s instructions (Bio-Rad).
RNA libraries for RNA-seq were prepared using KAPA Stranded mRNA-Seq Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.39
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR v2.7.8a
Read count extraction and normalization were performed using R packages DESeq2 v1.36.0
Assembly: GRCh38
Supplementary files format and content: csv file includes raw counts for each sample
|
| |
|
| Submission date |
Nov 13, 2023 |
| Last update date |
Jul 09, 2024 |
| Contact name |
Xiaodi Qin |
| Organization name |
Duke Cancer Institute
|
| Street address |
2424 Erwin Road
|
| City |
Durham |
| ZIP/Postal code |
27705 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE247592 |
Different doses of androgens induce the expression of distinct gene expression programs (RNA-Seq) |
| GSE247593 |
Different doses of androgens induce the expression of distinct gene expression programs |
|
| Relations |
| BioSample |
SAMN38237975 |
| SRA |
SRX22513272 |
