|
| Status |
Public on Nov 07, 2023 |
| Title |
VCaP_RNA_EtOH_rep5 |
| Sample type |
SRA |
| |
|
| Source name |
VCaP
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Vertebral Cancer of the Prostate
cell line: VCaP
enz treatment: 0
hormone treatment: EtOH vehicle
hormone concentration: 0.01%
|
| Treatment protocol |
VCaP and 22Rv1 cells were grown in the presence or absence of 10 µM enzalutamide (ENZ) for at least 16 (ENZ2w) or 21 days (ENZ3w) before the start of hormone treatments. VCaP and 22Rv1 cells were treated with vehicle (EtOH), 1 nM of dihydrotestosterone (DHT), or 100 nM of Dexamethasone (Dex) for 18 h before the start of RNA extraction.
|
| Growth protocol |
VCaP cells were grown in DMEM medium supplemented with 10% fetal bovine serum, 1 U/µl penicillin and 1 µg/ml streptomycin. 22Rv1 cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1 U/µl penicillin, 1 µg/ml streptomycin and 2 mM L-glutamine. All cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The isolation of RNA was conducted using NEB Monarch Total RNA Miniprep Kit following manufacturer’s protocol.
NEBNext Poly(A) mRNA Magnetic Isolation Module kit and NEBNext Ultra II Directional RNA Library Prep kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
75SE
|
| Data processing |
Basecalls performed using CASAVA
Alignment of RNA-seq data to human reference genome version hg38 was done with STAR. Differential expression of genes was analyzed using DESeq2 using HOMER.
Assembly: hg38
Supplementary files format and content: bedGraph (HOMER makeUCSCfile command) from alignment file.
|
| |
|
| Submission date |
Oct 04, 2022 |
| Last update date |
Nov 07, 2023 |
| Contact name |
Ville Paakinaho |
| E-mail(s) |
villepaakinaho@gmail.com
|
| Organization name |
University of Eastern Finland
|
| Department |
School of Medicine
|
| Lab |
Biomedicine
|
| Street address |
Yliopistonranta 8
|
| City |
Kuopio |
| ZIP/Postal code |
70210 |
| Country |
Finland |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE214756 |
Chromatin accessibility and pioneer factor FOXA1 restrict glucocorticoid receptor action in prostate cancer (RNA-Seq) |
| GSE214757 |
Chromatin accessibility and pioneer factor FOXA1 restrict glucocorticoid receptor action in prostate cancer |
|
| Relations |
| BioSample |
SAMN31150094 |
| SRA |
SRX17794518 |
