|
| Status |
Public on Nov 07, 2023 |
| Title |
22Rv1_RNA_ENZ3w_siARV7_Dex_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
22Rv1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CWR22 xenograft derived human prostate carcinoma epithelial cell line
cell line: 22Rv1
enz treatment: 3 weeks
sirna treatment: Custom AR-V7 siRNA (Dharmacon)
hormone treatment: dexamethasone
hormone concentration: 100 nM
|
| Treatment protocol |
22Rv1 cells were grown in the presence or absence of 10 µM enzalutamide (ENZ) for at least 21 days (ENZ3w) before the start of hormone treatments. For siRNA treatments, the 22Rv1 cells were transfected with 80 nM siRNA using Lipofectamine RNAiMAX reagent 96 h before hormone treatments. 22Rv1 cells were treated with vehicle (EtOH) or 100 nM of Dexamethasone (Dex) for 18 h before the start of RNA extraction.
|
| Growth protocol |
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 |
NextSeq 2000 |
| |
|
| Description |
50PE
|
| 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 |
Sep 20, 2023 |
| 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 |
GPL30173 |
| 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 |
SAMN37482438 |
| SRA |
SRX21838821 |
