|
| Status |
Public on Sep 26, 2024 |
| Title |
PC3, DMSO, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
PC3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PC3
treatment: DMSO
|
| Treatment protocol |
The cells were seeded in 6 well plates and left to attach for 24 hours. Subsequently, they were treated with 1.5 µM of the CDK8/CDK19 inhibitor SEL120-34A or DMSO vehicle for 3 days.
|
| Growth protocol |
22Rv1 cells were acquired from the American Type Culture Collection (ATCC) and cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, and 1% GlutaMAX.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was performed with the Blirt EXTRACTME TOTAL RNA KIT
Library prep was performed with the high throughput 3’ tag BRB-seq kit from Alithea genomics using early barcoding RT primers.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X Plus |
| |
|
| Description |
PC3_DMSO_rep1
|
| Data processing |
The multiplexed fastq file was split into individual per sample fastq files with STARsolo using the cellular barcodes and PCR duplicates were removed using the UMIs. Read alignment and counting of the individual fastq files were performed in R using the Rsubread package and the Gencode Release 43 (GRCh38.p13) genome assembly.
Assembly: GRCh38
Supplementary files format and content: count_file.txt: Tab-delimited text file with ensemble gene ID, gene symbol and gene counts for each sample
Supplementary files format and content: log2CPM_expression.txt: Tab-delimited text file with ensemble gene ID, gene symbol and log2 transformed CPM gene expression values for each sample
|
| |
|
| Submission date |
Jun 04, 2024 |
| Last update date |
Sep 26, 2024 |
| Contact name |
Florian Handle |
| E-mail(s) |
[email protected]
|
| Organization name |
Medical University of Innsbruck
|
| Department |
Institute of Pathology, Neuropathology and Molecular Pathology
|
| Street address |
Müllerstrasse 44
|
| City |
Innsbruck |
| ZIP/Postal code |
6020 |
| Country |
Austria |
| |
|
| Platform ID |
GPL34284 |
| Series (1) |
| GSE269071 |
Inhibition of CDK8/CDK19 with the small molecule inhibitor SEL120-34A in prostate cancer cell lines (3’ tag DGE) |
|
| Relations |
| BioSample |
SAMN41675438 |
| SRA |
SRX24802575 |
