|
| Status |
Public on Sep 26, 2024 |
| Title |
22Rv1 cells, vehicle treated, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
22Rv1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 22Rv1
treatment: DMSO vehicle
|
| Treatment protocol |
22Rv1 were treated with DMSO or 50 nM Lorecivivint (IC50) and harvested after 72h post-treatment
|
| Growth protocol |
22Rv1 were cultivated in standard conditions, as recommended by the ATCC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was performed with the Blirt EXTRACTME TOTAL RNA KIT
Library preparation for Oxford Nanopore long read sequencing was performed with the PCR-cDNA sequencing kit SQK-PCS109 together with the the PCR barcoding kit SQK- PBK004.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
| |
|
| Description |
DMSO_rep1
|
| Data processing |
Processing was performed using the EPI2Me wf-transcriptomes pipeline using the GENCODE release 43 (GRCh38.p13) transcriptome assembly.
Assembly: GRCh38
Supplementary files format and content: all_gene_counts.tsv: Tab-delimited text file with ensemble gene ID and gene counts for each sample
Supplementary files format and content: all_counts_filtered.tsv: Tab-delimited text file with ensemble gene ID, ensemble transcript ID and transcript counts for each sample
|
| |
|
| Submission date |
Feb 27, 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 |
GPL26167 |
| Series (2) |
| GSE259334 |
Targeting the CLK2/SRSF9 splicing axis in prostate cancer leads to decreased ARV7 expression in an rs5918762 allele-dependent manner (ONT long read sequencing) |
| GSE259335 |
Targeting the CLK2/SRSF9 splicing axis in prostate cancer leads to decreased ARV7 expression in an rs5918762 allele-dependent manner |
|
| Relations |
| BioSample |
SAMN40154662 |
| SRA |
SRX23759265 |
