|
| Status |
Public on Sep 11, 2023 |
| Title |
CWR22Rv1-AR-EK cells 72h DNA-PKcs knockdown/24h DMSO n1 |
| Sample type |
SRA |
| |
|
| Source name |
Prostate
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Prostate
cell line: CWR22Rv1-AR-EK
cell type: CRISPR edited CWR22Rv1 derivative, prostate epithelial cells
genotype: WT
treatment: siDNA-PKcs/DMSO
|
| Treatment protocol |
CWR22Rv1-AR-EK cells were transfected with 25 nm siRNA for 48 hours then treated with either DMSO or 1 µM NU7441, NU5455 or AZD7648 for a further 24 hours, CWR22Rv1 cells were reverse transfected with 25 nm siRNA for 72 hours
|
| Growth protocol |
CWR22Rv1-AR-EK and CWR22Rv1 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin antibiotics in humidified atmosphere with 5% CO2 at 37 °C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Phenol/chloroform extraction using TRIzol
Illumina-compatible library samples (performed by GeneWiz)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
KD_1
AREK_DNAPK_featureCounts.tsv
AREK_DNAPK_DESeq2_normalised_counts.csv
|
| Data processing |
Quality control using fastqC
Cutadapt to trim adapter sequences from reads (CWR22Rv1 experiment only)
sequence reads were aligned to the human geneome (GRCh38) using STAR
Gene count matrix was generated using FeatureCounts
Differential gene expression using DESeq2
Assembly: GENCODE GRCh38 primary assembly and associated GTF annotation (release v36 (CWR22Rv1-AR-EK) release v43 (CWR22Rv1).
Supplementary files format and content: tab-seperated featurecounts.tsv file contains raw count data
Supplementary files format and content: DESeq2 comma seperated csv file contains normalised counts
|
| |
|
| Submission date |
Sep 04, 2023 |
| Last update date |
Sep 11, 2023 |
| Contact name |
Beth Adamson |
| E-mail(s) |
beth.adamson@ncl.ac.uk
|
| Organization name |
Newcastle University
|
| Department |
Translational and Clinical Research Institute
|
| Lab |
Gaughan Lab
|
| Street address |
Paul O'Gorman Building, Framlington Place
|
| City |
Newcastle upon Tyne |
| ZIP/Postal code |
NE2 4HH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE242255 |
DNA-PKcs is a key transcriptional and splicing regulator of AR-Vs in advanced prostate cancer |
|
| Relations |
| BioSample |
SAMN37271736 |
| SRA |
SRX21618755 |
