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Sample GSM7757202 Query DataSets for GSM7757202
Status Public on Sep 11, 2023
Title CWR22Rv1-AR-EK cells 72h Scrambled siRNA/24h 1 µM NU5455 n2
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: siScr/NU5455
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 NU5455_2
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 SAMN37271741
SRA SRX21618750

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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