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Sample GSM7792268 Query DataSets for GSM7792268
Status Public on Nov 07, 2023
Title 22Rv1_RNA_ENZ3w_siARV7_Dex_rep1
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 SAMN37482440
SRA SRX21838819

Supplementary file Size Download File type/resource
GSM7792268_22Rv1_RNA_ENZ3w_siARV7_Dex_rep1.bedGraph.gz 71.0 Mb (ftp)(http) BEDGRAPH
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