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| Status |
Public on Jul 28, 2021 |
| Title |
04_VPC220010_DHT_rep1 |
| Sample type |
SRA |
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| Source name |
LNCaP cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: LNCaP cells
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| Treatment protocol |
Cells were treated with 10nM DHT and either DMSO (Control) or 1.5µM Enzalutamide, or 6µM VPC-220010 for 6 hours before RNA isolation.
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| Growth protocol |
LNCaP cells (6 x 10^6) were seeded in RPMI 1640 media containing 10% FBS and 1% penicillin/streptomycin. Following O/N incubation, the media was changed to RPMI 1640 containing 5% CSS and the cells were then grown for 48hrs at 37C with 5% CO2.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol and the Qiagen RNeasy RNA Extraction Kit. Three biological replicas were collected for each condition. The concentrations and the qualities of the RNA samples were checked by Nanodrop and tape station. All RIN values were between 9.5 and 10.
Library was constructed by BGI using library construction methods underlying the BGISEQ-500 platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Data processing |
Base calling was performed using the BGISeq500 platform. The raw reads were pre-filtered by removing adaptor sequences, contamination and low-quality reads.
The high quality of the filtered reads was confirmed using the FastQC (Andrews, 2014) quality control tool.
Reads were quantified using Salmon version 1.1.0 (Patro, R., et al. 2017)
Differential gene expression analysis for different treatments was performed using the DESeq2 (Love, Huber, & Anders, 2014).
Genome_build: hg38 transcriptome
Supplementary_files_format_and_content: DESeq2 Differential Expression Analyses of DHT vs Ethanol, Enzalutamide vs DHT and VPC-220010 vs DHT, as a Microsoft Excel Spreadsheet.
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| Submission date |
Apr 26, 2021 |
| Last update date |
Jul 28, 2021 |
| Contact name |
Ayse Derya Cavga |
| E-mail(s) |
acavga13@ku.edu.tr
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| Organization name |
Koc University
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| Street address |
Rumelifeneri Yolu, Sariyer
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| City |
Istanbul |
| ZIP/Postal code |
34450 |
| Country |
Turkey |
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| Platform ID |
GPL23227 |
| Series (1) |
| GSE173331 |
Development of an Androgen Receptor Inhibitor Targeting the N-Terminal Domain of Androgen Receptor for Treatment of Castration Resistant Prostate Cancer |
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| Relations |
| BioSample |
SAMN18871719 |
| SRA |
SRX10680831 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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