{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Konsta Kukkonen"],"organism":["Homo sapiens"],"software":["Trim Galore v0.6.5; Kallisto v0.45.0; tximport v1.34.0; deepTools v3.5.5","Trim Galore! v0.6.5; STAR v2.7.11b; Picard toolkit v1.8; deepTools v3.5.5"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15758"],"description":["RNA-sequencing from RWPE-Ctrl (empty vector control), RWPE-1-AR (transduced with androgen receptor cDNA), LNCaP-pcDNA3.1 (empty vector control), and LNCaP-ARhi (transfected with androgen receptor cDNA) cells treated with 0, 1, 10, or 100 nM DHT for 4 hours before RNA extraction. Biological triplicate samples from each cell line in all conditions were collected. Aim of the experiment was to study androgen regulated gene expression in nonmalignant and cancer cells."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Performed by Novogene using Illumina NovaSeq 6000, aiming at 6G of data with 150 bp PE reads.","Library Construction - Standard Illumina polyA enrichment libraries, done by Novogene in the seuquencing center in Hong Kong, or in Cambridge Sequencing Center","Growth Protocol - For androgen induction studies, RWPE-1 cells were grown in phenol red-free RPMI-1640 medium with 5% charcoal/dextran-treated (CCS) FBS and 1% glutamine for 3 days. LNCaP were grown in same medium but with 10% charcoal/dextran-treated(CCS) FBS.","Sample Collection - Cells were lyzed directly to cell culture vessels with TRIzol reagent (Thermo Fisher Scientific)","Nucleic Acid Extraction - TRIzol protocol (Thermo Fisher Scientific) + RNEasy kit (Qiagen) for on-column DNase I treatment with RNase-Free DNase Set (Qiagen)","Sample Treatment - For androgen induction studies, hormone-deprived cells were treated with 0, 1, 10 or 100 nM of dihydrotestosterone (DHT) for 4 hours before cell lysis."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - The raw reads were first trimmed with Trim Galore! (https://github.com/FelixKrueger/TrimGalore) using the parameters --phred33 --stringency 5 --paired and aligned with STAR and indexed with Picard toolkit. The BigWig files were generated from these BAM-files using deepTools with the following parameters: --binSize 1 --effectiveGenomeSize 2862010578 --maxFragmentLength 1250000 --minMappingQuality 10 --normalizeUsing CPM --ignoreDuplicates.","Data Transformation - For the tabular results (length_scaled_TPMs_all_samples.tsv), the read counts were acquired with pseudoalignment with Kallisto using protein coding genes subset of Gencode comprehensive gene annotation of the primary assembly v30 as reference. The counts were normalized to average transcript length and library size using tximport package in R. The gene level summarized raw kallisto counts are also provided (raw_counts_all_samples.tsv). BigWig files were normalized to CPM using deepTools."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Konsta Kukkonen","Tapio Visakorpi"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of dihydrotestosterone (DHT) stimulated prostate epithelial cell lines RWPE-1-Ctrl, RWPE-1-AR and prostate cancer cell lines LNCaP-pcDNA3.1 and LNCaP-Arhi","description":"RNA-sequencing from RWPE-Ctrl (empty vector control), RWPE-1-AR (transduced with androgen receptor cDNA), LNCaP-pcDNA3.1 (empty vector control), and LNCaP-ARhi (transfected with androgen receptor cDNA) cells treated with 0, 1, 10, or 100 nM DHT for 4 hours before RNA extraction. Biological triplicate samples from each cell line in all conditions were collected. Aim of the experiment was to study androgen regulated gene expression in nonmalignant and cancer cells.","dates":{"release":"2026-07-31T00:00:00Z","modification":"2026-07-31T13:26:31.312Z","creation":"2025-10-16T12:46:59.641Z"},"accession":"E-MTAB-15758","cross_references":{"ENA":["ERP182306"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}