{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Konsta Kukkonen"],"organism":["Homo sapiens"],"software":["Trim Galore! v.0.6.10; Bowtie2 v2.4.523; Samtools v1.15.124; Picard toolkit v2.27.1","deepTools v3.5.0"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15731"],"description":["ATAC-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 2 hours before nuclei isolation. Biological duplicate samples from each cell line in all conditions were collected. Aim of the experiment was to study genomic effect of androgen receptor activation in nonmalignant and cancer cells."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Nuclei isolation was performed using published Omni-ATAC protocol (Corces et al. 2017) with the following modification: cell centrifugation was performed with 700 g for 5 min.","Nucleic Acid Extraction - Does not apply to ATAC-sequencing. See published Omni-ATAC protocol (Corces et al. 2017)","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.","Library Construction - ATAC-library preparation was performed using published Omni-ATAC protocol (Corces et al. 2017) with the following modifications: For Tagmentation reaction conditions were adjusted to 45 min in 37 °C at 900 RPM. And for the PCR purification steps, MinElute kit (Qiagen) was used and the library purification was finalized using AMPure Xp beads (Beckman Coulter).","Sequencing - Sequencing was performed in Novogene Cambrige Sequencing Center using Illumina NovaSeq 6000","Sample Treatment - For androgen induction studies, hormone-deprived cells were treated with 0, 1, 10 or 100 nM of dihydrotestosterone (DHT) for 2 hours before nuclei isolation."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - The raw reads were first trimmed using Trim Galore! (https://github.com/FelixKrueger/TrimGalore) using parameters --phred33 -q 20 --fastqc --length 36 --paired --retain_unpaired. Reads were then aligned against the analysis set reference genome (i.e., GRCh38_no_alt_plus_hs38d1_analysis_set) to avoid multimapping to alternative chromosomes with Bowtie2 with parameters -X 2000 –very-sensitive -q and converted to BAM format using Samtools. Picard toolkit (https://broadinstitute.github.io/picard/) was used to assign read groups based on flow cell, to fix read mate information, to remove duplicate reads and reads with MAPQ < 30, and finally to index the BAM-files. These BAM files were used with deepTools to make the bigwigs.","Data Transformation - The background correction for the reproducible ATAC-peaks was performed as previously described (Uusi-Mäkelä et al. 2020). Briefly: average signal was calculated for whole genome in bins of 10 kbp, 100 kbp and whole chromosome arms. The highest of these background values was subtracted from each reproducible peak region. bg_cor_signal_rep_peaks_all_samples.tsv.gz contains these background corrected signal values for all samples. The bigwig files were normalized to CPM using deepTools bamCoverage with parameters: bamCoverage --binSize 50 --effectiveGenomeSize 2862010578 --normalizeUsing CPM --ignoreDuplicates. Additionally Encode blacklist (Amemiya, Kundaje & Boyle 2019) and blacklist for GRCh38 genomic DNA regions with mitochondrial homology (Uusi-Mäkelä et al. 2020) were used."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["ATAC-seq"],"species":["Homo sapiens"],"pubmed_authors":["Konsta Kukkonen","Tapio Visakorpi"],"additional_accession":[]},"is_claimable":false,"name":"ATAC-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":"ATAC-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 2 hours before nuclei isolation. Biological duplicate samples from each cell line in all conditions were collected. Aim of the experiment was to study genomic effect of androgen receptor activation in nonmalignant and cancer cells.","dates":{"release":"2026-07-31T00:00:00Z","modification":"2026-07-31T13:26:36.22Z","creation":"2025-10-15T14:01:50.673Z"},"accession":"E-MTAB-15731","cross_references":{"ENA":["ERP182235"],"EFO":["EFO_0002944","EFO_0007045","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}