{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Arkaitz Carracedo"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13764"],"description":["Determine a comprehensive transcriptome sequencing profiling of tumor-adjacent (contralateral lobe) benign prostatic hyperplasia, 10X genomics single-cell RNA-sequencing analysis on human surgical specimen."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Single cell library was prepared using “Chromium Next GEM Chip G Single Cell Kit”, 16 rxns PN-1000127, “Chromium Next GEM Single Cell 3ʹ Kit v3.1”, 4 rxns PN-1000269 and “Dual Index Kit TT Set A”, 96 rxns PN-1000215, following “Chromium Next GEM Single Cell 3 ’ Reagent Kits v3.1 (Dual Index) User Guide” (Document number CG000315).","Nucleic Acid Extraction - Single cell library was prepared using “Chromium Next GEM Chip G Single Cell Kit”, 16 rxns PN-1000127, “Chromium Next GEM Single Cell 3ʹ Kit v3.1”, 4 rxns PN-1000269 and “Dual Index Kit TT Set A”, 96 rxns PN-1000215, following “Chromium Next GEM Single Cell 3 ’ Reagent Kits v3.1 (Dual Index) User Guide” (Document number CG000315).","Sequencing - Approximately 10,000 cells were sequenced with an average sequencing depth of 400 million reads on Illumina NovaSeq 6000 sequencer","Sample Collection - A benign prostate sample was collected adjacent to the tumor (contralateral lobe) from a patient with prostate cancer at the Basurto University Hospital at the time of robotic prostatectomy following Ugalde-Olano et al., Mehods, 2015. The biopsy was kept in MACS medium, tissue storage solution until dissociation. The tumor was washed with cold phosphate-buffered saline (PBS; GIBCO) and minced into fragments under 0.4 mm. The tissue was chemically dissociated in a sterilized filter with Liberase TH solution (2.5mg/ml; REF QZY-5401135001, Thomas Scientific) in complete media composed of Advanced DMEM/F-12 (REF 12-634-010, Fisher Scientific), Pen/strep (REF 15-140122, GIBCO), MgCl2 (5mM, REF M4880, Sigma Aldrich), DNAse I (200 μg/ml, REF 11284932001, Sigma Aldrich) and Y-27632 dihydrochloride (10 μM; AbMole) at 37ºC shaking at 800 r.p.m for 40 minutes. The tissue solution was manually disaggregated with a pipette every 10 min during the incubation followed by centrifugation at 2400xg for 5 min. Next, a second chemical dissociation was performed with TrypLE (REF 12605010, Thermo Scientific) supplemented with Y-27632 dihydrochloride under constant pipetting for 2 minutes. The inactivation of TrypLE was done by adding FBS (GIBCO) and centrifuged at 2400xg for 5 minutes. The cell pellet was resuspended in PBS, filtered through 40 μm filter and washed with PBS. The suspension was centrifuged at 2400xg for 5 minutes and resuspended in 200ul of PBS. Cells were counted on a Neubauer chamber and 20000 cells were then centrifuged at 2400xg for 5 minutes and resuspended in PBS for scRNAseq analysis according to manufacturers´ indications."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The matrixes generated by “cellranger count” were loaded into Seurat package (version 4.3.0) in R (version 4.2.1). Low quality cells expressing less than 200 unique genes were filtered out together with those cells under 80% of calculated novelty score (The novelty score is computed by taking the ratio of number of genes over number of UMIs. If there are many captured transcripts and a low number of genes detected in a cell, this likely means that you only captured a low number of genes and simply sequenced transcripts from those lower number of genes repeatedly. These low novelty cells could represent a specific cell or could be due to some other strange artifact or contamination). In addition, cells with greater than 20% of their transcriptome being mitochondrial genes were excluded. Finally, only genes expressed in more than 10 cells were shortlisted for subsequent analyses. The filtered gene expression matrix was normalised using Seurat. We applied a global-scaling normalization method “LogNormalize” that normalizes the feature expression measurements for each cell by the total expression, multiplies this by a scale factor, and log-transforms the result.","Sequence Alignment - The sequenced data was processed for analysis with Cell Ranger (version 7.0.1), “cellranger count” was used to perform the alignment analysis using human reference genome GRCh38."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Arkaitz Carracedo"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell RNA-seq from human prostate cancer-adjacent benign prostatic hyperplasia","description":"Determine a comprehensive transcriptome sequencing profiling of tumor-adjacent (contralateral lobe) benign prostatic hyperplasia, 10X genomics single-cell RNA-sequencing analysis on human surgical specimen.","dates":{"release":"2025-12-16T00:00:00Z","modification":"2025-12-16T16:26:52.096Z","creation":"2024-02-05T15:10:40.168Z"},"accession":"E-MTAB-13764","cross_references":{"ENA":["ERP157161"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}