Chromium scRNA-seq data of hormone therapy-naïve localised prostate cancer and adjacent benign tissue

This dataset contans proceseed scRNA-seq data associated with the 10X Chromium experiments in Apostolov et al, Single-Cell and Spatial Transcriptomic Profiling Reveals Epithelial Functional States and Fibroblast Phenotypes in Hormone Therapy-Naïve Localized Prostate Cancer. This is the first of two datasets associated with this study. Processed Visium spatial transcriptomic data can be found in the related Visium dataset. The Chromium experiments consist of 16 multiplexed captures (PCa1 ~ PCa16), each containing three samples of either localised prostate tumour or adjacent benign tissue from 24 patients naïve to hormone therapy. This dataset contains outputs from cellranger v3.1 for each of the 16 captures, excluding bam files (*). Individual barcodes from each multiplexed capture were assigned to samples via souporcell (commit 790b281dbe) based on genotypes derived from SNP microarray experiments(*). This dataset also includes clusters_annotated.tsv for each of the sixteen captures, showing the barcode-sample assignments from souporcell. For each capture we have also included full_GPb_diff_scores_cluster_genotype.tsv and matched_GPb_diff_scores_cluster_genotype.tsv from vireosnp, which were used to souporcell results by comparing the genotypes from the SNP clusters identified by souporcell to the known genotypes derived from microarray data. The full dataset can be explored interactively at CELLxGENE, which includes rich cell-type and other annotations. Working AnnData and Seurat objects can be downloaded from CELLxGENE for the full cohort as well as cell type specific subsets. (*) Raw fastqs and raw and processed microarray data have been deposited on EGA as part of EGAS00001008332, along with bam files produced by cellranger and a VCF file containing genotypes for all samples derived from microarrays.