Visium spatial transcriptomic data of hormone therapy-naïve localised prostate cancer and adjacent benign tissue

This dataset contans proceseed Visium spatial transcriptomic data associated with the 10X Visium 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 second of two datasets associated with this study. Processed 10X Chromium scRNA-seq data can be found in the related Chromium dataset. The Visium experiments consist of 10 slides captured with different Visium protocols, including fresh frozen (OCT) and FFPE (using both v1 and v2 probe sets). See the included metadata for a mapping between samples and Visium experiments. This dataset contains MEX-format count matrices produced by spaceranger (v1.3.1 for OCT and FFPE v1; v3.0.1 for FFPE v2), filtered for spots under tissue, as well as the spatial/ directory produced by spaceranger for each experiment. Other spaceranger outputs are available on request. OCT-derived Visium libraries were generated using the standard 10x Genomics reference transcriptome refdata-gex-GRCh38-2020-A (based on the GRCh38 genome assembly with GENCODE v32 annotations) while FFPE-derived Visium libraries were generated using the Visium Human Transcriptome Probe Set v2.0 (GRCh38-2020-A; 10x Genomics).