Loupe Files with Spot Annotations for GBM Visium Samples

This archive contains cloupe files, generated by the 10X Genomics spaceranger pipeline, for all Visium samples in "Mapping the spatial architecture of glioblastoma from core to edge delineates niche-specific tumor cell states and intercellular interactions" (https://www.biorxiv.org/content/10.1101/2025.04.04.647096v1). Loupe files that include detailed histologic annotations are labeled with “ann.” For other samples, typically those with more uniform histology and/or low quality H&E images, only broad whole-sample annotations (i.e. ‘core,’ ‘edge,’ or ‘transition’) were provided by Pathology. Notes on specific sample annotations: TWBK-B172-02 (aka B172-02): Approximate tumor edge indicated, uncategorized spots are tumor core B176-02-01: Approximate tumor edge indicated, uncategorized spots are tumor core B178-02-01: Approximate tumor core indicated, uncategorized spots are tumor core B186-04: ‘Tumor edge/gray matter’ and ‘tumor edge/white matter’ are indicated ST073021-2: Notable features and approximate tumor content are indicated ST073021-4: Notable features and approximate tumor content are indicated WU1220-1: Notable features are indicated, uncategorized spots are tumor WU1220-2: ‘Tumor edge/gray matter’ and ‘tumor edge/white matter’ are indicated WU1220-3: Notable features are indicated, uncategorized spots are core tumor WU1221-Core2: Tumor and dense tumor are indicated WU1221-Edge1: Notable features are indicated, uncategorized spots are tumor edge WU1227-Core5: Notable features are indicated, uncategorized spots are tumor core