Visium HD FFPE Human Carotid Plaque Dataset

Le résumé fourni par la source

This repository contains Space Ranger–processed Visium HD spatial transcriptomic data generated from an FFPE section of a human carotid atherosclerotic plaque (Patient08, Cohort 1). A serial FFPE section from the same plaque was analyzed by imaging mass cytometry (IMC), enabling region-level comparison between transcriptomic patterns and protein-defined cellular niches. The deposited files include processed feature–barcode matrices, spatial coordinate files, tissue-image registration outputs, tissue images, quality-control summaries, clustering results, downstream analysis files, and ROI-specific CSV files. Nine regions of interest (ROIs) were manually delineated in Loupe Browser v8 (10x Genomics), guided by tissue histology and spatial molecular features. These included one necrotic-core region, three non-necrotic regions, two T-cell-enriched regions, two neovascularization regions, and one extracellular matrix (ECM)-enriched macrophage region. Data corresponding to each ROI were exported as CSV files for region-specific downstream analyses. These data were used to characterize spatial gene-expression patterns across pathological plaque regions and to provide transcriptomic context and cross-modal support for the macrophage/myeloid states and multicellular niches identified by IMC.

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