SpatialDB

SpatialDB provides a manually curated database of spatially resolved transcriptomics datasets to organize, standardize, and annotate spatial gene expression across tissues and species for comparative and functional analyses.

Key Features:

• Manually curated database: Datasets and metadata are manually curated to ensure consistent annotation and high-quality organization.
• Extensive dataset collection: Contains 24 datasets (305 sub-datasets) from five species generated by eight spatially resolved transcriptomic techniques.
• Standardized data integration: Integrates and standardizes data from multiple spatial transcriptomic techniques into a unified format to enable comparability across studies.
• Spatially variable gene annotation: Identifies and records spatially variable genes within datasets.
• Functional enrichment annotation: Provides functional enrichment annotations for spatially variable genes to aid biological interpretation.
• Centralized repository for comparative analysis: Aggregates spatial transcriptomic datasets to support cross-study and cross-species comparative analyses.

Scientific Applications:

• Characterize tissue architecture: Enables characterization of cellular spatial organization within tissues through spatial gene expression profiles.
• Investigate disease mechanisms: Supports examination of molecular underpinnings of disease by analyzing spatial patterns of gene expression in specific cellular contexts.
• Identify functional spatially variable genes: Facilitates identification of spatially variable genes that may play roles in physiological processes or pathological conditions, with associated functional enrichment.

Methodology:

Integration and manual curation of diverse datasets obtained from multiple spatial transcriptomic techniques, with standardization into a unified dataset format.