STOmicsDB

STOmicsDB provides a centralized repository and analysis resource for spatial transcriptomics data, aggregating 218 manually curated datasets across 17 species to enable single-cell-resolution and spatially resolved gene expression and cell–cell interaction studies.

Key Features:

• Comprehensive Data Integration: Integrates 218 manually curated spatial transcriptomics datasets spanning 17 species to support cross-species and comparative analyses.
• Detailed Annotations and Analyses: Contains annotations of cell types, spatial regions, and genes and supports cell–cell interaction analysis within datasets.
• Visualization at Scale: Supports visualization of spatial transcriptomics datasets comprising millions of cells for spatially resolved exploration of gene expression.
• Customizable Sub-Databases: Enables creation of customized sub-databases for tailored organization and visualization of specific spatial transcriptomic analyses.
• Data Archiving Standards and System: Implements defined standards and a data archiving system to store datasets in a consistent, interoperable format.

Scientific Applications:

• Biological Insight Generation: Enables detailed examination of gene expression patterns in relation to cellular spatial organization to study tissue development, function, and disease.

Methodology:

Manual curation of 218 spatial transcriptomics datasets; annotation of cell types, spatial regions, and genes; computation of cell–cell interactions; and data archiving implemented according to the database's developed standards.