OrganoidDB

OrganoidDB provides a curated repository and analysis resource of bulk and single-cell transcriptomic profiles from 16,218 organoid samples derived from pluripotent or adult stem cells in human and mouse to support comparative and molecular studies.

Key Features:

• Extensive Transcriptome Data Integration: Curates bulk and single-cell transcriptomic profiles for 16,218 organoid samples from human and mouse and integrates primary tissues and cell lines for comparative analyses.
• Multi-Perspective Exploration: Enables queries across different organoid types, derivation sources or protocols, comparisons between organoids and other sample types, developmental stages, and correlation analyses.
• Detailed Data Browsing: Provides dataset- and sample-level results including organoid characteristics, differentially expressed genes, enriched biological pathways, and single-cell clustering results.

Scientific Applications:

• Enhanced Understanding of Organoids: Facilitates investigation of molecular underpinnings of organoid composition, architecture, and function using transcriptomic data.
• Optimization of Culture Protocols: Supports refinement of organoid culture techniques to produce more physiologically relevant models.

Methodology:

Data are curated and integrated across studies; analyses explicitly include differential expression, pathway enrichment, single-cell clustering, and correlation analyses on bulk and single-cell transcriptomic data.