ProximID

ProximID identifies preferential cellular interactions by integrating single-cell mRNA sequencing with physical proximity information to map cellular networks in native tissue environments.

Key Features:

• Integration of single-cell mRNA sequencing and spatial data: Combines single-cell mRNA sequencing with physical proximity information to link transcriptional identities to neighboring cells.
• Unsupervised detection of preferential interactions: Detects novel preferential cellular interactions without requiring prior knowledge of component cell types.
• Spatial analysis in native tissue contexts: Analyzes spatial relationships between cells within native environments such as bone marrow and intestinal crypts.
• Construction of cellular interaction maps: Builds detailed maps of cellular interactions to reveal interaction networks and tissue architecture.
• Discovery of previously unrecognized interactions: Identifies interactions that are not evident from traditional niche studies relying on assumed cell populations.

Scientific Applications:

• Mouse bone marrow interaction mapping: Identified interactions between megakaryocytes and mature neutrophils, and between plasma cells and myeloblasts or promyelocytes in mouse bone marrow.
• Small intestine crypt niche discovery: Revealed an interaction between Tac1+ enteroendocrine cells and Lgr5+ stem cells in small intestine crypts.
• Discovery of novel cellular niches across organs: Enables identification of new cellular niches and interactions relevant to tissue organization, developmental biology, disease pathology, and regenerative medicine.

Methodology:

Analyzes spatial relationships between cells in native tissues and integrates single-cell mRNA sequencing with physical proximity information to construct maps of cellular interactions.