This pipeline is for the STellaris webserver: https://spatial.rhesusbase.com.
Single-cell RNA sequencing (scRNA-seq) has enabled comprehensive profiling of molecular signatures of diverse cell types. However, the spatial information was lost during the tissue dissociation step, hindering the further interpretation of crosstalk between different cell types that coordinates tissue formation and pathological states. Emerging spatial transcriptomics (ST) methods enable measuring gene expression while preserving spatial information. The expanding ST datasets offer the potential for serving as a reference atlas for guiding spatial mapping of existing scRNA-seq data, thereby increasing their value in deciphering intercellular communications in the spatial context.
STellaris is an integrated web server for accurate and flexible spatial mapping of user-uploaded scRNA-seq data. It is founded on a manually curated compilation of ST datasets across diverse organs, developmental stages and pathological states in humans and mice. With the inferred spatial information of single cells, STellaris can thus characterize spatial distances between cell type pairs and identify intercellular LRIs between them. Notably, the spatial construction of other single-cell omics data that were jointly profiled with the transcriptome can be resolved simultaneously if provided.
STellaris also provides a dataset browser tool for navigating ST datasets collected in our local database, as well as a gene search tool for retrieving gene expression characteristics from a spatial perspective.
Please cite: Li, X. et al. STellaris: a web server for accurate spatial mapping of single cells based on spatial transcriptomics data. Nucleic Acids Res. 1–9 (2023) doi:10.1093/nar/gkad419.