Faculty, Staff and Student Publications
Publication Date
1-6-2023
Journal
Nucleic Acids Research
Abstract
In recent years, the explosive growth of spatial technologies has enabled the characterization of spatial heterogeneity of tissue architectures. Compared to traditional sequencing, spatial transcriptomics reserves the spatial information of each captured location and provides novel insights into diverse spatially related biological contexts. Even though two spatial transcriptomics databases exist, they provide limited analytical information. Information such as spatial heterogeneity of genes and cells, cell-cell communication activities in space, and the cell type compositions in the microenvironment are critical clues to unveil the mechanism of tumorigenesis and embryo differentiation. Therefore, we constructed a new spatial transcriptomics database, named SPASCER (https://ccsm.uth.edu/SPASCER), designed to help understand the heterogeneity of tissue organizations, region-specific microenvironment, and intercellular interactions across tissue architectures at multiple levels. SPASCER contains datasets from 43 studies, including 1082 sub-datasets from 16 organ types across four species. scRNA-seq was integrated to deconvolve/map spatial transcriptomics, and processed with spatial cell-cell interaction, gene pattern and pathway enrichment analysis. Cell-cell interactions and gene regulation network of scRNA-seq from matched spatial transcriptomics were performed as well. The application of SPASCER will provide new insights into tissue architecture and a solid foundation for the mechanistic understanding of many biological processes in healthy and diseased tissues.
Keywords
Humans, Carcinogenesis, Cell Communication, Cell Differentiation, Gene Expression Profiling, Single-Cell Analysis, Transcriptome, Tumor Microenvironment, Databases, Genetic
DOI
10.1093/nar/gkac889
PMID
36243975
PMCID
PMC9825565
PubMedCentral® Posted Date
10-16-2022
PubMedCentral® Full Text Version
Post-print
Published Open-Access
yes
