High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq

In this study, we extended co-indexing of transcriptomes and epitopes (CITE) to the spatial dimension and demonstrated high-plex protein and whole transcriptome co-mapping. We profiled 189 proteins and whole transcriptome in multiple mouse tissue types with spatial CITE sequencing and then further applied the method to measure 273 proteins and transcriptome in human tissues, revealing spatially distinct germinal center reactions in tonsil and early immune activation in skin at the Coronavirus Disease 2019 mRNA vaccine injection site. Co-indexing of transcriptomes and epitopes is extended to the spatial dimension with large protein panels.

Automated summary

In this study, the researchers extended the co-indexing of transcriptomes and epitopes (CITE) to the spatial dimension and successfully mapped a large number of proteins and the whole transcriptome. They applied this method to analyze multiple mouse tissue types and human tissues, revealing spatially distinct reactions and immune activation. The co-indexing of transcriptomes and epitopes in the spatial dimension with large protein panels proved to be effective.