Spatial-CITE-seq: spatially resolved high-plex protein and whole transcriptome co-mapping

We present spatial-CITE-seq for high-plex protein and whole transcriptome co-mapping, which was firstly demonstrated for profiling 189 proteins and transcriptome in multiple mouse tissue types. It was then applied to human tissues to measure 273 proteins and transcriptome that revealed spatially distinct germinal center reaction in tonsil and early immune activation in skin at the COVID-19 mRNA vaccine injection site. Spatial-CITE-seq may find a range of applications in biomedical research. ### Competing Interest Statement R.F., Y.L., and Y.D. are inventors of a patent application related to this work. R.F. is scientific founder and advisor of IsoPlexis, Singleron Biotechnologies, and AtlasXomics. The interests of R.F. were reviewed and managed by Yale University Provost Office in accordance with the University conflict of interest policies. PB and MC are employees at Lunaphore Technologies SA