Journal Article

DKFZ-2026-02817

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Protocol for integrated multimodal spatial RNA and protein profiling using Xenium and MACSima.

Scheuermann, S. (First author)DKFZ* ; Rosenbauer, J. (First author)DKFZ* ; Bortolomeazzi, M.DKFZ* ; Sant, P.DKFZ* ; Ulloa Guerrero, C. P.DKFZ* ; Schütze, L.DKFZ* ; Platten, M.DKFZ* ; Mallm, J.-P.DKFZ* ; Seitz, C. (Last author)DKFZ*

2026
Cell Press Cambridge, MA

Abstract: Combining same-section spatial transcriptomics with high-plex protein imaging enables comprehensive characterization of the tissue microenvironment while preserving spatial information. Here, we present a protocol for multimodal spatial RNA and protein profiling using Xenium transcriptomics and MACSima cyclic protein imaging. We describe steps for tissue preparation, hybridization, and RNA imaging, followed by slide recovery, antigen retrieval, and MACSima imaging cyclic staining (MICS). We provide Python scripts for data registration and integration to generate a single-cell multimodal map of the tissue microenvironment.

Keyword(s): Cancer ; Computer sciences ; Genomics ; Immunology ; Microscopy ; Proteomics ; Single Cell

Note: #EA:B310#EA:D170#LA:B310# / #NCTZFB26# / #DKTKZFB26#

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Contributing Institute(s):

1. KKE Pädiatrische Onkologie (B310)
2. KKE Neuroimmunologie und Hirntumorimmunologie (D170)
3. DKTK HD zentral (HD01)
4. Single-cell Open Lab (W192)
5. Koordinierungsstelle NCT Heidelberg (HD02)

Research Program(s):

1. 312 - Funktionelle und strukturelle Genomforschung (POF4-312) (POF4-312)

Appears in the scientific report 2026

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Database coverage:
; ; Article Processing Charges ; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; DOAJ Seal ; Emerging Sources Citation Index ; Fees ; SCOPUS ; Web of Science Core Collection

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