High-Plex Spatial Profiling of RNA and Protein Using Digital Spatial Profiler

Nan Wang; Xia Li; Zhiyong Ding

doi:10.1007/978-1-0716-3163-8_6

High-Plex Spatial Profiling of RNA and Protein Using Digital Spatial Profiler

Methods Mol Biol. 2023:2660:69-83. doi: 10.1007/978-1-0716-3163-8_6.

Authors

Nan Wang¹, Xia Li¹, Zhiyong Ding²

Affiliations

¹ Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd, Jinan City, Shandong Province, P. R. China.
² Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd, Jinan City, Shandong Province, P. R. China. [email protected].

PMID: 37191791
DOI: 10.1007/978-1-0716-3163-8_6

Abstract

The rapid emergence of spatial multi-omics technologies in recent years has revolutionized biomedical research. Among these, the Digital Spatial Profiler (DSP, commercialized by nanoString) has become one of the dominant technologies in spatial transcriptomics and proteomics and has assisted in deconvoluting complex biological questions. Based on our practical experience in the past 3 years with DSP, we share here a detailed hands-on protocol and key handling notes that will allow the broader community to optimize their work procedure.

Keywords: Cancer Transcriptome Atlas (CTA); Companion diagnostics (CDs); Digital Spatial Profiler (DSP), Whole Transcriptome Atlas (WTA); Next-generation sequencing (NGS)-based barcode; Spatial biology, Transcriptomics, Proteomics, Formalin-fixed paraffin-embedded (FFPE) specimens.

MeSH terms

Formaldehyde
Gene Expression Profiling* / methods
Paraffin Embedding
RNA* / genetics
Tissue Fixation

Substances

RNA
Formaldehyde