Journal: Nature Reviews. Genetics

Article Title: Methods and applications for single-cell and spatial multi-omics

doi: 10.1038/s41576-023-00580-2

Figure Lengend Snippet: Spatial multi-ome profiling of tissue samples can be achieved by applying spatial mono-omics assays separately on adjacent or serial tissue sections (part a ) or in a combined way on the same tissue section (parts b – e ). a , Serial fresh-frozen or formalin-fixed paraffin-embedded (FFPE) tissue sections can be analysed using different spatial mono-omic assays, potentially also combining with morphological stainings and annotations on the same or adjacent sections, followed by computational data integration. b , Microfluidic deterministic barcoding strategies in tissue allow next-generation sequencing (NGS)-based spatial multi-omics profiling of transcriptome-plus-proteins, as in DBiT-seq and Spatial-CITE-seq , and epigenome-plus-transcriptome, as in ATAC&RNA-seq and CUT&Tag-RNAseq . Using dual microfluidic chip-based spatial barcoding of poly(A) RNAs together with proteins or epigenome information at the crossroads of chip channels, a spatially barcoded 2D pixel map of the tissue is created. c , Advanced fluorescence in situ hybridization (FISH)-based methods, including MERFISH , , and seqFISH+ , , , allow microscopy-based identification of thousands of transcripts together with genomic loci in single cells, in addition to being compatible with limited protein readouts using fluorescent or DNA-conjugated antibody readout strategies. These high-resolution imaging methods leverage predefined optical barcoding schemes and complex encoding and readout probe designs. d , Array-based assays, including Spatial Transcriptomics (ST) and 10x Genomics Visium , make use of slides with arrayed oligo-dT spots for capturing and spatial barcoding of poly(A) RNAs followed by NGS profiling. This can be combined with upfront haematoxylin and eosin (H&E) staining or limited protein antibody staining and tissue imaging for spatial mapping. In SM-Omics and SPOTS , these technologies have also been shown to be compatible with antibody-derived tag (ADT)-conjugated antibody-based co-profiling of a larger number of proteins. e , NanoString GeoMx digital spatial profiling (DSP) , , allows quantification of RNAs and proteins in specific regions of interest (ROIs) by counting uniquely barcoded oligonucleotides that are covalently linked through a UV-photocleavable linker with probes or antibodies. Tissue marker staining, imaging, ROI selection and illumination by directed UV light causes disintegration of the photocleavable linkers that are collected and profiled by NGS, followed by spatial mapping to the ROIs. cDNA, complementary DNA; gDNA, genomic DNA; OCT, optimal cutting temperature compound; UMI, unique molecular identifier.

Article Snippet: These high-resolution imaging methods leverage predefined optical barcoding schemes and complex encoding and readout probe designs. d , Array-based assays, including Spatial Transcriptomics (ST) and 10x Genomics Visium , make use of slides with arrayed oligo-dT spots for capturing and spatial barcoding of poly(A) RNAs followed by NGS profiling.

Techniques: Formalin-fixed Paraffin-Embedded, Next-Generation Sequencing, Biomarker Discovery, RNA Sequencing, Fluorescence, In Situ Hybridization, Microscopy, Imaging, Staining, Derivative Assay, Marker, Selection