Spatial transcriptomic technologies and available paths for analysis

Deciphering the principles and mechanisms by which gene activity orchestrates complex cellular arrangements in multicellular organisms has far-reaching implications for research in the life sciences. Recent technological advances in next-generation sequencing- and imaging-based approaches have established the power of spatial transcriptomics to measure expression levels of all or most genes systematically throughout tissue space, and have been adopted to generate biological insights in neuroscience, development and plant biology as well as to investigate a range of disease contexts, including cancer. Similar to datasets made possible by genomic sequencing and population health surveys, the large-scale atlases generated by this technology lend themselves to exploratory data analysis for hypothesis generation.

Researchers from NYU Langone Health discuss spatial transcriptomic technologies and describe the repertoire of operations available for paths of analysis of the resulting data. Spatial transcriptomics can also be deployed for hypothesis testing using experimental designs that compare time points or conditions—including genetic or environmental perturbations. Finally, spatial transcriptomic data are naturally amenable to integration with other data modalities, providing an expandable framework for insight into tissue organization.

The technologies of spatial transcriptomics provide a gene-expression matrix

Fig. 1

a, NGS-based spatial transcriptomic methods barcode transcripts according to their location in a lattice of spots. b, ISS approaches directly read out the transcript sequence within the tissue. c, ISH methods detect target sequences by hybridization of complementary fluorescent probes. d, The product of spatial transcriptomics is the gene-expression matrix, in which the rows and columns correspond to genes and locations.

Rao A, Barkley D, França GS, Yanai I (2021). Exploring tissue architecture using spatial transcriptomics. Nature 596, 211–220 [abstract]

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