Advance Single-Cell Studies with Spatial Insights

Capturing spatial information is essential to elucidate how cells function and interact within their native tissue environment. However, the initial spatial transcriptomics techniques have several limitations.

Researchers often categorize spatial approaches into two types: microscopy-based and capture-based. Microscopy-based methods use labeled probes to visualize RNA molecules within tissue sections. However, they rely on cell segmentation algorithms to assign the RNA signal to individual cells. Many capture-based methods use spatially barcoded probes to collect transcripts from overlaid tissue before sequencing. But they require cell deconvolution algorithms to estimate each cell’s contribution to the RNA mixture at a capture site.

To enable more precise spatial analysis, Takara Bio released the Trekker Single-Cell Spatial Mapping Kita nuclear labeling method that allows scientists to acquire spatial and single-cell data in a single experiment. The technology, which adds only an hour upstream to single-cell assays, uses a monolayer of spatially barcoded beads and ultraviolet light to tag individual nuclei in spatial context prior to single-cell library preparation.¹ Following tissue dissociation, scientists perform single-nucleus RNA sequencing to analyze the mRNA and spatial barcodes. By spatially labeling individual nuclei before tissue dissociation, researchers can “directly map the spatial location of each single cell in its spatial context, representing a direct measurement and bypassing any guesstimates of a cell’s contribution via complex algorithms,” said Christina Fan, Vice President, Spatial Genomics R&D at Takara Bio USA and cofounder of Curio Bioscience.

This innovative technology can profile cell types often missed by previous approaches, such as small immune cells. Additionally, Trekker technology opens up the possibility for scientists to study spatial omes, including chromatin accessibility, immune repertoire, and beyond.