= Solution
The central principle is to \b[attach a recoverable spatial address to an RNA-derived molecule before the tissue's positional organization is destroyed]. After sequencing, each read identifies both a transcript and a capture location.
In the original array-based <spatial transcriptomics> method, a thin tissue section is placed on a slide carrying spatially indexed capture primers. The tissue is imaged for <histology>, then permeabilized. Polyadenylated <messenger RNA> binds the oligo(dT) region of the primers and is copied by <reverse transcription>. The resulting <cDNA> carries the positional barcode. Sequencing identifies the expressed <gene>, and a barcode lookup places its counts back on the tissue image. The first published array used approximately $100\,\mu\mathrm m$ capture features, so a feature could contain contributions from several cells; it was not a single-cell measurement by construction.<Visualization and analysis of gene expression in tissue sections by spatial transcriptomics by Patrik L. Ståhl and others>[pp. 78–80, spatially localized cDNA synthesis, positional barcodes and array features]{ref}
<Slide-seq> applies the same addressing idea using a dense monolayer of roughly $10\,\mu\mathrm m$ barcoded beads. The bead barcode–position map is decoded in advance. A tissue section is transferred onto the beads, released <RNA> is captured, and the sequenced molecular addresses recover the bead-level expression map. This gives much finer spatial sampling than the original coarse array, although RNA capture efficiency and assignment to individual cells remain limiting.<Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution by Samuel G. Rodriques and others>[pp. 1463–1465, bead puck construction, positional decoding and RNA capture]{ref}
Some assays also incorporate a <unique molecular identifier> so that amplified reads from one captured molecule can be collapsed, reducing <polymerase chain reaction> duplication bias. Spatial barcodes identify capture locations; <unique molecular identifiers> identify molecules within those locations. Neither alone supplies cell boundaries.
For either method, align the coordinate map with <histology>, account for capture efficiency and background, and use independent tissue specimens as <biological replicates>. A smaller capture feature improves sampling granularity but does not guarantee equal effective <spatial resolution> or a pure single-cell transcriptome: tissue thickness, diffusion and mixed cell boundaries still matter.
Back to article page
