Measurement of gene expression together with positions within a tissue. Its spatial units can be individual molecules, segmented cells or capture regions; these units should not be conflated.
Slide-seq measures gene expression with spatial information by transferring tissue-associated RNA onto a surface carrying position-mapped barcoded beads. Sequencing associates captured transcripts with bead barcodes and hence with locations. The original study used approximately ten-micrometre beads and demonstrated tissue expression patterns at high spatial resolution. A bead measurement is a capture region rather than an automatic identification of one intact cell; tissue geometry and capture efficiency still affect interpretation. [ref]
Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution by Samuel G. Rodriques and others. 2019, bead array, barcode-position mapping and tissue demonstrations
Spatial barcoding attaches a location-associated sequence label to a measured molecule or its derivative. In spatial transcriptomics, sequencing the barcode together with captured RNA connects expression measurements to tissue position. The barcode identifies the sampling location rather than necessarily the exact original molecular coordinate or a unique cell. Slide-seq implements the principle with individually barcoded, position-mapped beads. [ref]
Visualization and analysis of gene expression in tissue sections by spatial transcriptomics by Patrik L. Ståhl and others. 2016, spatially barcoded capture probes
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