Trekker Single-Cell Spatial Mapping Kit resources

The core of the Trekker technology lies in its spatially barcoded surface, composed of a bead monolayer. A 25 µm frozen tissue section is placed onto this barcoded substrate. Upon exposure to UV light, oligonucleotides carrying spatial barcodes are cleaved from the beads and attach to the nuclei in their vicinity. The tissue is then dissociated from the substrate, and the nuclei are isolated. Single-nucleus RNA sequencing (snRNA-seq) is performed on these isolated nuclei containing spatial barcode oligos. Spatial barcode oligos are captured and amplified alongside cellular RNA. For each sample, two sequencing libraries are generated—one for gene expression data and another for spatial barcodes. A custom analysis pipeline is used to map the position of each nucleus based on the spatial barcodes it contains. Integrating the Trekker protocol adds just one hour upstream of standard snRNA-seq workflows.