Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics v1

Seq-Scope is a high-resolution spatial transcriptomics platform that repurposes Illumina sequencing flow cells to generate submicrometer-scale spatial gene expression maps. Here, we outline five general steps of the workflow: (1) generation of a spatially barcoded flow cell array through initial sequencing, (2) preparation and mounting of fresh-frozen tissue sections onto the array, (3) mRNA capture and reverse transcription on the chip surface, (4) spatial library construction and second-round sequencing, and (5) computational integration of spatial barcodes with transcriptome data to produce a spatial gene expression matrix for downstream analysis. This entry provides a conceptual overview of the experimental and computational framework. Detailed step-by-step procedures, reagent formulations, optimization guidelines, troubleshooting, and computational instructions are described in the full peer-reviewed protocol: Kim, Y., Cheng, W., Cho, C.-S. et al. Seq-Scope: repurposing Illumina sequencing flow cells for high-resolution spatial transcriptomics. Nat Protoc 20, 643–689 (2025). https://doi.org/10.1038/s41596-024-01065-0