Feb 26, 2026
Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics
- Anna Park1,
- Jun Hee Lee1
- 1University of Michigan
Protocol Citation: Anna Park, Jun Hee Lee 2026. Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics. protocols.io https://dx.doi.org/10.17504/protocols.io.dm6gp1qmjgzp/v1
Manuscript citation:
Kim, Y., Cheng, W., Cho, CS. 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
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: February 25, 2026
Last Modified: February 26, 2026
Protocol Integer ID: 244037
Keywords: Seq-Scope, Spatial, resolution spatial transcriptomics seq, spatial transcriptomic, spatial transcriptomics platform, resolution spatial transcriptomics platform, resolution spatial transcriptomic, spatial gene expression matrix for downstream analysis, repurposing illumina sequencing flow cell, repurposing illumina sequencing flow cells for high, flow cell array through initial sequencing, sequencing flow cell, scale spatial gene expression map, spatial gene expression matrix, spatial gene expression map, transcriptome data, initial sequencing, barcoded flow cell array, computational integration of spatial barcode, transcription on the chip surface, flow cell, mrna capture, round sequencing, transcription, spatial barcode, downstream analysis, frozen tissue sections onto the array
Funders Acknowledgements:
NIH
Grant ID: UH3CA268091
Abstract
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
Troubleshooting
Seq-Scope Overview (Find the details in the citation)
Generate the spatially barcoded flow cell array (1st-Seq).
Prepare and mount fresh-frozen tissue onto the chip.
Capture mRNA on the spatial array.
Construct and sequence the spatial library (2nd-Seq).
Build the spatial gene expression matrix and analyze.