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Seq-Scope: repurposing Illumina sequencing flow cells for high-resolution spatial transcriptomics
Yongsung Kim1, Weiqiu Cheng2, Chun-Seok Cho1
1Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA.
Nature Protocols
|November 1, 2024
Summary
Seq-Scope enhances spatial transcriptomics by repurposing Illumina sequencing for high-resolution gene expression analysis. This cost-effective method offers submicrometer resolution and rapid results for molecular biology and histology research.
Area of Science:
- Genomics
- Molecular Biology
- Histology
Background:
- Spatial transcriptomics enables gene expression profiling with spatial context.
- Current methods face limitations in resolution, cost, and scalability.
Purpose of the Study:
- To introduce Seq-Scope, a novel protocol for high-resolution spatial transcriptome analysis.
- To overcome limitations of existing spatial transcriptomics technologies.
Main Methods:
- Repurposing the Illumina NovaSeq 6000 platform for spatial transcriptomics.
- Detailed protocol for tissue section preparation, library construction, and computational analysis.
- Integration of histological imaging with transcriptomic data at submicrometer resolution.
Main Results:
- Seq-Scope achieves submicrometer resolution and high capture efficiency.
- The protocol enables rapid turnaround time (within 3 days) and cost-effectiveness.
- Demonstrates precise annotation of histopathology alongside transcriptomic data.
Conclusions:
- Seq-Scope provides a scalable and affordable solution for high-resolution spatial transcriptome analysis.
- The method is adaptable across various biological tissues.
- It serves as a valuable tool for molecular biology and histology researchers.
