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University of Michigan Medical School

Nat. Protoc., Oct 31 2024, | https://doi.org/10.1038/s41596-024-01065-0 Seq-Scope: repurposing Illumina sequencing flow cells for high-resolution spatial transcriptomics

Yongsung Kim^1,9, Weiqiu Cheng^2,9, Chun-Seok Cho^1,9, Yongha Hwang1,3, Yichen Si2, Anna Park1, Mitchell Schrank1, Jer-En Hsu1, Angelo Anacleto1, Jingyue Xi2, Myungjin Kim1, Ellen Pedersen4, Olivia I. Koues4, Thomas Wilson4,5,6, ChangHee Lee7, Goo Jun8, Hyun Min Kang2 & Jun Hee Lee1

¹Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA.

²Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA.

³Space Planning and Analysis, University of Michigan Medical School, Ann Arbor, MI, USA.

⁴Biomedical Research Core Facilities Advanced Genomics Core, University of Michigan, Ann Arbor, MI, USA.

⁵Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA.

⁶Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.

⁷Department of Genetics, Harvard Medical School, Boston, MA, USA.

⁸Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA.

⁹These authors contributed equally: Yongsung Kim, Weiqiu Cheng, Chun-Seok Cho

Corresponding authors

Correspondence to Hyun Min Kang or Jun Hee Lee.

Abstract

Spatial transcriptomics technologies aim to advance gene expression studies by profiling the entire transcriptome with intact spatial information from a single histological slide. However, the application of spatial transcriptomics is limited by low resolution, limited transcript coverage, complex procedures, poor scalability and high costs of initial setup and/or individual experiments. Seq-Scope repurposes the Illumina sequencing platform for high-resolution, high-content spatial transcriptome analysis, overcoming these limitations. It offers submicrometer resolution, high capture efficiency, rapid turnaround time and precise annotation of histopathology at a much lower cost than commercial alternatives. This protocol details the implementation of Seq-Scope with an Illumina NovaSeq 6000 sequencing flow cell, allowing the profiling of multiple tissue sections in an area of 7 mm × 7 mm or larger. We describe the preparation of a fresh-frozen tissue section for both histological imaging and sequencing library preparation and provide a streamlined computational pipeline with comprehensive instructions to integrate histological and transcriptomic data for high-resolution spatial analysis. This includes the use of conventional software tools for single-cell and spatial analysis, as well as our recently developed segmentation-free method for analyzing spatial data at submicrometer resolution. Aside from array production and sequencing, which can be done in batches, tissue processing, library preparation and running the computational pipeline can be completed within 3 days by researchers with experience in molecular biology, histology and basic Unix skills. Given its adaptability across various biological tissues, Seq-Scope establishes itself as an invaluable tool for researchers in molecular biology and histology.

논문정보

형식Review Paper
게재일2024년 10월 (BRIC 등록일 2024-11-12)
연구진국외 연구진
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