Abstract
Abstract10X Visium, a popular Spatial transcriptomics (ST) method, faces limited adoption due to its high cost and restricted sample usage per slide. To address these issues, we propose Microarray Integrated Spatial Transcriptomics (MIST), combining conventional tissue microarray (TMA) with Visium, using laser-cutting and 3D printing to enhance slide throughput. Our design facilitates independent replication and customization in individual labs to suit specific experimental needs. We provide a step-by-step guide from designing TMAs to the library preparation step. We demonstrate MIST’s cost-effectiveness and technical benefits over Visium and GeoMx Nanostring. We also introduce ‘AnnotateMap’, a novel computational tool for efficient analysis of multiple ROIs processed through MIST.
Publisher
Cold Spring Harbor Laboratory
Reference9 articles.
1. Tissue Microarray: A rapidly evolving diagnostic and research tool
2. Fine needle aspiration and core needle biopsy of metastatic malignancy of unknown primary site;Mod Pathol,2019
3. Fine-needle aspiration and core needle biopsy: An update on 2 common minimally invasive tissue sampling modalities;Cancer Cytopathol,2016
4. Challenges and Opportunities for Immunoprofiling Using a Spatial High-Plex Technology: The NanoString GeoMx® Digital Spatial Profiler
5. NanoString [Internet]. NanoString Technologies, Inc.; 2021 [cited 2023 Dec 1]. GeoMx Manuals & Guides. Available from: https://nanostring.com/resources/geomx-manuals-guides/