Microarray Integrated Spatial Transcriptomics (MIST) for Affordable, Robust, and Comprehensive Digital Pathology

Juwayria; Priyansh Shrivastava; Kaustar Yadav; Sourabh Das; Shubham Mittal; Sunil Kumar; Deepali Jain; Prabhat Singh Malik; Ishaan Gupta

doi:10.1038/s41540-024-00462-1

Bioinformaticsnpj Systems Biology and ApplicationsNov 30, 2024

Peer-reviewed journal article

Microarray Integrated Spatial Transcriptomics (MIST) for Affordable, Robust, and Comprehensive Digital Pathology

Juwayria, Priyansh Shrivastava, Kaustar Yadav, Sourabh Das, Shubham Mittal iD, Sunil Kumar iD, Deepali Jain iD, Prabhat Singh Malik iD, Ishaan Gupta iD

Abstract

10X 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 MISTs 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.

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