Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology.
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| Titel: | Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology. |
|---|---|
| Autoren: | Juwayria; Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India., Shrivastava P; Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India., Yadav K; Department of Pathology, All India Institute of Medical Sciences, New Delhi, India., Das S; Department of Mechanical Engineering, Indian Institute of Technology, New Delhi, India., Mittal S; Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India., Kumar S; Department of Surgical Oncology, All India Institute of Medical Sciences, New Delhi, India., Jain D; Department of Pathology, All India Institute of Medical Sciences, New Delhi, India., Malik PS; Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India., Gupta I; Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India. ishaan@dbeb.iitd.ac.in. |
| Quelle: | NPJ systems biology and applications [NPJ Syst Biol Appl] 2024 Nov 30; Vol. 10 (1), pp. 142. Date of Electronic Publication: 2024 Nov 30. |
| Publikationsart: | Journal Article |
| Sprache: | English |
| Info zur Zeitschrift: | Publisher: Nature Publishing Group in partnership with SBI, The Systems Biology Institute Country of Publication: England NLM ID: 101677786 Publication Model: Electronic Cited Medium: Internet ISSN: 2056-7189 (Electronic) Linking ISSN: 20567189 NLM ISO Abbreviation: NPJ Syst Biol Appl Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: [London] : Nature Publishing Group in partnership with SBI, The Systems Biology Institute, [2015]- |
| MeSH-Schlagworte: | Gene Expression Profiling*/methods, Humans ; Tissue Array Analysis/methods ; Oligonucleotide Array Sequence Analysis/methods ; Transcriptome/genetics ; Computational Biology/methods |
| 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 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. (© 2024. The Author(s).) |
| Competing Interests: | Competing interests: All authors have reviewed potential conflicts of interest and declare that there are no competing interests related to the manuscript. This declaration is made to maintain transparency and uphold the integrity of our research. |
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| Entry Date(s): | Date Created: 20241130 Date Completed: 20241130 Latest Revision: 20241203 |
| Update Code: | 20250114 |
| PubMed Central ID: | PMC11608264 |
| DOI: | 10.1038/s41540-024-00462-1 |
| PMID: | 39616155 |
| Datenbank: | MEDLINE |
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