{"title":"A practical guide to spatial transcriptomics: lessons from over 1000 samples.","authors":"Daniela Grases, Eduard Porta-Pardo","doi":"10.1016/j.tibtech.2025.08.020","DOIUrl":null,"url":null,"abstract":"<p><p>Spatial transcriptomics (ST) enables the in situ mapping of gene expression, revolutionizing our ability to study tissue organization and cellular interactions. However, many groups struggle with practical barriers to implementation, including platform selection, sample quality, and experimental scalability. We provide a practical guide to ST, informed by the processing and analysis of over 1000 spatial samples across multiple ST platforms. We outline best practices for experimental design, tissue handling, sequencing, and computational analysis, with special attention to clinical samples. Our goal is to translate hands-on experience into recommendations that support robust, reproducible spatial workflows. This guide is designed to assist researchers at all levels: from those designing their first spatial experiment to groups aiming to integrate ST into large-scale studies.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":""},"PeriodicalIF":14.9000,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Trends in biotechnology","FirstCategoryId":"5","ListUrlMain":"https://doi.org/10.1016/j.tibtech.2025.08.020","RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Spatial transcriptomics (ST) enables the in situ mapping of gene expression, revolutionizing our ability to study tissue organization and cellular interactions. However, many groups struggle with practical barriers to implementation, including platform selection, sample quality, and experimental scalability. We provide a practical guide to ST, informed by the processing and analysis of over 1000 spatial samples across multiple ST platforms. We outline best practices for experimental design, tissue handling, sequencing, and computational analysis, with special attention to clinical samples. Our goal is to translate hands-on experience into recommendations that support robust, reproducible spatial workflows. This guide is designed to assist researchers at all levels: from those designing their first spatial experiment to groups aiming to integrate ST into large-scale studies.
期刊介绍：
Trends in Biotechnology publishes reviews and perspectives on the applied biological sciences, focusing on useful science applied to, derived from, or inspired by living systems.
The major themes that TIBTECH is interested in include:
Bioprocessing (biochemical engineering, applied enzymology, industrial biotechnology, biofuels, metabolic engineering)
Omics (genome editing, single-cell technologies, bioinformatics, synthetic biology)
Materials and devices (bionanotechnology, biomaterials, diagnostics/imaging/detection, soft robotics, biosensors/bioelectronics)
Therapeutics (biofabrication, stem cells, tissue engineering and regenerative medicine, antibodies and other protein drugs, drug delivery)
Agroenvironment (environmental engineering, bioremediation, genetically modified crops, sustainable development).
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