{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Blick T"],"funding":["Queensland Children's Hospital","Wesley Research Institute","Cooper Rice-Brading Foundation, Australia","Richie's Rainbow Foundation","University of Queensland","National Breast Cancer Foundation","Medical Research Future Fund","Australian Academy of Sciences","PA Research Foundation"],"pagination":["lqag007"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12838529"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["8(1)"],"pubmed_abstract":["We developed Standardised Minimum 3D Distance (SM3DD), an entirely cell segmentation/annotation-free approach to the analysis of spatial RNA datasets, using it to compare lung tissue from 16 clinically normal individuals to that of 18 SARS-CoV-2 patients who died from acute respiratory distress syndrome. RNA spatial coordinates were determined using the CosMx™ Spatial Molecular Imager (Bruker Spatial Biology, US). For each individual transcript location, we calculated the three-dimensional distances to the nearest transcript of each transcript type, standardising the distances to each transcript type. Mean SM3DDs were compared between normal and SARS-CoV-2 patients. Notably, hierarchical clustering of the directional log10(P) values organized genes by functionality, making it easier to int"],"journal":["NAR genomics and bioinformatics"],"pubmed_title":["SM3DD with segmented PCA: a comprehensive method for interpreting 3D spatial transcriptomics."],"pmcid":["PMC12838529"],"funding_grant_id":["2019485","2023/IIRS0063"],"pubmed_authors":["Belz GT","Nam A","Liang Y","Blick T","Guimaraes PSF","Fraser JF","Martins APC","Monkman J","Kilgallon A","Kulasinghe A","de Noronha L","Nagashima S","Tan CW","Killingbeck EE","Leon M","Machado-Souza C","Kim Y","Cooper C","Pan L","Souza-Fonseca-Guimaraes F"],"additional_accession":[]},"is_claimable":false,"name":"SM3DD with segmented PCA: a comprehensive method for interpreting 3D spatial transcriptomics.","description":"We developed Standardised Minimum 3D Distance (SM3DD), an entirely cell segmentation/annotation-free approach to the analysis of spatial RNA datasets, using it to compare lung tissue from 16 clinically normal individuals to that of 18 SARS-CoV-2 patients who died from acute respiratory distress syndrome. RNA spatial coordinates were determined using the CosMx™ Spatial Molecular Imager (Bruker Spatial Biology, US). For each individual transcript location, we calculated the three-dimensional distances to the nearest transcript of each transcript type, standardising the distances to each transcript type. Mean SM3DDs were compared between normal and SARS-CoV-2 patients. Notably, hierarchical clustering of the directional log10(P) values organized genes by functionality, making it easier to int","dates":{"release":"2026-01-01T00:00:00Z","publication":"2026 Mar","modification":"2026-06-12T03:19:28.69Z","creation":"2026-06-12T03:11:51.993Z"},"accession":"S-EPMC12838529","cross_references":{"pubmed":["41608733"],"doi":["10.1093/nargab/lqag007"]}}