Wang, T.Roach, M.J.Harvey, K.Morlanes, J.E.Kiedik, B.Al-Eryani, G.Greenwald, A.Kalavros, N.Dezem, F.S.Ma, Y.Pita-Juarez, Y.H.Wise, K.Degletagne, C.Elz, A.Hadadianpour, A.Johanneson, J.Pakiam, F.Ryu, H.Newell, E.W.Tonon, L.et al.2025-03-122025-03-122024Communications Biology, 2024; 7(1):1340-1-1340-122399-36422399-3642https://hdl.handle.net/2440/143845Formalin-fixed paraffin-embedded (FFPE) samples are valuable but underutilized in single-cell omics research due to their low RNA quality. In this study, leveraging a recent advance in single-cell genomic technology, we introduce snPATHO-seq, a versatile method to derive high-quality single-nucleus transcriptomic data from FFPE samples. We benchmarked the performance of the snPATHO-seq workflow against existing 10x 3' and Flex assays designed for frozen or fresh samples and highlighted the consistency in snRNA-seq data produced by all workflows. The snPATHO-seq workflow also demonstrated high robustness when tested across a wide range of healthy and diseased FFPE tissue samples. When combined with FFPE spatial transcriptomic technologies such as FFPE Visium, the snPATHO-seq provides a multi-modal sampling approach for FFPE samples, allowing more comprehensive transcriptomic characterization.en© The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.RNA sequencing; TranscriptomicsHumansFormaldehydeParaffin EmbeddingTissue FixationGene Expression ProfilingSequence Analysis, RNAWorkflowSingle-Cell AnalysisTranscriptomeJournal article10.1038/s42003-024-07043-2714029Roach, M.J. [0000-0003-1488-5148]Butler, L.M. [0000-0003-2698-3220]Martelotto, L.G. [0000-0002-9625-1183]