1. snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives
- Author
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Taopeng Wang, Michael J. Roach, Kate Harvey, Javier Escudero Morlanes, Beata Kiedik, Ghamdan Al-Eryani, Alissa Greenwald, Nikolaos Kalavros, Felipe Segato Dezem, Yuling Ma, Yered H. Pita-Juarez, Kellie Wise, Cyril Degletagne, Anna Elz, Azi Hadadianpour, Jack Johanneson, Fiona Pakiam, Heeju Ryu, Evan W. Newell, Laurie Tonon, Andrew Kohlway, Tingsheng Drennon, Jawad Abousoud, Ryan Stott, Paul Lund, Jens Durruthy, Andres F. Vallejo, Wenyan Li, Robert Salomon, Dominik Kaczorowski, Joanna Warren, Lisa M. Butler, Sandra O’Toole, Jasmine Plummer, Ioannis S. Vlachos, Joakim Lundeberg, Alexander Swarbrick, and Luciano G. Martelotto
- Subjects
Biology (General) ,QH301-705.5 - Abstract
Abstract Formalin-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.
- Published
- 2024
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