{"entity": "researcher", "timestamp": "2026-08-20T21:42:24.381Z", "family": "Greenwald", "given": "Alissa", "initials": "A", "orcid": "0000-0001-5428-9645", "affiliations": ["Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/6997859be9f546829facb356d6e9a6d0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/6997859be9f546829facb356d6e9a6d0"}}, "publications": [{"entity": "publication", "iuid": "eaa1671d4d2e4f69af8f1d4c38e3dd81", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/eaa1671d4d2e4f69af8f1d4c38e3dd81.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/eaa1671d4d2e4f69af8f1d4c38e3dd81"}}, "title": "snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives.", "authors": [{"family": "Wang", "given": "Taopeng", "initials": "T", "orcid": "0000-0002-9184-609X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/01e933430f5c4715b4f8551eb21d8158.json"}}, {"family": "Roach", "given": "Michael J", "initials": "MJ", "orcid": "0000-0003-1488-5148", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f8258e46da264256b9735267e451ab6e.json"}}, {"family": "Harvey", "given": "Kate", "initials": "K", "orcid": "0000-0002-2155-5203", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/afb60b0fb41a4fb998ea9fa280bde92d.json"}}, {"family": "Morlanes", "given": "Javier Escudero", "initials": "JE"}, {"family": "Kiedik", "given": "Beata", "initials": "B", "orcid": "0000-0001-8517-5253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ee049740d8e4ae7879d456ddcd08ef5.json"}}, {"family": "Al-Eryani", "given": "Ghamdan", "initials": "G"}, {"family": "Greenwald", "given": "Alissa", "initials": "A", "orcid": "0000-0001-5428-9645", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6997859be9f546829facb356d6e9a6d0.json"}}, {"family": "Kalavros", "given": "Nikolaos", "initials": "N", "orcid": "0000-0001-5503-9808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4839d734d7d04fb08cc1aa05df8da1df.json"}}, {"family": "Dezem", "given": "Felipe Segato", "initials": "FS"}, {"family": "Ma", "given": "Yuling", "initials": "Y"}, {"family": "Pita-Juarez", "given": "Yered H", "initials": "YH"}, {"family": "Wise", "given": "Kellie", "initials": "K"}, {"family": "Degletagne", "given": "Cyril", "initials": "C"}, {"family": "Elz", "given": "Anna", "initials": "A"}, {"family": "Hadadianpour", "given": "Azi", "initials": "A"}, {"family": "Johanneson", "given": "Jack", "initials": "J", "orcid": "0009-0002-7612-1290", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed3b76d318044ce18d854fa54451fbb9.json"}}, {"family": "Pakiam", "given": "Fiona", "initials": "F"}, {"family": "Ryu", "given": "Heeju", "initials": "H"}, {"family": "Newell", "given": "Evan W", "initials": "EW", "orcid": "0000-0002-2889-243X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/954fa28bfe19491c889a04d9dcdd7fb5.json"}}, {"family": "Tonon", "given": "Laurie", "initials": "L", "orcid": "0009-0005-8794-7276", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/15a0d18b94174c54b565af53459d81d4.json"}}, {"family": "Kohlway", "given": "Andrew", "initials": "A"}, {"family": "Drennon", "given": "Tingsheng", "initials": "T", "orcid": "0000-0002-8106-7981", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2f6bb092530e4ae980f89364447a5457.json"}}, {"family": "Abousoud", "given": "Jawad", "initials": "J"}, {"family": "Stott", "given": "Ryan", "initials": "R"}, {"family": "Lund", "given": "Paul", "initials": "P", "orcid": 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M", "initials": "LM", "orcid": "0000-0003-2698-3220", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e76885407d5c4fd2bdcd4a27e5520217.json"}}, {"family": "O'Toole", "given": "Sandra", "initials": "S"}, {"family": "Plummer", "given": "Jasmine", "initials": "J", "orcid": "0000-0001-7263-350X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/862458ea9eb541d9a9cbfcb74bd2bd37.json"}}, {"family": "Vlachos", "given": "Ioannis S", "initials": "IS", "orcid": "0000-0002-8849-808X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/486d1c8f0d984011ac065a50699bfa99.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}, {"family": "Swarbrick", "given": "Alexander", "initials": "A", "orcid": "0000-0002-3051-5676", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/09393c3690dc4ff8b42f5b39ec981a22.json"}}, {"family": "Martelotto", "given": "Luciano G", "initials": "LG", "orcid": "0000-0002-9625-1183", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/87031d582f3c44fc8cb8281fb45ce26f.json"}}], "type": "journal article", "published": "2024-10-16", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "7", "issue": "1", "pages": "1340", "issn-l": "2399-3642"}, "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.", "doi": "10.1038/s42003-024-07043-2", "pmid": "39414943", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11484811"}, {"db": "pii", "key": "10.1038/s42003-024-07043-2"}, {"db": "GEO", "key": "GSE268426"}, {"db": "GEO", "key": "GSE268427"}, {"db": "Dryad", "key": "10.5061/dryad.7m0cfxq4s"}], "notes": [], "created": "2026-08-20T09:25:19.884Z", "modified": "2026-08-20T09:25:20.607Z"}, {"entity": "publication", "iuid": "23cf806d59d1468c9e25ef36b9f29eef", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/23cf806d59d1468c9e25ef36b9f29eef.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/23cf806d59d1468c9e25ef36b9f29eef"}}, "title": "snPATHO-seq: unlocking the pathology archives", "authors": [{"family": "Wang", "given": "Taopeng", "initials": "T", "orcid": "0000-0002-9184-609X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/01e933430f5c4715b4f8551eb21d8158.json"}}, {"family": "Harvey", "given": "Kate", "initials": "K", "orcid": "0000-0002-2155-5203", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/afb60b0fb41a4fb998ea9fa280bde92d.json"}}, {"family": "Morlanes", "given": "Javier Escudero", "initials": "JE"}, {"family": "Kiedik", "given": "Beata", "initials": "B", "orcid": "0000-0001-8517-5253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0ee049740d8e4ae7879d456ddcd08ef5.json"}}, {"family": "Al-Eryani", "given": "Ghamdan", "initials": "G", "orcid": "0000-0002-1137-1726", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6869f7a561a443aaac3c157a28f6cb4c.json"}}, {"family": "Greenwald", "given": "Alissa", "initials": "A", "orcid": "0000-0001-5428-9645", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6997859be9f546829facb356d6e9a6d0.json"}}, {"family": "Kalavros", "given": "Nikolaos", "initials": "N", "orcid": "0000-0001-5503-9808", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4839d734d7d04fb08cc1aa05df8da1df.json"}}, {"family": "Dezem", "given": "Felipe Segato", "initials": "FS"}, {"family": "Ma", "given": "Yuling", "initials": "Y"}, {"family": "Pita-Juarez", "given": "Yered H", "initials": "YH"}, {"family": "Wise", "given": "Kellie", "initials": "K"}, {"family": "Degletagne", "given": "Cyril", "initials": "C"}, {"family": "Elz", "given": "Anna", "initials": "A"}, {"family": "Hadadianpour", "given": "Azi", "initials": "A"}, {"family": "Johanneson", "given": "Jack", "initials": "J"}, {"family": "Pakiam", "given": "Fiona", "initials": "F"}, {"family": "Ryu", "given": "Heeju", "initials": "H"}, {"family": "Newell", "given": "Evan W", "initials": "EW"}, {"family": "Tonon", "given": "Laurie", "initials": "L"}, {"family": "Kohlway", "given": "Andrew", "initials": "A"}, {"family": "Drennon", "given": "Tingsheng", "initials": "T"}, {"family": "Abousoud", "given": "Jawad", "initials": "J"}, {"family": "Stott", "given": "Ryan", "initials": "R"}, {"family": "Lund", "given": "Paul", "initials": "P"}, {"family": "Durruthy", "given": "Jens", "initials": "J"}, {"family": "Vallejo", "given": "Andres F", "initials": "AF"}, {"family": "Kaczorowski", "given": "Dominik", "initials": "D"}, {"family": "Warren", "given": "Joanna", "initials": "J"}, {"family": "Butler", "given": "Lisa M", "initials": "LM", "orcid": "0000-0003-2698-3220", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e76885407d5c4fd2bdcd4a27e5520217.json"}}, {"family": "O\u2019Toole", "given": "Sandra", "initials": "S", "orcid": "0000-0001-9912-0245", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d16101d8c115471a92b1f2c009881c8e.json"}}, {"family": "Plummer", "given": "Jasmine", "initials": "J", "orcid": "0000-0001-7263-350X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/862458ea9eb541d9a9cbfcb74bd2bd37.json"}}, {"family": "Vlachos", "given": "Ioannis S", "initials": "IS"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}, {"family": "Swarbrick", "given": "Alexander", "initials": "A", "orcid": "0000-0002-3051-5676", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/09393c3690dc4ff8b42f5b39ec981a22.json"}}, {"family": "Martelotto", "given": "Luciano", "initials": "L", "orcid": "0000-0002-9625-1183", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/87031d582f3c44fc8cb8281fb45ce26f.json"}}], "type": "posted-content", "published": "2023-12-08", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2023.12.07.570700", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:50:46.070Z", "modified": "2026-08-20T10:50:46.262Z"}]}