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Knowledge of host\u2010pathogen interactions and host responses to infection is crucial for conservation and management. Obtaining this knowledge quickly is made increasingly possible by a variety of genomic approaches, yet, for many species the bottleneck to understanding this, remains access to appropriate samples and data. Lack of sample availability has also limited our understanding of how pathogens and the immune responses of hosts change over time. Archival materials may provide a way to explore pathogen emergence and host responses over multiple\u2014possibly hundreds\u2014of years. Here, we tested whether formalin\u2010fixed paraffin\u2010embedded (FFPE) tissue samples could be used to understand an unknown pathology, lamprey reddening syndrome (LRS), affecting pouched lampreys (<jats:italic>Geotria australis<\/jats:italic>). Our differential expression analyses of dermal tissues from four unaffected lampreys and eight affected lampreys collected in 2012 alluded to several potential agents associated with LRS. Interestingly, the pathways associated with viral infections were overrepresented in affected versus unaffected lamprey. Gene ontology analyses of the affected and non\u2010affected lampreys also provided new insights into the largely understudied immune responses of pouched lampreys. Our work confirms that FFPE samples can be used to infer information about the transcriptional responses of a wildlife species affected by unknown historical pathologies\/syndromes. In addition, the use of FFPE samples for transcriptomics offers many opportunities to investigate the genomic responses of a species to a variety of environmental changes. We conclude with a discussion about how to best sample and utilize these unique archival resources for future wildlife transcriptomic studies.<\/jats:p>","DOI":"10.1111\/1755-0998.13805","type":"journal-article","created":{"date-parts":[[2023,5,8]],"date-time":"2023-05-08T04:28:31Z","timestamp":1683520111000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Formalin\u2010fixed paraffin\u2010embedded (<scp>FFPE<\/scp>) samples help to investigate transcriptomic responses in wildlife disease"],"prefix":"10.1111","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5334-2771","authenticated-orcid":false,"given":"Allison K.","family":"Miller","sequence":"first","affiliation":[{"name":"Anatomy Department University of Otago  Dunedin New Zealand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cara L.","family":"Brosnahan","sequence":"additional","affiliation":[{"name":"Animal Health Laboratory Ministry for Primary Industries  Upper Hutt New Zealand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anjali","family":"Pande","sequence":"additional","affiliation":[{"name":"Animal Health Laboratory Ministry for Primary Industries  Upper Hutt New Zealand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cindy F.","family":"Baker","sequence":"additional","affiliation":[{"name":"National Institute of Water and Atmospheric Research Limited  Hamilton New Zealand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jemma L.","family":"Geoghegan","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology University of Otago  Dunedin New Zealand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jane","family":"Kitson","sequence":"additional","affiliation":[{"name":"Kitson Consulting Ltd  Invercargill\/Waihopai New Zealand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0671-3637","authenticated-orcid":false,"given":"Neil J.","family":"Gemmell","sequence":"additional","affiliation":[{"name":"Anatomy Department University of Otago  Dunedin New Zealand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Edwina J.","family":"Dowle","sequence":"additional","affiliation":[{"name":"Anatomy Department University of Otago  Dunedin New Zealand"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2023,5,7]]},"reference":[{"key":"e_1_2_12_2_1","doi-asserted-by":"publisher","DOI":"10.1186\/1743-422X-11-120"},{"key":"e_1_2_12_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pt.2014.11.001"},{"key":"e_1_2_12_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"e_1_2_12_5_1","volume-title":"FastQC: A quality control tool for high throughput sequence data","author":"Andrews S.","year":"2010"},{"key":"e_1_2_12_6_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms17091579"},{"key":"e_1_2_12_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/75556"},{"key":"e_1_2_12_8_1","doi-asserted-by":"publisher","DOI":"10.1186\/1297-9716-42-20"},{"key":"e_1_2_12_9_1","doi-asserted-by":"publisher","DOI":"10.1139\/cjfas-2016-0292"},{"key":"e_1_2_12_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/0959-8030(91)90019-G"},{"key":"e_1_2_12_11_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.2517-6161.1995.tb02031.x"},{"key":"e_1_2_12_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_2_12_13_1","doi-asserted-by":"publisher","DOI":"10.1080\/00288330.2018.1556167"},{"key":"e_1_2_12_14_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00441-010-1026-0"},{"key":"e_1_2_12_15_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2016.12.063"},{"key":"e_1_2_12_16_1","volume-title":"Furunculosis and other diseases caused by Aeromonas salmonicida","author":"Cipriano R. 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