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We previously revealed that M cells in the FAE of the chicken lung, bursa of Fabricius (bursa), and caecum based on the expression of <jats:italic>CSF1R<\/jats:italic>. Here, we applied RNA-seq analysis on highly enriched <jats:italic>CSF1R<\/jats:italic>-expressing bursal M cells to investigate their transcriptome and identify novel chicken M cell-associated genes. Our data show that, like mammalian M cells, those in the FAE of the chicken bursa also express <jats:italic>SOX8<\/jats:italic>, <jats:italic>MARCKSL1<\/jats:italic>, <jats:italic>TNFAIP2<\/jats:italic> and <jats:italic>PRNP<\/jats:italic>. Immunohistochemical analysis also confirmed the expression of SOX8 in <jats:italic>CSF1R<\/jats:italic>-expressing cells in the lung, bursa, and caecum. However, we found that many other mammalian M cell-associated genes such as <jats:italic>SPIB<\/jats:italic> and <jats:italic>GP2<\/jats:italic> were not expressed by chicken M cells or represented in the chicken genome. Instead, we show bursal M cells express high levels of related genes such as <jats:italic>SPI1<\/jats:italic>. Whereas our data show that bursal M cells expressed <jats:italic>CSF1R<\/jats:italic>-highly, the M cells in the small intestine lacked <jats:italic>CSF1R<\/jats:italic> and both expressed SOX8. This study offers insights into the transcriptome of chicken M cells, revealing the expression of CSF1R in M cells is tissue-specific.<\/jats:p>","DOI":"10.1038\/s41598-024-59368-x","type":"journal-article","created":{"date-parts":[[2024,4,16]],"date-time":"2024-04-16T15:30:16Z","timestamp":1713281416000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Discrimination of distinct chicken M cell subsets based on CSF1R expression"],"prefix":"10.1038","volume":"14","author":[{"given":"Safieh","family":"Zeinali","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kate","family":"Sutton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masoud Ghaderi","family":"Zefreh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neil","family":"Mabbott","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lonneke","family":"Vervelde","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,4,16]]},"reference":[{"key":"59368_CR1","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1038\/mi.2007.9","volume":"1","author":"P Brandtzaeg","year":"2008","unstructured":"Brandtzaeg, P., Kiyono, H., Pabst, R. & Russell, M. 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