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In order to study the specificities of the GALT transcriptome in pigs, we compared the transcriptome profiles of jejunal and ileal Peyer\u2019s patches (PPs), mesenteric lymph nodes (MLNs) and peripheral blood (PB) of four male piglets by RNA-Seq. We identified 1,103 differentially expressed (DE) genes between ileal PPs (IPPs) and jejunal PPs (JPPs), and six times more DE genes between PPs and MLNs. The master regulator genes<jats:italic>FOXP3<\/jats:italic>,<jats:italic>GATA3<\/jats:italic>,<jats:italic>STAT4<\/jats:italic>,<jats:italic>TBX21<\/jats:italic>and<jats:italic>R<\/jats:italic><jats:italic>ORC<\/jats:italic>were less expressed in IPPs compared to JPPs, whereas the transcription factor<jats:italic>BCL6<\/jats:italic>was found more expressed in IPPs. In comparison between IPPs and JPPs, our analyses revealed predominant differential expression related to the differentiation of T cells into Th1, Th2, Th17 and iTreg in JPPs. Our results were consistent with previous reports regarding a higher T\/B cells ratio in JPPs compared to IPPs. We found antisense transcription for respectively 24%, 22% and 14% of the transcripts detected in MLNs, PPs and PB, and significant positive correlations between PB and GALT transcriptomes. Allele-specific expression analyses revealed both shared and tissue-specific<jats:italic>cis<\/jats:italic>-genetic control of gene expression.<\/jats:p>","DOI":"10.1038\/s41598-018-27019-7","type":"journal-article","created":{"date-parts":[[2018,6,7]],"date-time":"2018-06-07T13:30:03Z","timestamp":1528378203000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Immunome differences between porcine ileal and jejunal Peyer\u2019s patches revealed by global transcriptome sequencing of gut-associated lymphoid tissues"],"prefix":"10.1038","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3392-5363","authenticated-orcid":false,"given":"T.","family":"Maroilley","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M.","family":"Berri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"G.","family":"Lemonnier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"D.","family":"Esquerr\u00e9","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C.","family":"Chevaleyre","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S.","family":"M\u00e9lo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"F.","family":"Meurens","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. 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