Toll-like receptor signalling in the intestinal epithelium: how bacterial recognition shapes intestinal function, Nat. Rev. Immunol, vol.10, pp.131-144, 2010. ,
Lymph node dissection-understanding the immunological function of lymph nodes, Clin. Exp. Immunol, vol.169, pp.205-212, 2012. ,
Peyer's patches: organizing B-cell responses at the intestinal frontier, Immunol. Rev, vol.271, pp.230-245, 2016. ,
Morphological and functional comparisons of Peyer's patches in different parts of the swine small intestine, Vet. Immunol. Immunopathol, vol.6, pp.391-403, 1984. ,
Lymphocyte migration in the intestinal mucosa: entry, transit and emigration of lymphoid cells and the influence of antigen, Vet. Immunol. Immunopathol, vol.72, pp.157-165, 1999. ,
The evolutionary basis for differences between the immune systems of man, mouse, pig and ruminants, Vet. Immunol. Immunopathol, vol.152, pp.13-19, 2013. ,
Systematic characterization of porcine ileal Peyer's patch, I. apoptosis-sensitive immature B cells are the predominant cell type, Immunology, vol.98, pp.612-621, 1999. ,
Alternate mucosal immune system: organized Peyer's patches are not required for IgA responses in the gastrointestinal tract, J. Immunol, vol.164, pp.5184-5191, 2000. ,
Ileal Peyer's patches are not necessary for systemic B cell development and maintenance and do not contribute significantly to the overall B cell pool in swine, J. Immunol, vol.187, pp.5150-5161, 2011. ,
Differences in transcriptomic profile and IgA repertoire between jejunal and ileal Peyer's patches, Dev. Comp. Immunol, vol.34, pp.102-106, 2010. ,
Pattern recognition receptors in the gut: analysis of their expression along the intestinal tract and the crypt/villus axis, Physiol Rep, vol.3, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01194058
Extensive expression differences along porcine small intestine evidenced by transcriptome sequencing, PLoS ONE, vol.9, p.88515, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01193806
Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis, BMC Genomics, vol.18, p.967, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-02624041
Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, pp.2114-2120, 2014. ,
, Nucleic Acids Res, vol.44, pp.710-716, 2016.
, ScIEntIfIc REpoRTS |, vol.8, p.9077, 2018.
HTSeq-a Python framework to work with high-throughput sequencing data, Bioinformatics, vol.31, pp.166-169, 2015. ,
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, vol.26, pp.139-140, 2010. ,
A scaling normalization method for differential expression analysis of RNA-seq data, Genome Biology, vol.11, p.25, 2010. ,
STAR: ultrafast universal RNA-seq aligner, Bioinformatics, vol.29, pp.15-21, 2013. ,
From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline, Curr Protoc Bioinformatics, vol.43, issue.11, pp.10-11, 2013. ,
The variant call format and VCFtools, Bioinformatics, vol.27, pp.2156-2158, 2011. ,
QuASAR: quantitative allele-specific analysis of reads, Bioinformatics, vol.31, pp.1235-1242, 2015. ,
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res, vol.25, pp.3389-3402, 1997. ,
GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists, BMC Bioinformatics, vol.10, p.48, 2009. ,
KEGG: kyoto encyclopedia of genes and genomes, Nucleic Acids Res, vol.28, pp.27-30, 2000. ,
Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes, Genome Biol, vol.3, p.34, 2002. ,
Commensal bacteria and expression of two major intestinal chemokines, TECK/CCL25 and MEC/CCL28, and their receptors, PLoS ONE, vol.2, p.677, 2007. ,
Early immune response following Salmonella enterica subspecies enterica serovar Typhimurium infection in porcine jejunal gut loops, Vet. Res, vol.40, p.5, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00903086
Epithelial induction of porcine suppressor of cytokine signaling 2 (SOCS2) gene expression in response to Entamoeba histolytica, Dev. Comp. Immunol, vol.34, pp.562-571, 2010. ,
Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method, Methods, vol.25, pp.402-408, 2001. ,
Advances in swine biomedical model genomics, Int. J. Biol. Sci, vol.3, pp.179-184, 2007. ,
Anatomical particularities of the porcine immune system-a physician's view, Dev. Comp. Immunol, vol.33, pp.267-272, 2009. ,
Quantification of B, T and null lymphocyte subpopulations in the blood and lymphoid organs of the pig, Immunobiology, vol.201, pp.74-87, 1999. ,
Gene discovery and expression profiling in porcine Peyer's patch, Vet. Immunol. Immunopathol, vol.105, pp.301-315, 2005. ,
Gene expression profiling of jejunal Peyer's patches in juvenile and adult pigs, Mamm. Genome, vol.16, pp.599-612, 2005. ,
Lymphoid cells in afferent and efferent intestinal lymph: lymphocyte subpopulations and cell migration, Clin. Exp. Immunol, vol.92, pp.317-322, 1993. ,
The postnatal development of gut lamina propria lymphocytes: number, proliferation, and T and B cell subsets in conventional and germ-free pigs, Pediatr. Res, vol.29, pp.237-242, 1991. ,
Chemokine requirements for B cell entry to lymph nodes and Peyer's patches, J. Exp. Med, vol.196, pp.65-75, 2002. ,
Regionalized Development and Maintenance of the Intestinal Adaptive Immune Landscape, Immunity, vol.46, pp.532-548, 2017. ,
Differential expression of CTLA-4 among T cell subsets, Clin. Exp. Immunol, vol.136, pp.463-471, 2004. ,
Human G protein-coupled receptor GPR-9-6/CC chemokine receptor 9 is selectively expressed on intestinal homing T lymphocytes, mucosal lymphocytes, and thymocytes and is required for thymus-expressed chemokine-mediated chemotaxis, J. Exp. Med, vol.190, pp.1241-1256, 1999. ,
Mechanisms underlying lineage commitment and plasticity of helper CD4+ T cells, Science, vol.327, pp.1098-1102, 2010. ,
there and everywhere: T follicular helper cells on the move, Immunology, vol.152, pp.382-387, 2017. ,
T-cell subsets in the germinal center, Immunol. Rev, vol.252, pp.146-155, 2013. ,
Preferential generation of follicular B helper T cells from Foxp3+ T cells in gut Peyer's patches, Science, vol.323, pp.1488-1492, 2009. ,
T Follicular Helper Cells Promote a Beneficial Gut Ecosystem for Host Metabolic Homeostasis by Sensing Microbiota-Derived Extracellular ATP, Cell Rep, vol.18, pp.2566-2575, 2017. ,
Jejunal and ileal Peyer's patches in pigs differ in their postnatal development, Anat. Embryol, vol.195, pp.41-50, 1997. ,
Functional studies of Peyer's patches: evidence for their participation in intestinal immune responses, J. Immunol, vol.114, pp.1757-1760, 1975. ,
The antisense transcriptomes of human cells, Science, vol.322, pp.1855-1857, 2008. ,
A genome-wide investigation of expression characteristics of natural antisense transcripts in liver and muscle samples of pigs, PLoS ONE, vol.7, p.52433, 2012. ,
Extensive variation between tissues in allele specific expression in an outbred mammal, BMC Genomics, vol.16, p.993, 2015. ,
Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance, Nat. Genet, vol.47, pp.353-360, 2015. ,
Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans, Science, vol.348, pp.648-660, 2015. ,
The Genotype-Tissue Expression (GTEx) project, Nat. Genet, vol.45, pp.580-585, 2013. ,
Genetic effects on gene expression across human tissues, Nature, vol.550, pp.204-213, 2017. ,
, ScIEntIfIc REpoRTS |, vol.8, p.9077, 2018.
, Experiments were funded by the SUS-FLORA project (ANR-10-GENM-016) of the French National Agency and internal funds of INRA's Animal Genetics Division