Sus scrofa
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ABSTRACT:
PROVIDER: PRJNA90933 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To gain a comprehensive view of the host response to pathogens within these tissues, we determined the transcriptional profiles of intestinal lymphatic tissue infected with Y. enterocolitica. Expression analysis using Affymetrix GeneChips revealed a complex host response in the Peyer’s patches (PP) and mesenteric lymph nodes (MLN) following oral infection with Y. enterocolitica. Keywords: Disease state analysis
2006-05-04 | GSE4764 | GEO
Project description:Although immune mechanisms have been described for Peyer’s patch function, in discriminating food nutrients and commensal microflora from pathogenic challenge, an understanding of gene expression patterns associated with normal intestinal homeostasis is lacking. The effects of commensal bacterial colonization on global gene expression in the small intestine of germ-free mice have been described (1, 2). However, no studies have compared expression patterns of various healthy lymphoid tissues in conventionally-raised pigs or other species. The objective of this study was to investigate the pattern of normal gene expression in jejunal Peyer’s patches (JPP) of healthy pigs. We hypothesized that gene expression of intact jejunal Peyer's patch is characterized by genes associated with absorption and secretory functions as well as genes associated with GALT-specific immune functions. Eight hybridizations were performed, with dye swaps of JPP mRNA from four juvenile pigs. Each hybridization compared JPP from an individual pig to the jejunal mesenteric lymph node reference sample, which was pooled from all juvenile pigs in the study. However, two of the hybridizations resulted in poor quality data, and were excluded from further analysis. Normalization, hierarchical clustering, data visualization, and statistical analysis were performed by GeneSpring version 6.2 (Silicon Genetics, Redwood, CA). GeneSpring standardized the intensities for each spot by subtracting the local background, and then normalized globally by locally weighted linear regression (Lowess). A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead. Spots with a flag value of “0” were excluded. The intensity of negative control DNA-containing spots was used to additionally exclude low intensity data. Negative controls include the gene for Arabidopsis thaliana homeodomain-like protein (AY054571); 200 ng/microl Poly(dA) (Amersham, Piscataway, NJ); a 461 bp fragment of the kanamycin-resistant gene, amplified from the pET24b+ plasmid (Novagen, Madison, WI); PRRS virus strain VR-2332 (PRU87392) ORFs 2, 3, 4, 5, 6 and 7; pCMVSport 6 plasmid (Invitrogen, Carlsbad, CA); and pGEM-T plasmid (Promega, Madison WI). The mean intensity of the negative controls for both Cy3 and Cy5 was calculated for each slide, and spots with a mean intensity less than the mean intensity + 2SD were excluded from further analysis. After normalization, GeneSpring averaged replicate spots for each clone across hybridizations. GeneSpring used the Cross Gene Error Model, which was based on replicate values. A Student’s t-test with the Benjamini and Hochberg false discovery rate multiple testing correction (MTC) verified the difference between the natural log of the normalized gene expression ratio (JPP:j-MLN) and a ratio of 1.0. p-values less than 0.05 were considered significant. Series_references: 1.Fukushima K, Ogawa H, Takahashi K, Naito H, Funayama Y, Kitayama T, Yonezawa H, and Sasaki I. Non-pathogenic bacteria modulate colonic epithelial gene expression in germ-free mice. Scand J Gastroenterol 38: 626-634, 2003. 2. Hooper LV, Wong MH, Thelin A, Hansson L, Falk PG, and Gordon JI. Molecular analysis of commensal host-microbial relationships in the intestine. Science 291: 881-884, 2001.
2004-11-04 | E-GEOD-1913 | biostudies-arrayexpress
Project description:scRNAseq of stromal cells isolated from mesenteric lymph nodes (MLN), peripheral lymph nodes (PLN) and mandibular lymph nodes (mandLN)
2022-09-01 | E-MTAB-11644 | biostudies-arrayexpress
Project description:Expression data from non-infected and Salmonella Choleraesuis infected mesenteric lymph nodes
| PRJNA97971 | ENA
Project description:Expression data from non-infected and Salmonella Typhimurium infected mesenteric lymph nodes
| PRJNA97969 | ENA
Project description:Regulatory role of microRNAs in mesenteric lymph nodes after Salmonella Typhimurium infection
| PRJNA392048 | ENA
Project description:In this study, we applied the isobaric tags for relative and absolute quantitation (iTRAQ) technique to detect alterations in the proteomic profile of the jejunal mucosa using a porcine model in which piglets were offered the protein-limited (PL) diet. Protein identification and quantification for iTRAQ experiments were performed using ProteinPilot (v4.0.8085) software. The LC-MS/MS data were searched against the UniProtKB (sus scrofa). To minimize the false discovery rate (FDR), a threshold for protein identification was applied, with the confident value > 95% (amount to the confident value “unused ProtScore” > 1.3 in ProteinPilot software), and at least one unique peptide was considered for protein identification. Proteins that were quantified with fold change > 2.0 were considered to be differentially expressed proteins. We identified 5275 proteins, 202 of which were differentially expressed. Furthermore, we adopted function annotation analysis of all identified proteins and function enrichment analysis of all differentially expressed proteins to explore more meaningful proteins and pathways.
2016-12-22 | PXD004069 | Pride
Project description:RNA-seq analysis of spleen and mesenteric lymph node (mLN) hematopoietic cells
| PRJNA890599 | ENA
Project description:Obesity has emerged as a worldwide problem in human health. Dietary lipids are taken up and transported via lymphatics into the circulatory system. During this process, lipids pass the mesenteric lymph node (mLN). These organs filter the lymph fluid for foreign antigens to induce and control immune responses. Alteration of that function during obesity has only slightly been studied. Here, we characterize changes within the microarchitecture of the mLN during high levels of lipid transport and highlight the role of stromal cells. Microarray experiments detected gene probes expressed by mLN stromal cells. Transmission electron microscopy enabled us to identify lipid droplets in different stromal cells, and in macrophages. Sizes, numbers and intercellular distances increased after 10 weeks of a high-fat diet. Thus, we propose that changes in the microarchitecture and increased accumulation of lipid droplets in stromal cells and macrophages have an influence on the immunological function of the mLN.
2020-05-14 | GSE138594 | GEO