Porcine small intestinal mucosa
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ABSTRACT:
PROVIDER: PRJNA1162586 | ENA |
REPOSITORIES: ENA
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Project description:Porcine intestinal microbes Raw sequence reads
| PRJNA1124503 | ENA
Project description:The alternative (non-canonical) nuclear factor-kappa B (NF-κB) signalling pathway predominantly regulates the function of the p52/RelB heterodimer. Germline Nfkb2 deficiency in mice leads to loss of p100/p52 protein and offers protection against a variety of gastrointestinal conditions, such as azoxymethane/dextran sulfate sodium (DSS)-induced colitis-associated cancer and lipopolysaccharide (LPS)-induced small intestinal epithelial apoptosis. However, the common underlying protective mechanisms are not yet fully understood. Here we applied RNA sequencing and identified a B-lymphocyte defect as the major signature in the small intestinal mucosa of naïve adult Nfkb2-/- mice. Proteomics analysis also revealed a dramatic decrease in small intestinal immunoglobulin A levels, and this was validated by quantitative ELISA in both small intestinal lysates and serum. Moreover, the numbers of IgA-producing, CD138+ve plasma cells were also reduced in the lamina propria of the small intestinal villi of Nfkb2-/- mice. This phenotype was even more striking in the small intestinal mucosa of RelB-/- mice, although these mice were equally sensitive to LPS-induced intestinal apoptosis as their RelB+/+ wild-type counterparts. Therefore, p52 deficiency offers resistance to LPS-induced intestinal apoptosis and appears to regulate the plasma cell population within the gut.
2022-07-31 | E-MTAB-11018 | biostudies-arrayexpress
Project description:The GeneChip Porcine Genome Array was used to identify the transcriptional response upon Salmonella typhimurium infection in three porcine intestinal sections (jejumun, ileum and colon) along a time course of 1,2 and 6 days post infection. The objetives in this study were i) characterize transcriptional changes upon S. typhimurium infection in the intestinal mucosa; ii) identify differences among porcine intestinal sections in inmune resposes against S. typhimurium; iii) identify change that could be associated to salmonellosis pathogenesis and symtomatology; and finally, iv) identify transcriptional changes that could be induced by S. typhimurium in order to get bacterial survival and successful colonization.
2012-06-20 | GSE22596 | GEO
Project description:the human in vivo transcriptional response of small intestinal mucosa to Lactobacillus plantarum
2008-10-17 | E-MEXP-1328 | biostudies-arrayexpress
Project description:The goal of the present study was to determine whether loss of the insulin receptor alters the molecular landscape of the intestinal mucosa, using intestinal-epithelial insulin receptor knockout (IE-irKO) mice and both genetic (IRfl/fl and Villin-cre) controls. Quantitative proteomic analysis by Liquid Chromatography Mass Spectrometry (LC-MS) was deployed on jejunal and colonic mucosa from mice fed a chow- or Western diet (WD). Jejunal mucosa from IE-irKO mice demonstrated alterations in all intestinal cell linages, Paneth, goblet, absorptive and enteroendocrine cells, whereas only goblet and absorptive cells were affected in the colon. There was also a significant effect of the WD on the gut proteome. A significant reduction was detected in Paneth cell proteins with anti-microbial activity, including lysozyme C-1, angiogenin-4, cryptdin-related sequence1C-3 and -2, a-defensin 17 and intelectin-1a. The key protein expressed by goblet cells, mucin-2, was also reduced in the IE-irKO mice. Proteins involved in lipid metabolism, including aldose reductase-related protein 1, 15-hydroxyprostaglandin dehydrogenase [NAD(+)], apolipoprotein A-II and pyruvate dehydrogenase kinase isozyme 4, were increased in the mucosa of WD-fed IE-irKO mice as compared to controls. In contrast, expression of the nutrient-responsive gut hormones, glucose-dependent insulinotropic polypeptide and neurotensin, was reduced in the jejunal mucosa of IE-irKO mice, and there was a reduction in proteins of the P-type ATPases and the solute carrier-transporter family in the colon of WD-fed IE-irKO mice. In conclusion, IE-irKO mice display a distinct molecular phenotype, suggesting a biological role of insulin and its receptor in determining differentiated cell-specificity in the intestinal epithelium.
2017-08-18 | PXD005932 | Pride
Project description:In this experiment, m6A-seq sequencing technology was used to study the functional role of methylated molecules in the process of CPB2 processing porcine small intestinal epithelial cells. In this experiment, an IP library and an input library were built together. The IP library was enriched with m6A specific antibodies to generate methylated RNA, and the influence of m6A methylation modification on its expression was analyzed by bioinformatics. We finally concluded that m6A methylation modification may play a very important role after CPB2 toxin treats small intestinal epithelial cells.
2021-10-05 | GSE167267 | GEO
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:Nfkb2 deficiency and its impact on the murine small intestinal mucosa
| PRJEB47948 | ENA
Project description:The APC (Adenomatous Polyposis Coli) gene encodes a large multidomain protein that plays an integral role in the Wnt/beta-catenin signaling pathway. The loss-of-function mutation in APC is considered the earliest genetic alteration in the course of adenoma-carcinoma sequence of colorectal cancer progression, and the resulting constitutive activation of Wnt/beta-catenin signaling is required for the maintenance of advanced colorectal cancer. In order to identify genes affected by loss of Apc function, we performed transcription profiling of mouse small intestinal tissues comparing polyps with normal mucosa of Apc+/Delta716 mice. We isolated total RNA from intestinal polyps and normal intestinal mucosa from 3 individual Apc+/Delta716 mice. Total RNA samples were then employed to perform microarray analysis (Agilent Whole Mouse Genome Microarray Ver. 2.0, 4x44K).
2020-11-01 | E-MTAB-9187 | biostudies-arrayexpress
Project description:Background While more than 700 microRNAs (miRNAs) are known in human, a comparably low number has been identified in swine. Because of the close phylogenetic distance to humans, pigs serve as a suitable model for studying e.g. intestinal development or disease. Recent studies indicate that miRNAs are key regulators of intestinal development and their aberrant expression leads to intestinal malignancy. Results Here, we present the identification of hundreds of apparently novel miRNAs in the porcine intestine. MiRNAs were first identified by means of deep sequencing followed by miRNA precursor prediction using the miRDeep algorithm as well as searching for conserved miRNAs. Second, the porcine miRNAome along the entire intestine (duodenum, proximal and distal jejunum, ileum, ascending and transverse colon) was unraveled using customized miRNA microarrays based on the identified sequences as well as known porcine and human ones. In total, the expression of 332 intestinal miRNAs was discovered, of which 201 represented assumed novel porcine miRNAs. The identified hairpin forming precursors were in part organized in genomic clusters, and most of the precursors were located on chromosomes 3 and 1, respectively. Hierarchical clustering of the expression data revealed subsets of miRNAs that are specific to distinct parts of the intestine pointing to their impact on cellular signaling networks. Conclusions In this study, we have applied a straight forward approach to decipher the porcine intestinal miRNAome for the first time in mammals using a piglet model. The high number of identified novel miRNAs in the porcine intestine points out their crucial role in intestinal function as shown by pathway analysis. On the other hand, the reported miRNAs may share orthologs in other mammals such as human still to be discovered.
2010-05-05 | GSE21628 | GEO