E-MEXP-1335
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ABSTRACT:
PROVIDER: E-MEXP-1335 | ExpressionAtlas | 2015-10-22
REPOSITORIES: ExpressionAtlas
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Project description:Genome wide DNA methylation profiling in paired saliva and intestinal mucosa samples from individuals undergoing gastroscopies. The Illumina Infinium 450k Human DNA methylation BeadChip was used to obtain DNA methylation profiles across approximately 485,500 CpGs. The aim of the study was to determine the utility of saliva as a surrogate for intestinal mucosa in DNA methylation studies.
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Project description:Genome wide expression profiling of ulcerative colitis, and normal colon mucosa samples. The GeneChip PrimeView Human Gene Expression Array was used to obtain expresion profiles across colon mucosa samples. Samples came from 5 ulcerative colitis affected, and 5 normal individuals.
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Project description:We developed a non-invasive ex vivo HT29 cell-based minimal model to fingerprint the mucosa-associated microbiota fraction in humans. HT29 cell-associated fractions were characterized by the universal phylogenetic array platform HTF-Microbi.Array, both in presence or in absence of a TNF-M-NM-1-mediated pro-inflammatory stimulus. A high taxonomical level fingerprint profiling of the mucosa-associated microbiota was performed on a group of 12 breast-fed infants and 6 adults (used as controls). Relative abundance of the bacterial species was assessed by using a so-called HTF-Microbi.Array, based on a ligation detection reaction (LDR) - Univerasal array (UA) assay, capable of correctly identify up to 31 intestinal bacterial groups, covering up to 95% of the human gut microbiota
2013-09-26 | E-GEOD-51177 | biostudies-arrayexpress
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:To analyse roles of HAI-1/Spint1 in intestinal tumorigenesis, we examined the effect of intestine-specific deletion of Spint1 gene on Apc(Min/+) mice. The loss of Hai-1/Spint1 significantly accelerated tumor formation in ApcMin/+ mice and shortened their survival periods. Mouse small intestine tumor tissue or background mucosa lacking macroscopically visible tumors were proceeded to RNA extraction and hybridization on microarrays (Affymetrix Mouse Genome 430 2.0 Array). Non-tumor or tumor intestinal mucosa tissues of Apc (Min/+)/Spint1 (flox/flox) mice and non-tumor or tumor intestinal mucosa tissues of Apc (Min/+)/Spint1 (flox/flox)/Vil-Cre mice were analysed. The experiment was repeated respectively.
2013-04-01 | E-GEOD-40856 | biostudies-arrayexpress
Project description:Molecular adaptation of the intestinal mucosa occurs during microbial conventionalization to maintain a balanced immune response. However, the genetic regulation of such adaptation is obscure. Here, combined analysis of germ free and conventionalized mice revealed that the major molecular adaptations were initiated at day 4 of conventionalization with a strong induction of innate immune functions followed by stimulation of adaptive immune functions. We identified central regulatory genes and reconstructed a common regulatory network that appeared to be sufficient to regulate the dynamic adaptation of the intestinal mucosa to the colonizing microbiota. The majority of the genes within this regulatory network play roles in mucosal inflammatory diseases in mouse and human. We propose that the identified central regulatory network may serve as a genetic signature for control of intestinal homeostasis in healthy mice and may help to unravel the genetic basis of pathway dysregulation in human intestinal inflammatory diseases. Expression profiling of jejunum, ileum, and colon tissue from germ-free and colonized mice at day 1,2,4,8,16 and 30.
2012-07-10 | E-GEOD-32513 | biostudies-arrayexpress
Project description:Resident human lamina propria immune cells serve as powerful effectors in host defense. Molecular events associated with the initiation of an intestinal inflammatory response in these cells are largely unknown. Here, we aimed to characterize phenotypic and functional changes induced in these cells at the onset of intestinal inflammation using a human intestinal organ culture model. In this model, healthy human colonic mucosa was depleted of epithelial cells by EDTA treatment. Following loss of the epithelial layer, expression of the inflammatory mediators IL-1β, IL-6, IL-8, IL-23p19, TNF-α, CXCL2 and the surface receptors CD14, TLR2, CD86, CD54 was rapidly induced in resident lamina propria cells in situ as determined by qRT-PCR and immunohistology. Gene microarray analysis of lamina propria cells obtained by laser-capture microdissection provided an overview of global changes in gene expression occurring during the initiation of an intestinal inflammatory response in these cells. Bioinformatic analysis gave insight into signalling pathways mediating this inflammatory response. Furthermore, comparison with published microarray datasets of inflamed mucosa in vivo (ulcerative colitis) revealed a significant overlap of differentially regulated genes underlining the in vivo relevance of the organ culture model. The organ culture model characterized may be useful to study molecular mechanisms underlying the initiation of an intestinal inflammatory response in normal mucosa as well as potential alterations of this response in inflammatory bowel disease. Gut specimens were derived from individuals undergoing resection for localized colon cancer. Microscopically normal colonic mucosa was dissected from the surgical specimen near the resection margin and immediately subjected to the experimental procedures. After extensive washing the mucus layer was removed by dithiothreitol (DTT) treatment. Subsequently, punches of defined surface area were prepared and denuded of epithelial cells by exposure to EDTA. Samples were collected prior to culturing and washing (control, t = 0 h, total mucosa, TM) as well as after loss of the epithelial layer (t = 5 h, mucosa after loss of epithelial layer, LEL-M) and snap frozen in liquid nitrogen. Lamina Propria (LP) was subsequently isolated via Laser Capture Microdissection (LMD) followed by RNA isolation. Microarray analysis of TM-LP (control) and LEL-LP samples was performed using the WG-DASL Human HT_12 V4 Expression BeadChip Assay from Illumina employing a minimum of 200 ng total RNA per sample. Four replicates from individual experiments were measured for each time point.
2014-04-03 | E-GEOD-56448 | biostudies-arrayexpress
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:Genome wide miRNA profiling of ulcerative colitis, and normal colon mucosa samples. The GeneChip miRNA 3.0 Array was used to obtain miRNA profiles across colon mucosa samples. Samples came from 5 ulcerative colitis affected, and 5 normal individuals.
2015-01-01 | GSE43009 | GEO
Project description:The early interaction of Salmonella enterica serovar typhimurium DT104 with intact small intestinal mucosa was studied in a Small Intestinal Segment Perfusion (SISP) model. Intestinal segments were infected with or without Salmonella. Scrapings from jejunal segments were collected after perfusion for 0, 2, 4, or 8 hours. Details of the SISP experiment are described in: Niewold TA, Veldhuizen EJ, van der Meulen J, Haagsman HP, de Wit AA, Smits MA, Tersteeg MH, Hulst MM. Using the Operon 13K pig oligonucleotide array differences in host gene expression were recorded between infected and uninfected segments within a single pig (isogenic comparisons), and between identical treated segments collected from 3 individual SISP pigs, all responding markedly different to infection with Salmonella (inter-animal comparisons). A Small Intestinal Segment Perfusion (SISP) test was performed with 3 pigs (pig no. 2, 3, and 4) (cross-bred YorkshireM-CM-^W(Large WhiteM-CM-^WLandrace)). Two adjacent segments prepared in the mid-jejunum of each pig were perfused for 1 hour with Salmonella enterica serovar typhimurium DT104 suspended in peptone solution (10E-09 CFU/ml) or with peptone solution alone (mock infected segment) respectively. Subsequently, segments were perfused with peptone solution alone for a maximum period of 8 hours. At 2, 4, and 8 hours a part of the infected segment was dissected to obtain mucosal scrappings. The same was done at 0 and 8 hours for the uninfected (mock) control segment. RNA isolated from scrappings was used for microarray comparisons using the Operon 13K pig oligonucleotide array. 9 comparisons were done. For each of the 3 SISP pigs, expression in the 8 hours perfused infected segment, perfused for 8 hours, was compared to expression in its adjacent mock infected segment (3 isogenic comparisons, 8 hpi.). Expression in the infected segment of each SISP pig, dissected after 2 or 4 hours of perfusion, was compared to expression in an infected segment dissected from another SISP pig (2 versus 3, 2 versus 4, and 3 versus 4 / 3 comparisons at 2 hpi., and 3 comparisons at 4 hpi.). Dye-swaps were performed for each comparison. jejunum pig, host-microbe interaction, Salmonella enterica serovar typhimurium DT104.
2013-04-17 | E-GEOD-41630 | biostudies-arrayexpress