Gene expression profile of mouse intestinal epithelial cells during homeostasis and villus atrophy
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PROVIDER: PRJNA707420 | ENA |
REPOSITORIES: ENA
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Project description:The epithelium that lines small intestinal villi is critically important for nutrient absorption, defense against pathogens, and mucosal homeostasis. Atrophy or blunting of the villi as a result of epithelial damage is commonly observed in celiac disease, viral gastroenteritis, and various other pathologies. Whereas adaptive responses during epithelial stem cell injury are increasingly well understood, how epithelial tissues, and particularly the intestine, cope with drastic loss of differentiated cells remains unclear. Using an acute model of viral gastroenteritis induced by poly(I:C), we aimed to dissect the cellular adaptations that follow severe intestinal villus injury.
2021-03-09 | GSE168439 | GEO
Project description:The epithelium that lines small intestinal villi is critically important for nutrient absorption, defense against pathogens, and mucosal homeostasis. Atrophy or blunting of the villi as a result of epithelial damage is commonly observed in celiac disease, viral gastroenteritis, and various other pathologies. Whereas adaptive responses during epithelial stem cell injury are increasingly well understood, how epithelial tissues, and particularly the intestine, cope with drastic loss of differentiated cells remains unclear. Using an acute model of viral gastroenteritis induced by poly(I:C), we aimed to dissect the cellular adaptations that follow severe intestinal villus injury.
2021-03-27 | GSE169718 | GEO
Project description:Gene expression profile of mouse intestinal epithelial cells during homeostasis and villus atrophy at single-cell resolution
| PRJNA717757 | ENA
Project description:We molecularly characterized thousands of intestinal cells including epithelial, masenchymal and immune cells using scRNAseq. This enable us to uncover the important role of villus tip telocytes as master regulators of the epithelial spatial expression programs along the villus axis
2020-02-05 | GSE134479 | GEO
Project description:Genes encoding transcription factors function as hubs in gene regulatory networks because they encode DNA-binding proteins, which bind to promoters that carry their binding sites. In the present work we have studied gene regulatory networks defined by genes with transcripts belonging to different mRNA abundance classes in the small intestinal epithelial cell. The focus is the rewiring that occurs in transcription factor hubs in these networks during the differentiation of the small intestinal epithelial cell while it migrates along the crypt-villus axis and during its development from a fetal endodermal cell to a mature adult villus epithelial cell. We have generated transcriptome data for mouse small intestinal villus, crypt and fetal intestinal epithelial cells. In addition we have generated metabolome data from crypt and villus cells. Our results show that the intestinal crypt transcription factor hubs that are rewired during differentiation are involved in the cell cycle process (E2F, NF-Y) and stem cell maintenance (c-Myc). In contrast the villi are dominated by a HNF-4 villus hub, which is rewired during differentiation by the addition of network genes with relevance for lipoprotein synthesis and lipid absorption. Moreover, we have identified a villus NF-kB hub, which was revealed by comparison of the villus and endoderm transcriptomes. The rewiring of the NF-kB villus hub during intestinal development reflects transcriptional activity established by host and microflora interactions. To aid in the mining of our results we have developed a web portal (http://gastro.imbg.ku.dk/mousecv/) allowing easy linkage between the transcriptomic data, biological processes and functions. Keywords: Cell type comparison
2005-11-29 | GSE3216 | GEO
Project description:Genes encoding transcription factors function as hubs in gene regulatory networks because they encode DNA-binding proteins, which bind to promoters that carry their binding sites. In the present work we have studied gene regulatory networks defined by genes with transcripts belonging to different mRNA abundance classes in the small intestinal epithelial cell. The focus is the rewiring that occurs in transcription factor hubs in these networks during the differentiation of the small intestinal epithelial cell while it migrates along the crypt-villus axis and during its development from a fetal endodermal cell to a mature adult villus epithelial cell. We have generated transcriptome data for mouse small intestinal villus, crypt and fetal intestinal epithelial cells. In addition we have generated metabolome data from crypt and villus cells. Our results show that the intestinal crypt transcription factor hubs that are rewired during differentiation are involved in the cell cycle process (E2F, NF-Y) and stem cell maintenance (c-Myc). In contrast the villi are dominated by a HNF-4 villus hub, which is rewired during differentiation by the addition of network genes with relevance for lipoprotein synthesis and lipid absorption. Moreover, we have identified a villus NF-kB hub, which was revealed by comparison of the villus and endoderm transcriptomes. The rewiring of the NF-kB villus hub during intestinal development reflects transcriptional activity established by host and microflora interactions. To aid in the mining of our results we have developed a web portal (http://gastro.imbg.ku.dk/mousecv/) allowing easy linkage between the transcriptomic data, biological processes and functions. Experiment Overall Design: Four different sample categories were analyzed. Experiment Overall Design: 1) Small intestinal crypts isolated form 12-weeks old C57BL/6 mice. These samples are in triplicates. Experiment Overall Design: 2) Small intestinal villi isolated form 12-weeks old C57BL/6 mice. These samples are in triplicates. Experiment Overall Design: 3) Embryonic day 12 mesenchyme. These samples are in quadruplicate. each sample is derived from a pool of mesenchymes (10-40) Experiment Overall Design: 4) Embryonic day 12 endoderm. These samples are in quadruplicate. each sample is derived from a pool of endoderms (10-40)
2008-06-12 | E-GEOD-3216 | biostudies-arrayexpress
Project description:We analyzed gene expression profiles in isolated mouse LGR5+ intestinal stem cells, lineage-specific enterocyte and secretory progenitors, and terminally differentiated villus enterocytes. Gene Ontology analyses of cell type-specific transcripts indicated their expected biological functions. We hybridized Affmetrix 430A 2.0 mouse microarrays with processed RNA isolated from purified Lgr5+ intestinal stem cells, secretory (Sec-Pro) and enterocyte (Ent-Pro) crypt progenitors, and mature villus enterocytes (ENT).
2014-01-06 | E-GEOD-51398 | biostudies-arrayexpress
Project description:To assess the role of LSD1 in mouse small intestinal epithelium, we isolated small intestinal crypts and villus from wild type (WT) (Villin-Cre -; Lsd1f/f) and intestinal-epithelial-specific knock-out (cKO) (Villin-Cre+; Lsd1f/f) mice. This experiment uses a new Cre strain with 100% deletion efficiency. RNA was directly isolated from intestinal crypt and villus, and this was used for RNAseq. Gene expression analysis of cKO derived crypt and villus provides a spatially restricted outlook on the maturation status of the intestinal epithelium in the villi and the absence of Paneth cells in the crypt.
2023-08-02 | E-MTAB-10498 | biostudies-arrayexpress
Project description:The three-dimensional epithelial differentiation model, in which T84 epithelial cells are induced to differentiate either with TGFbeta1 or IMR-90 mesenchymal cell-secreted soluble factors, is previously shown to model differentiation seen in jejunal crypt-villus axis (Halttunen et al. 1996). The gene expression changes were studied in fully undifferentiated and fully differentiated three-dimensional T84 cultures with cDNA microarray method. Keywords: developmental stage
2007-06-27 | GSE5170 | GEO
Project description:We analyzed gene expression profiles in isolated mouse LGR5+ intestinal stem cells, lineage-specific enterocyte and secretory progenitors, and terminally differentiated villus enterocytes. Gene Ontology analyses of cell type-specific transcripts indicated their expected biological functions.
2014-01-06 | GSE51398 | GEO