Transcriptomics of mouse ileal stem cell-derived epithelium grown on transwells
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ABSTRACT:
PROVIDER: PRJNA513853 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8418160.fastq.gz | Fastqsanger.gz | |||
| SRR8418170.fastq.gz | Fastqsanger.gz | |||
| SRR8418161.fastq.gz | Fastqsanger.gz | |||
| SRR8418162.fastq.gz | Fastqsanger.gz | |||
| SRR8418163.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The goal of this study was to identify transcriptional changes that occur in mouse ileal stem cell-derived epithelium plated on transwells after the establishment of an air-liquid interface (ALI). Methods: Mouse ileal stem cell spheroids were plated on transwells and grown in L-WRN conditioned medium (top and bottom compartment) for 7 days, at which point the top medium was removed to establish ALI. Samples were collected for sequencing on the day of ALI initiation (non-ALI Day 0) and three days post top medium removal (ALI Day 3). Control samples were also collected from transwells submerged for all 10 days of the experiment (non-ALI Day 3) and from the initial stem cell spheroid cultures. Results: Non-ALI Day 0 and non-ALI Day 3 samples had similar transcriptional profiles, whereas ALI transwells showed upregulation of transcriptional factors that induce secretory cell lineages, as well as a general upregulation of metabolic genes involved in oxidative phosphorylation and downregulation of those involved in glycolysis. Conclusions: Removal of L-WRN conditioned medium from the top compartment of transwells plated with stem cell-derived intestinal epithelial cells establishes an air-liquid interface that changes the metabolic profile of the cultures and initiates a differentiation cascade for intestinal secretory cells such as goblet cells and paneth cells.
2019-07-29 | GSE124815 | GEO
Project description:Gene expression was compared between adult wildtype (WT) CD1 jejunual epithelium (J) and ileal epithleium (I). Gene expression was compared between adult control ileal epithleium and Gata4 conditional knockin (cKI) ileal epithelium. Gene expression was compared between adult wildtype CD1 jejunum and Gata4 conditional knockout (cKO) jejunal epithelium.
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Project description:Identification of significant regulated genes of the ileal epithelium in patients suffering from Crohn disease (normal vs. activ and non activ CD).
2009-02-27 | E-MEXP-1225 | biostudies-arrayexpress
Project description:Background and aims: Intestinal fibrosis is a common complication of Crohn’s disease (CD). It is characterised by an excessive accumulation of fibroblasts differentiating into activated myofibroblasts secreting excessive extracellular matrix. The potential role of the intestinal epithelium in this fibrotic process remains poorly defined. Methods: A total of 113 CD and control subjects were studied. We performed a pilot proteomic study comparing the proteome of surface epithelium isolated by laser capture microdissection in normal and fibrotic zones of resected ileal CD strictures (n=5). Selected proteins were validated by immunohistochemistry (IHC) in colonic and ileal samples of stricturing CD patients (n=44), pure inflammatory CD (n=29) and control subjects (n=40). Functional assays with cell lines cultures and a fibroblast to myofibroblast differentiation model were used to assess the role of the highlighted epithelial proteins in CD fibrosis. Results: Proteomic study revealed an endoplasmic reticulum (ER) stress and unfolded protein response (UPR) markers increase in the epithelium overlying ileal fibrotic strictures, involving Anterior gradient protein 2 homolog (AGR2) and Binding immunoglobulin protein (BiP). This was confirmed by IHC. The ER stress induction in intestinal epithelial cells increased AGR2 as well as BiP expression and led to an extracellular secreted AGR2. A fibroblast to myofibroblast differentiation was obtained with the supernatant of intestinal epithelial cells pre-conditioned by ER stress and with recombinant AGR2. Conclusions: AGR2 and other ER stress markers are increased within the intestinal epithelium overlying fibrotic strictures and might contribute to profibrotic signals involved in CD fibrosis.
2022-04-04 | PXD022214 | Pride
Project description:Dose-dependent ileal gene expression was examined following repeated exposure (every 4 days for 28 days) to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). These data were used to examine the effect of repeated TCDD exposure on gene expression in the intestinal epithelium of C57BL/6 male mice.
2017-02-28 | GSE89430 | GEO
Project description:Dose-dependent ileal gene expression was examined following repeated exposure (every 4 days for 28 days) to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). These data were used to examine the effect of repeated TCDD exposure on gene expression in the intestinal epithelium of C57BL/6 male mice.
2021-12-31 | GSE171942 | GEO
Project description:Epithelium-only cultured stem cells isolated from human pluripotent stem cell derived intestinal organoids grown in matrigel and alginate
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Project description:In both vertebrates and invertebrates, generating a functional appendage requires interactions between ectoderm-derived epithelia and mesoderm-derived cells. To investigate such interactions, we used single-cell transcriptomics to generate a temporal cell atlas of the Drosophila wing disc from two developmental time points. Using these data, we visualized gene expression using a multi-layered model of the wing disc and catalogued ligand-receptor pairs that could mediate signaling between epithelial cells and adult muscle precursors (AMPs). We found that localized expression of the FGF ligands, Thisbe and Pyramus, in the disc epithelium regulates the number and location of the AMPs. In addition, Hedgehog ligand from the epithelium activates a specific transcriptional program within adjacent AMP cells, defined by AMP-specific targets Neurotactin and midline, that is critical for proper formation of direct flight muscles. More generally, our annotated temporal cell atlas provides an organ-wide view of potential cell-cell interactions between epithelial and myogenic cells.
2021-03-23 | GSE155543 | GEO
Project description:Salmonella enterica serotype Typhimurium cause a localized enteric infection in immunocompetent patients while human immunodeficiency virus (HIV)-infected patients develop a life threatening bacteremia. We used a rhesus macaque ileal loop model to study how simian immunodeficiency virus (SIV) infection triggers defects in mucosal barrier function that enhance S. Typhimurium dissemination. SIV infection resulted in significant depletion of CD4+ T cells in the intestinal mucosa. Gene expression profiling revealed a defective TH17 response (with suppression of IL-17 and IL-22 expression) and impaired homeostasis of the intestinal epithelium in SIV-infected animals during NTS infection. These findings correlated with an impaired ability of lamina propria CD4+ T cells from SIV-infected macaques to produce IL-17 upon ex vivo stimulation, while production of IFNï§ was not affected. This cytokine imbalance in SIV-infected animals was associated with reduced expression of genes required for intestinal epithelial maintenance and repair, increased fluid secretion during NTS infection, epithelial damage and translocation of a non-invasive S. Typhimurium mutant. Although no defects in neutrophil recruitment were noted, the ileum of SIV-infected animals contained lower levels of the enzyme myeloperoxidase, which may indicate defects in neutrophil killing capacity. S. Typhimurium was recovered in markedly increased numbers from the mesenteric lymph nodes of SIV-infected macaques, illustrating the increased potential for systemic dissemination during co-infection. Our data suggest that SIV-infection causes a multi-factorial defect in mucosal barrier function that promotes bacterial dissemination. Keywords: Disease state analysis Comparison of ileal gene expression profiles in SIV infected rhesus macaques in response to Salmonella challange.
2010-05-26 | E-GEOD-10567 | biostudies-arrayexpress