Project description:The usage of IGF1 and FGF2 instead of EGF and p38 inhibitor during human intestinal organoid culture enables to preserve differentiated cell populations. We analyzed gene expression of human small intestinal organoids cultured with either IGF1/FGF2 or EGF/p38i.
Project description:To assess the role of LSD1 in mice small intestinal epithelium, small intestinal organoids were treated with an inhibitor for LSD1 (GSK-LSD1) and compared to untreated organoids. Similar to intestinal epithelium from mice with an intestinal epithelium specific LSD1-KO, paneth cells dissappear upon GSK-LSD1 treatment. We used these sequencing data to show that these small intestinal organoids have a similar phenotype as mice epithelium without LSD1.
Project description:Using 3' droplet-based single cell sequencing, we profiled single cells derived from a fresh human small intestinal epithelial tissue and human small intestinal organoids cultured with either IGF1/FGF2 or EGF/p38i.
Project description:To assess the role of LSD1 in mouse small intestinal epithelium, we grew small intestinal organoids in vitro from mice with an epithelial specific deletion of LSD1 (Villin-Cre+; Lsd1f/f) and from wild type (Villin-Cre-; Lsd1f/f) mice. This experiment uses a new Cre strain with 100% recombination efficiency. Similar to intestinal epithelium from mice with an intestinal epithelium specific LSD1-KO, Paneth cells are not present in LSD1-KO small intestinal organoids. We used these sequencing data to show intrinsic epithelial changes in the intestinal epithelium caused by LSD1 deletion in the absence of microbiota and surrounding in vivo cell types.
Project description:Small intestinal organoids generated from Opa1KO mice and Opa1fl/fl. Organoids were generated from young adult mice and stimulated in vitro with tamoxifen 4-oht for 3 days. Opa1KO organoids are smaller and more round than their WT counterparts. Organoids were collected and their transcriptome was extracted for RNAseq.
Project description:Bcl9/9l fl/fl;Rosa26-CreERT2 small intestinal organoids were exposed to 1uM 4-OHT (or EtOH as a control) for 24 hours to induce recombination and induce a conditional Bcl9 and Bcl9l knockout. Intestinal epithelial cells were isolated 72 hours later for single cell RNA sequencing. BCL9 is a beta-catenin transcriptional cofactor involved in the transcriptional machinery of Wnt target genes. We found that BCL9/9L is a key player in coordinating the balance between Wnt mediated proliferation and differentiation in the intestinal epithelium by engaging with GATA transcription factors. In line with this observation, we observed an increase in secretory lineage cells upon loss of Bcl9/9l in intestinal organoids.
Project description:We aimed to analyse the effect of different extra-cellular matrices on the growth of small intestinal organoids. Small intestinal crypts of wildtype mice were harvested and grown under standard Matrigel organoid conditions. After establishment of organoids (passaged 1-2), organoids were grown in Matrigel, on collagen or in a drop of collagen. Growth in a droplet of collagen requires addition of Wnt3a, therefore all samples are either provided with standard culture conditions (ENR) or with ENR+50%Wnt3a-CM (WENR). Samples were grown in specified matrix for at least 1-2 passages before RNA was purified.
Project description:To assess the role of LSD1 in human intestinal epithelium, human small intestinal organoids were treated with an inhibitor for LSD1 (GSK-LSD1) and compared to untreated organoids. The organoids were grown with specific conditions where Paneth cells are present in the organoids as similar experiments in mice show that Paneth cells disappear upon GSK-LSD1 treatment. Similar to mouse intestinal organoids, Paneth cells dissappear upon GSK-LSD1 treatment. Furthermore, we used these gene set enrichment analysis on these microarray data to show that these human intestinal organoids have a similar phenotype as mice epithelium without LSD1.
Project description:We treated intestinal organoids continuously for 5 days with or without TgfbR1/2 inhibitor (LY2109761) or Tgfb1 ligand Organoids were continuously treated for 5 days, then RNA was extracted and hybridized to Affymetrix Mouse Genome 430 2.0