Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA255303 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Single-cell RNA-sequencing of murine small intestinal organoid cultured with and without lymphatic endothelial cells: Purpose: To identify differences in cell composition in murine organoids upon coculture with lymphatic endothelial cells Results: We recovered 818 cells with a median of 37750 UMIs per cell for the organoid alone and 1233 cells with a median of 79354 UMIs per cells for the cocultured organoid condition. Conclusions: scRNASeq reveals different cell composition in organoids cocultured with lymphatic endothelial cells compared to control Single-cell RNA-Sequencing of murine small and large intestinal tissue: Purpose: To generate a reference dataset of all major cell types present in the small and large intestine of the mouse Results: For the small intestine we recovered 8842 cells with a median of 4088 UMIs per cell compared to 8646 cells with a median of 10009 UMIs per cell for the large intestine. Conclusions: scRNASeq recovers all of the major epithelial, immune and stromal cell types in the intestine. Spatial transcriptomic profiling of murine small and large intestine: Purpose: To spatially map the major cell types in the mouse intestine and infer cell:cell communication from neighboring cells Conclusions: Spatial transcriptomic profiling of the mouse small and large intestine reveals all major cell types and allows for cell:cell signaling analyses upon integration with our matching scRNA-Seq data
2022-06-21 | GSE190037 | GEO
Project description:Differentiation and specialisation of epithelial cells in the small intestine is regulated in two ways. First, there is differentiation along the crypt-villus axis of the intestinal stem cells into absorptive enterocytes, Paneth, goblet, tuft, enteroendocrine or M-cells, which is mainly regulated by WNT. Second, there is specialization along the cephalocaudal axis with different absorptive and digestive functions in duodenum, jejunum and ileum that is controlled by several transcription factors such as GATA4. However, so far it is unknown whether location-specific functional properties are intrinsically programmed within stem cells or if continuous signalling from mesenchymal cells is necessary to maintain the location-specific identity of the small intestine. By using the pure epithelial organoid technique, we show that region-specific gene expression profiles are conserved throughout long-term cultures of both mouse and human intestinal stem cells and correlated with differential Gata4 expression. Furthermore, the human organoid culture system demonstrates that Gata4-regulated gene expression is only allowed in absence of WNT signalling. These data show that location-specific function is intrinsically programmed in the adult stem cells of the small intestine and that their differentiation fate is independent of location-specific extracellular signals. In light of the potential future clinical application of small intestine-derived organoids, our data imply that it is important to generate GATA4-positive and GATA4-negative cultures to regenerate all essential functions of the small intestine. RNA sequencing of intestinal crypts, villi and cultured organoids derived from mouse duodenum, jejunum and ileum
2014-01-07 | E-GEOD-53297 | biostudies-arrayexpress
Project description:The organoids heterogenously expressed mCherry by the lentivirus transduction were dissociated into single cells. A single mCherry- positive and -negative cell were collected and grown up to the organoids, respectivery. The difference of the gene expression profile between mCherry- positive and -negative organoids was assessd by maicroarray.
2014-07-16 | GSE59425 | GEO
Project description:In this experiment, we determined the differences in the transcriptomes of freshly isolated murine small intestine and colon derived crypts. The data shows that the mRNA profiles of the two tissues significantly differ in their ground state. Interestingly, we found that the expression levels of ERK pathway components as well as their positive and negative regulators significantly differ between small intestinal and colonic crypts. This observation indicates that the ERK pathway displays higher basal activity in the small intestine compared to the colon.
2021-06-30 | GSE132546 | GEO
Project description:Patient-derived gastrointestinal epithelium-only organoids from the small and large intestine, also referred to as colonoids and enteroids, were generated as part of the development of an on-going organoid biobank at the Michigan Medicine Translational Tissue Modeling Laboratory (TTML) (www.UmichTTML.org). Gene expression in organoids was characterized using RNA-sequencing
2020-07-24 | E-MTAB-9339 | biostudies-arrayexpress
Project description:Human intestinal epithelial organoids (IEO) culture models are rapidly emerging as novel experimental tools to investigate fundamental aspects of intestinal epithelial (patho)physiology. Cellular source and culture protocols vary between different IEO models and reliable markers for their characterization/validation are currently limited. Here, we provide the following reference datasets of transcriptomic profiling by RNA-sequencing: Purified intestinal epithelial cells (EpCAM+) from paediatric ileum and colon, Intestinal organoid cultures from paediatric ileum and colon, Purified intestinal epithelial cells (EpCAM+) from foetal small intestine and foetal large intestine, Intestinal organoid cultures from foetal small intestine and foetal large intestine, Intestinal organoid cultures derived from induced pluripotent stem cells.<br> Complementary data from methylation profiling on the same samples have been deposited at ArrayExpress under accession number E-MTAB-4957 ( https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4957 ).</br>
2018-01-20 | E-MTAB-5015 | biostudies-arrayexpress
Project description:Differentiation and specialisation of epithelial cells in the small intestine is regulated in two ways. First, there is differentiation along the crypt-villus axis of the intestinal stem cells into absorptive enterocytes, Paneth, goblet, tuft, enteroendocrine or M-cells, which is mainly regulated by WNT. Second, there is specialization along the cephalocaudal axis with different absorptive and digestive functions in duodenum, jejunum and ileum that is controlled by several transcription factors such as GATA4. However, so far it is unknown whether location-specific functional properties are intrinsically programmed within stem cells or if continuous signalling from mesenchymal cells is necessary to maintain the location-specific identity of the small intestine. By using the pure epithelial organoid technique, we show that region-specific gene expression profiles are conserved throughout long-term cultures of both mouse and human intestinal stem cells and correlated with differential Gata4 expression. Furthermore, the human organoid culture system demonstrates that Gata4-regulated gene expression is only allowed in absence of WNT signalling. These data show that location-specific function is intrinsically programmed in the adult stem cells of the small intestine and that their differentiation fate is independent of location-specific extracellular signals. In light of the potential future clinical application of small intestine-derived organoids, our data imply that it is important to generate GATA4-positive and GATA4-negative cultures to regenerate all essential functions of the small intestine.
2014-01-07 | GSE53297 | GEO