Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profiles of mouse colonic epithelial monolayer cultured in air-liquid interface

ABSTRACT: The colonic epithelium can undergo multiple rounds of damage and repair, often in response to excessive inflammation. Our understanding of how this process occurs is limited by a lack of in vitro models that recapitulate key aspects of in vivo responses. We established a long-term, self-organizing 2D epithelial monolayer system to model the cyclic nature of epithelial alterations during injury-repair. Through RNA-seq analysis, we seek to evaluate the transcriptomic profiles of the cultured epithelial cells under select phases of “homeostasis-injury-repair” in vitro.

ORGANISM(S): Mus musculus

PROVIDER: GSE127172 | GEO | 2019/12/29

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA sequencing of chronically damage human colon organoids via Air-liquid interface submergence

Project description:We report that repeated rounds of media submergence damage of human colon organoids led to the inability of cells to regrow and respond appropriately to TLR stimulation. We also identified mRNA expression and DNA methylation changes in genes associated with IBD and colon cancer.

2021-06-23 | GSE178698 | GEO

Human ileum stem cell differentiation by air-liquid interface

Project description:Despite major advances with embryonic and induced pluripotent stem cells or lineage-committed, p63-expressing stem cells of stratified epithelia, we know less about the indigenous stem cells of the gastrointestinal tract, pancreas, liver, and other columnar epithelia which collectively resist cloning in their elemental states. Here we demonstrate the cloning of highly immature epithelial stem cells from defined regions of the human intestine and colon. In this study, we have isolated ileal stem cells and performed air-liquid interface method to induce differentiation of human ileal stem cells. The differentiated structure showed villi-like epithelia which contains enterocytes, goblet cells, endocrine cells and paneth cells.

2015-05-29 | GSE66115 | GEO

SARS-CoV-2-infected human nasal epithelial air-liquid interface cultures

Project description:Continuous assessment of the impact of SARS-CoV-2 on the host at the cell-type level is crucial for understanding key mechanisms involved in host defense responses to viral infection. We investigated host response to ancestral-strain and Alpha-variant SARS-CoV-2 infections within air-liquid-interface human nasal epithelial cells from younger adults (26-32 Y) and older children (12-14 Y) using single-cell RNA-sequencing. Ciliated and secretory-ciliated cells formed the majority of highly infected cell-types, where the latter derived from ciliated lineages. Strong innate immune responses were observed across lowly-infected and un-infected bystander cells and heightened in Alpha-infection. Alpha highly-infected cells showed increased expression of protein-refolding genes compared with ancestral-strain-infected cells in children. Furthermore, oxidative phosphorylation-related genes were down-regulated in bystander cells versus infected and mock-control, underscoring the importance of these biological functions for viral replication. Overall, this study highlights the complexity of cell-type-, age- and viral strain-dependent host epithelial responses to SARS-CoV-2.

2024-05-23 | GSE241292 | GEO

Exposure of Air-Liquid-Interface bronchial epithelial cells to whole birch pollen

Project description:Human BEAS-2B were exposed to whole birch pollen using a Pollen Sedimentation Chamber. The chamber was designed to be able to dose cells to dry whole pollen. The goal was to understand the reaction of human epithelial cells to a human real life pollen exposure.

2021-11-03 | GSE179942 | GEO

Gene expression profiles of mouse colonic epithelial monolayer cultured in air-liquid interface

Project description:Gene expression profiles of mouse colonic epithelial monolayer cultured in air-liquid interface

| PRJNA524283 | ENA

Do Airway Epithelium Air-liquid Cultures Represent the In Vivo Airway Epithelium Transcriptome?

Project description:Human airway epithelial cells cultured in vitro at air-liquid interface (ALI) form a pseudostratified epithelium that forms tight junctions and cilia, and produces mucin, and are widely used as a model of differentiation, injury, and repair. To assess how closely the transcriptome of ALI epithelium matches that of in vivo airway epithelial cells, we used microarrays to compare the transcriptome of human large airway epithelial cells cultured at ALI with the transcriptome of large airway epithelium obtained via bronchoscopy and brushing. Gene expression profiling showed global gene expression correlated well between ALI cells and brushed cells, but there were some differences. Gene expression patterns mirrored differences in proportions of cell types (ALI have higher percentages of basal cells, brushed cells have higher percentages of ciliated cells), with ALI cells expressing higher levels of basal cell-related genes and brushed cells expressing higher levels of cilia-related genes. Pathway analysis showed ALI cells had increased expression of cell cycle and proliferation genes, while brushed cells had increased expression of cytoskeletal organization and humoral immune response genes. Overall, ALI cells are a good representation of the in vivo airway epithelial transcriptome, but for some biologic questions, the differences in the in vitro vs in vivo environments need to be considered. Affymetrix arrays were used to assess the gene expression of large airway cells cultured in vitro at air-liquid interface (12 samples) and large airway epithelial cells obtained by fiberoptic bronchoscopy of 20 healthy nonsmokers. *** Air-liquid interface Samples not provided in this Series. ***

2010-07-07 | E-GEOD-18637 | biostudies-arrayexpress

miRNA expression in differentiating primary human bronchial epithelial cells cultured at air-liquid-interface

Project description:We performed microarray analysis of miRNA expression in differentiating primary human bronchial epithelial cells. The goal was to identify miRNAs that are dynamically expressed under airway epithelial development. Cells were cultured at air-liquid-interface and were harvested day 4, 6, 8, 11, 13, 15, 18, 20 and 22 for analysis.

2021-01-09 | GSE164448 | GEO

Transcriptional profiling by array to investigate the effect of interfacial stress on rat alveolar type II cell signalling and gene expression (conventional air-liquid interface)

Project description:Many epithelia have contact with air-liquid interfaces. This applies particularly to the lung, where one of the epithelial cell types (the surfactant secreting alveolar type II [AT II] cells) even project into the air. This specific environment may be of considerable physiological relevance; however, only few data exist to provide a satisfying description. This is mainly due to the difficulty to manipulate cell-air contacts in a specific way. In previous investigations, using new microscopic approaches, we found that the presence of an air-liquid interface leads to a paradoxical situation: it is a potential threat that may cause cell injury, but also a potent stimulus for the cells: AT II cells respond promptly, and show sustained Ca2+-signals that activate exocytosis. In this report, gene chip analysis was performed to test the concept of an Air-liquid interface IAL as a mechanical stimulus, stress factor and/or regulator of the AT II cells. For this purpose, cultured AT II cells were exposed to two different interfacial conditions (inverted and conventional interface). The results support the concept that the IAL is a strong stimulus for AT II cells inducing cellular responses that seem to be closely associated with mechanotransduction, stress response, and alveolar repair.

2012-07-20 | E-MEXP-3363 | biostudies-arrayexpress

Transcriptional profiling by array to investigate the effect of interfacial stress on rat alveolar type II cell signalling and gene expression (inverted air-liquid interface)

2012-07-20 | E-MEXP-3372 | biostudies-arrayexpress

scRNA-seq of canalicular stage human fetal lung cultured under air-liquid interface

Project description:Small pieces (<0.5 cm of diameter) were isolated from distal regions of 125 day male human fetal lung and cultured on floating poly-carbonate membranes on top of serum and growth factor free medium under air-liquid interface conditons (ALI). ALI explants underwent changes in gene expression indicative of alveolar epithelial cell differentiation under these conditions. scRNA-sequencing was performed on fetal tissue prior to culture (day 0) and day 3, 6, 9 and 12 of ALI explant culture.

2023-06-15 | E-MTAB-12959 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data