Expression data from regenerating human airway epithelium in vitro.
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE197142 | GEO | 2022/11/14
REPOSITORIES: GEO
Similar Datasets
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
Project description:Expression data from airway brush biopsy samples, differentiated primary cultures of human airway epithelia, CaLu3 cultures at the air liquid interface, and primary cultures of human airway epithelia submerged in nutrient media Organotypic cultures of primary human airway epithelial cells have been used to investigate the morphology, ion and fluid transport, innate immunity, transcytosis, infection, inflammation, signaling, cilia and repair functions of this complex tissue. However, we do not know how close these cultures resemble the epithelia in vivo. In this study, we examine the genome-wide expression profile of human airway epithelial cells in vivo obtained from brush biopsies of the trachea and bronchus of healthy volunteers and compare it to the expression profile of primary cultures of human airway epithelia grown at the air-liquid interface. For comparison we also investigate the expression profile of Calu3 cells grown at the air-liquid interface and primary cultures of human airway epithelia submerged in nutrient media. We compare the transcriptional profile of human in vivo airway epithelia from trachea and bronchus to differentiated primary human airway epithelia cultures, also from trachea and bronchus, and grown at the air-liquid interface. We also included the profile of Calu3 cultures grown at the air-liquid interface and primary cultures submerged in nutrient media.
2010-04-15 | E-GEOD-20502 | biostudies-arrayexpress
Project description:Expression data from airway brush biopsy samples, differentiated primary cultures of human airway epithelia, CaLu3 cultures at the air liquid interface, and primary cultures of human airway epithelia submerged in nutrient media Organotypic cultures of primary human airway epithelial cells have been used to investigate the morphology, ion and fluid transport, innate immunity, transcytosis, infection, inflammation, signaling, cilia and repair functions of this complex tissue. However, we do not know how close these cultures resemble the epithelia in vivo. In this study, we examine the genome-wide expression profile of human airway epithelial cells in vivo obtained from brush biopsies of the trachea and bronchus of healthy volunteers and compare it to the expression profile of primary cultures of human airway epithelia grown at the air-liquid interface. For comparison we also investigate the expression profile of Calu3 cells grown at the air-liquid interface and primary cultures of human airway epithelia submerged in nutrient media.
2010-04-15 | GSE20502 | GEO
Project description:The mucus secreted by airway epithelial cells plays a key role in the protection against and clearance of particles and pathogens. In this project, a 3D model of the bronchial epithelium was established using Calu-3 cells grown on porous inserts at the air-liquid interface. The secreted proteins were characterized in long-term cultures and compared to the apical secretome of primary normal human bronchial epithelial (NHBE) cells. The apical secretome was collected and characterized in the Calu-3 model at day 4, day 11, and day 18 after air-liquid interface and in the NHBE model at day 4, day 12, and day 18 after air-liquid interface. "This project received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement no 760928 (BIORIMA)."
2021-03-26 | PXD024242 | Pride
Project description:Rat airway epithelial cells were cultured at the air-liquid interface and their total RNA was extracted for transcriptomic sequence analysis.
2023-09-03 | GSE234815 | GEO
Project description:Primary culture airway epithelial cells, grown under physiologic air-liquid interface conditions, with, or without IL-13 in order to study the effects of this cytokine on mucous cell metaplasia, an important feature of asthma and COPD. Keywords: IL13, mucus, goblet cell RNA was isolated from primary culture airway epithelial cells grown at air-liquid interface, treated with or without IL-13 for 21 days.
2012-12-04 | E-GEOD-37693 | biostudies-arrayexpress
Project description:scRNA-seq of air-liquid interface airway epithelial cultures derived from a human fluorescent reporter hPSC line labeling MUC5B-expressing cells
2023-05-04 | GSE202313 | GEO
Project description:We report the application of RNA sequencing technology for high-throughput profiling of gene expression responses to human rhinovirus infection at 24 hours in air-liquid interface human airway epithelial cell cultures derived from 6 asthmatic and 6 non-asthmatic donors. RNA-seq analysis identified sets of genes associated with asthma specific viral responses. These genes are related to inflammatory pathways, epithelial remodeling and cilium assembly and function, including those described previously (e.g. CCL5, CXCL10 and CX3CL1), and novel ones that were identified for the first time in this study (e.g. CCRL1, CDHR3). We concluded that air liquid interface cultured human airway epithelial cells challenged with live HRV are a useful in vitro model for the study of rhinovirus induced asthma exacerbation, given that our findings are consistent with clinical data sets. Furthermore, our data suggest that abnormal airway epithelial structure and inflammatory signaling are important contributors to viral induced asthma exacerbation. Differentiated air-liquid interface cultured human airway epithelial cell mRNA profiles from 6 asthmatic and 6 non-asthmatic donors after 24 hour treatment with either HRV or vehicle control were generated by deep sequencing, using Illumina HiSeq 2000.
2015-03-01 | E-GEOD-61141 | biostudies-arrayexpress
Project description:Oligonucleotide microarrays were used to establish a profile for gene expression in wild-type airway epithelial cells after paramyxoviral infection. Analysis was performed on mRNA isolated from SeV-infected primary-culture mouse tracheal epithelial cells that were maintained under physiologic conditions (air-liquid interface). Experiment Overall Design: Primary-culture mouse tracheal epithelial cells (mTECs) were established on Transwell membranes using air-liquid interface (ALI) conditions. Sendai virus (SeV), strain 52, was obtained from American Type Culture Collection and stored at -70°C. Cultures were inoculated with SeV or an equivalent amount of UV-inactivated SeV (SeV-UV) in the apical compartment for 1 h at 37 °C. Air-liquid-interface conditions were re-established by washing the membrane with PBS. Each culture well was subjected to one of two treatments (SeV, or UV-SeV) for 1 day. N = 4 SeV wells, N = 6 UV-SeV wells, with each well independently analyzed by microarray. No technical replicates were performed, but arrays were evaluated for quality control using the SimpleAffy package (Miller CJ, 2004) in Bioconductor 2.0.
2009-04-25 | E-GEOD-10211 | biostudies-arrayexpress
Project description:The aim of this study was to analyze gene expression of primary airway epithelial cells during their differentiation in air-liquid interface ALI culture. Cells from one healthy donor were collected at different days of ALI culture (0,6,9,14 and 21). All samples were sequenced on Illumina NovaSeq6000 platform, in 2x150 mode, with a coverage of 100M reads/sample. Obtained data was later correlated with expression of 14 genes known to be related to airway epithelium differentiation obtained using qRT-PCR technique (TaqMan low density array, TLDA cards).
2021-11-29 | E-MTAB-11209 | biostudies-arrayexpress