Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic Analysis of Air–Liquid Interface Culture in Human Lung Organoids Reveals Regulators of Epithelial Differentiation

ABSTRACT: We comprehensively analyzed differentiation effects of the air–liquid interface (ALI) culture method on adult tissue-derived human lung organoids and examined the similarity with in vivo human airway epithelium compared to submerged cultures using single-cell RNA sequencing.

ORGANISM(S): Homo sapiens

PROVIDER: GSE280502 | GEO | 2024/12/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Mouse Tracheal Epithelial Cell Air-Liquid Interface Primary Culture Time Course (ALI d0, d2, d7)

Project description:Mouse tracheal epithelial cells were cultured at air-liquid interface (ALI), RNA was harvested at days 0, 2, and 7 post-ALI, and hybridized to two-channel MEEBO arrays. The experiment was designed to allow investigators to identify genes differentially expressed during airway epithelial cell differentiation and development, including ciliogenesis.

2014-08-12 | GSE60364 | GEO

3D and Air Liquid Interface culture of human iPSC-derived alveoar epithelial type I-like cells (iAT1s) [NGAT LDCI]

Project description:The goal of this study is to understand transcriptomic differences of human iPSC derived alveolar epithelial type I-like cells cultured in 3D and at Air Liquid Interface (ALI).

2023-08-08 | GSE221342 | GEO

Intermittent exposure to whole cigarette smoke alters the differentiation of primary small airway epithelial cells in the air-liquid interface culture

Project description:Cigarette smoke (CS) is the leading cause to develop COPD. Therefore, we investigated the pathologic effects of whole CS on the differentiation of primary small airway epithelial cells (SAEC), from three healthy donors and three COPD patients, cultured under ALI (air-liquid interface) conditions. The analysis of the epithelial physiology demonstrated that CS impaired barrier formation and reduced cilia beat activity. Although, COPD-derived ALI cultures preserved some features known from COPD patients, the CS-induced effects were similarly pronounced in ALI cultures from patients compared to healthy controls. A RNA sequencing analysis revealed the deregulation for marker genes for basal cells and secretory cells upon CS exposure. The comparison between gene signatures obtained from our in vitro model (CS vs. air) with a published data set from human epithelial brushes (smoker vs. non-smoker) reveals a high degree of similarity between the deregulated genes and pathways. ALI culture has been generated utilising cells obtained from 3 COPD and 3 healthy subjects. Subsequently cultures have been treated with CS and air respectively for 33 days. Gene expression profiles were generated using next generation sequencing.

2019-12-31 | GSE135188 | GEO

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

Effect of air-liquid interface stimulation on gene expression during keratinocyte differentiation by three-dimensional culture

Project description:To investigate how air-liquid interface stimulation induces epidermal differentiation, we carried out RNA-seq on three-dimensional culture with and without air exposure.

2022-12-08 | GSE205727 | GEO

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

Single-cell analysis of Kaposi’s sarcoma-associated herpesvirus infection in three-dimensional air-liquid interface culture model

Project description:The oral cavity has previously been identified as the major site for transmission of Kaposi’s sarcoma-associated herpesvirus (KSHV), but how KSHV establishes infection and replication in the oral epithelia remains unclear. Here, we report a KSHV spontaneous lytic replication model using fully differentiated, three-dimensional (3D) oral epithelial organoids at an air-liquid interface (ALI). This model revealed that KSHV infected the oral epithelia when the basal epithelial cells were exposed by damage. Unlike two-dimensional (2D) cell culture, 3D oral epithelial organoid ALI culture allowed high levels of spontaneous KSHV lytic replication, where lytically replicating cells were enriched at the superficial layer of epithelial organoid. Single cell RNA sequencing (scRNAseq) showed that KSHV infection induced drastic changes of host gene expression in infected as well as uninfected cells at the different epithelial layers, resulting in altered epithelial differentiation and morphogenesis. Moreover, we identified a unique population of infected cells containing lytic gene expression at the KSHV K2-K5 gene locus and distinct host and viral gene expression compared to latency or lytic replication. This study demonstrates an in vitro 3D epithelial organoid ALI culture model that recapitulates KSHV infection in the oral cavity, where KSHV undergoes the epithelial differentiation-dependent spontaneous lytic replication with a unique cell population carrying distinct viral gene expression.

2022-07-28 | GSE184257 | GEO

Single cell transcriptomic profiling of pluripotent stem cell-derived alveolar type 2 cells expressing SFTPC-tdTomato cultured in 3D spheres, 2D submerged culture, and air-liquid interface culture with and without cigarette smoke exposure

Project description:We performed transcriptomic profiling of cells derived from human induced pluripotent stem cells (iPSCs) using previously described distal lung directed differentiation protocol to generate alveolar type 2 cells (iAT2s). We used the SPC2-ST-B2 (“SPC2”) line containing a SFTPC-tdTomato knock in reporter. iAT2s were cultured as 3D spheres (3D), on Transwells in 2D submerged conditions (2D), or at ALI for a total of 10 days post passaging. iAT2s in ALI culture were exposed to cigarette smoke 12 hours prior to cell collection (Smoke) or air (ALI). On day 10, and at 12 hours post cigarette smoke exposure, cultures were dissociated to single cells and live cells were sorted on calcein blue on a Mo-Flo Astrios Cell Sorter. Capture and library preparation was performed using a 10X Chromium system. Libraries were sequenced using a NextSeq 500. We find that ALI culture promotes maturation of iAT2s compared to 3D, and that iAT2s mount an inflammatory and xenobiotic metabolism response to cigarette smoke exposure at ALI.

2022-04-30 | GSE184142 | GEO

RNA-seq analysis identifies the effect of PM2.5 on human nasal epithelial cells cultured under air-liquid interface (ALI) conditions until differentiated.

Project description:In this study, we performed high-throughput sequencing to evaluate the gene expression profiles of human nasal epithelial cells (HNECs) cultured under air-liquid interface (ALI) conditions until differentiated and then stimulated with PM2.5 (100 μg/ml) for 24 hours.

2023-09-25 | GSE243618 | GEO

Bulk-RNA Sequencing of Nasopharyngeal Carcinoma Cell Lines infected with Epstein-Barr virus (EBV) subjected to air-liquid interface (ALI)-induced reactivation

Project description:The HK1-EBV cell line is a human nasopharyngeal carcinoma cell line (RRID:CVCL_7084) infected in vitro with recombinant Epstein-Barr virus (EBV) Akata strain expressing EGFP and neoR inserted into the BXLF1 locus (PMIDs: 16611410). This cell line has been authenticated to be free of HeLa contaminants (PMIDs: 18196576; 24991015). We used bulk RNA sequencing techniques to analyze these cell lines reactivated at the air liquid interface (ALI) in a 3D cell culture model for ALI-induced EBV reactivation.

2024-12-31 | GSE231687 | GEO

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