Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

4 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of air-liquid interface co-cultures of A549 and THP-1 cells exposed to Saharan dust or DQ12 against unexposed controls

ABSTRACT: Although desert dust is known to cause increased respiratory morbidity and mortality, the underlying biological pathways remain unclear. We used RNA-seq on an advanced human alveolar in vitro model to find yet unidentified genes dysregulated by Saharan dust exposure. For comparison, DQ12 quartz dust was used as a well-established pulmonary toxicant. Co-cultures of A549 cells and phorbol 12-myristate-13-acetate (PMA)-differentiated THP-1 cells were cultivated at the air-liquid interface (ALI) for one day before exposure. For exposure, a Vitrocell Cloud 12α system was used. In the exposure chamber, SD or DQ12 suspensions were nebulized onto ALI co-cultures. In parallel, in the control chamber, the vehicle was nebulized onto ALI co-cultures. After exposure for 24 h, RNA was isolated and used for RNA-seq.

INSTRUMENT(S): MinION

ORGANISM(S): Homo sapiens

SUBMITTER: Gerrit Bredeck

PROVIDER: E-MTAB-13372 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of human airway epithelial cells sampled at multiple time points to examine mucociliary differentiation

Project description:Microarray analysis was performed to identify transcriptional changes that occur during mucociliary differentiation of human primary bronchial epithelial cells cultured at an air-liquid interface (ALI). Experiment Overall Design: Cells from three different donors were cultured and collected at 11 different time points from day 0 to day 28 of ALI culture.

2007-11-11 | E-GEOD-5264 | biostudies-arrayexpress

Single-cell RNA sequencing of pandemic influenza A virus-infected human airway epithelial cells

Project description:To characterize the host response to pandemic IAV infection in its natural target cells, we infected primary human airway epithelial cell (hAEC) cultures wild-type pandemic IAV (WT) or a NS1 mutant virus (NS1R38A) with abrogated dsRNA binding capacity at a multiplicity of infection (MOI) of 0.03. We then profiled the transcriptomes of uninfected cells as well as cells harvested 18 hours post-infection (hpi) using single-cell RNA sequencing (scRNA-seq).

2022-09-22 | E-MTAB-12159 | biostudies-arrayexpress

Transcription profiling by array of human biopsies from normal esophageal epithelium and in vitro cell lines

Project description:Comparison of expression profiles of in vitro cell lines with biopsies from human normal esophageal epithelium.

2010-09-01 | E-MEXP-2795 | biostudies-arrayexpress

Characterization of a tetra-culture system combining lung alveolar epithelial cells, endothelial cells, macrophages, and mast cells in a three-dimensional orientation

Project description:To more accurately model inhalation toxicity in vitro, we developed a tetra-culture system that combines lung alveolar epithelial cells, endothelial cells, macrophages, and mast cells in a three-dimensional orientation. We characterized the influence of the added complexity, using network perturbation analysis and gene expression data, to gain an insight into the steady-state profile of the assembled complete three-dimensional model using all four cell types and of simpler models of one, two, or three of the cell types. Gene expression data were analyzed using cause-and-effect biological network models, together with a quantitative network-scoring algorithm to determine the biological impact of co-culturing the various cell types. In the assembled tetra-culture, macrophages appeared to be the largest contributors to overall network perturbations, promoting high basal levels of oxidative stress and inflammation. This finding led to further optimization of the model using rested macrophages; the addition of rested macrophages decreased the basal inflammatory and cell stress status of the co-culture. Finally, we compared transcriptional profiles from publicly available datasets of conventional in vitro models representative of the airways and of healthy human lung tissues, to assess similarities between our model and other in vitro models and the human lung. On the transcriptional level, we found an increasing correlation between airway models and normal human lung tissue, particularly as cell types became more physiologically relevant and the complexity of the system increased. This indicates that the combination of multiple lung-relevant cell types in vitro does indeed increase similarity to the physiological counterpart.

2019-02-12 | E-MTAB-7072 | biostudies-arrayexpress

SBRI_AB Host response in primary mouse tracheal epitelial cells (mTEC) to influenza infection with PR8, VN or X31 at MOI of 0.015 at 12 hours

Project description:Array analysis of total RNA from mTECs 12 h post infection with influenza. Strains used were Mock, PR8, X31, VN6+2 (MOI 0.015) Time Point: 12 h post infection (Mock, PR8, X31, VN) MOI 0.015; in biological triplicates. Total samples: 12.

2012-09-26 | E-GEOD-37246 | biostudies-arrayexpress

SBRI_AC Host response in primary mouse tracheal epitelial cells (mTEC) to influenza infection with PR8, VN or X31 at MOI of 3 at 12 hours

Project description:Array analysis of total RNA from mTECs 12 h post infection with influenza. Strains used were Mock, PR8, X31, VN6+2 (MOI 3) Time Point: 12 h post infection (Mock, PR8, X31, VN) MOI 3.0; in biological triplicates. Total samples: 12.

2012-09-26 | E-GEOD-37247 | biostudies-arrayexpress

Secretome profiling of human airway epithelial cultures infected with respiratory syncytial virus

Project description:The respiratory epithelium is a polarised layer at the interface between the outside environment and deeper lung structures, overlaid by the epithelial lining fluid (ELF). This provides a mechanical and immunological barrier to inhaled particulates, such as viruses. Human respiratory syncytial virus (hRSV) is a major cause of disease in humans, and targets the respiratory epithelium. However, little is known of the disruption of the ELF proteome in the context of virus-driven respiratory illnesses. To address this, a proteomics approach was combined with an ex-vivo human airway epithelial model (HAE) to investigate the apical and basolateral secretome in hRSV-infected cultures. This demonstrated that several apically- and basolaterally-restricted proteins were subsequently secreted in both directions upon infection, while a number of proteins saw their apical/basolateral abundance ratios significantly altered. Furthermore, another 35 proteins were uniquely identified after hRSV treatment. Importantly, some of these changes were correlated in nasal aspirates (NA) from children with and without hRSV. This study showed that hRSV could affect airway secretions, and disrupted the directionality of the respiratory epithelium.

2022-03-01 | PXD004430 | Pride

Changes in microRNA and mRNA expression with differentiation of human bronchial epithelial cells [mRNA]

Project description:Normal human bronchial epithelial (NHBE) cells cultured in an air-liquid interface (ALI) system form a polarized, pseudostratified epithelium composed of basal, ciliated and goblet cells that closely resemble the in vivo airway epithelium structure. ALI cultures of NHBE cells provide a unique in vitro system to investigate airway epithelial biology, including developmental, structural and physiologic aspects. In this study, we wanted to investigate mRNA expression patterns during airway epithelium differentiation. By using microarrays, we studied the changes in expression of mRNAs in normal human bronchial epithelial cells as they differentiate from an undifferentiated monolayer to a differentiated pseudostratified epithelium after 28 days of air-liquid interface (ALI) culture, when epithelial cells differentially express basal, ciliated and goblet cell markers. Normal human bronchial epithelial cells were cultured in an air-liquid interface (ALI) system and harvested at three different time-points: subconfluent, confluent and day 28 of ALI. Samples were processed for total RNA extraction and hybridization on Affymetrix microarrays. All the experiments were performed by triplicate.

2012-10-01 | E-GEOD-39059 | biostudies-arrayexpress

Secretome and Proteome of WT and CFTR-KO pancreatic duct epithelial cells

Project description:Loss of CFTR function in the pancreatic duct leads to dysregulated luminal pH causing premature activation of digestive enzymes and tissue necrosis. Drastic alterations in pancreatic tissue architecture and cellular composition changes the microenvironment of the islets. Given that CFTR is expressed in the pancreatic ducts, we hypothesized that loss of functional CFTR impacts islet function by modifying the ductal secretome. To this end, we developed a long-term in vitro pancreatic duct epithelial cell culture system and polarized both WT and CFTR-KO (CF) ferret duct epithelial cells. We profiled the apical and basolateral secretome, and the cellular proteome of both WT and CF duct epithelium using quantitative mass spectrometry. Bioinformatic analysis of differentially secreted proteins mapped to their cognate receptors provided a list of putative paracrine interactions that affect islet function. Signaling pathways and upstream regulators that alter the secretome and cellular proteome profile were computationally mined to characterize disease causing mechanisms. In this study, we provide a proteomic roadmap of perturbed autocrine and paracrine signals from the CF pancreatic duct.

2021-05-27 | PXD025126 | Pride

Changes in microRNA and mRNA expression with differentiation of human bronchial epithelial cells [miRNA]

Project description:Normal human bronchial epithelial (NHBE) cells cultured in an air-liquid interface (ALI) system form a polarized, pseudostratified epithelium composed of basal, ciliated and goblet cells that closely resemble the in vivo airway epithelium structure. ALI cultures of NHBE cells provide a unique in vitro system to investigate airway epithelial biology, including developmental, structural and physiologic aspects. MicroRNAs (miRNAs) are short, single-stranded, non-coding RNAs of 20-23 nucleotides that down-regulate gene expression by either inducing degradation of target mRNAs or impairing their translation. They are phylogenetically well conserved, which probably implies an important role of miRNAs in biological processes. In this way, we wanted to shed some light on miRNA specific roles and the relationship with their mRNA targets during airway epithelium differentiation. By using microarrays, we studied the changes in expression of microRNAs in normal human bronchial epithelial cells as they differentiate from an undifferentiated monolayer to a differentiated pseudostratified epithelium after 28 days of air-liquid interface (ALI) culture, when epithelial cells differentially express basal, ciliated and goblet cell markers. Normal human bronchial epithelial cells were cultured in an air-liquid interface (ALI) system and harvested at three different time-points: subconfluent, confluent and day 28 of ALI. Samples were processed for total RNA (including small RNAs) extraction and hybridization on Affymetrix microarrays. All the experiments were performed by triplicate.

2012-10-01 | E-GEOD-39060 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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