Ontology highlight
ABSTRACT:
PROVIDER: PRJEB88083 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR14821572.fastq.gz | Fastqsanger.gz | |||
| ERR14821573.fastq.gz | Fastqsanger.gz | |||
| ERR14821574.fastq.gz | Fastqsanger.gz | |||
| ERR14821575.fastq.gz | Fastqsanger.gz | |||
| ERR14821576.fastq.gz | Fastqsanger.gz |
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Project description:We used RNA sequencing to identify differentially expressed genes during esophageal epithelial differentiation and in the presence of interleukin 13 using an air-liquid interface culture system. RNA sequencing was performed on a human esophageal epithelial cell line (EPC2-hTERT) grown submerged (day 8) or at the air-liquid interface (ALI) (day 14, untreated or treated with interleukin 13 [100 ng/mL])
2015-02-01 | E-GEOD-65335 | biostudies-arrayexpress
Project description: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.
2024-12-02 | GSE280502 | GEO
Project description:Air-liquid interface (ALI) model using the immortalized Calu-3 cells has been used to model lung diseases. From submerged to ALI culture condition, Calu-3 cells polarize and change to a ciliary mucus-producing cell. Polarized Calu-3 molecular and phenotypic similarity with primary cells has been proven; however, no studies have been focused on the pathways differentially expressed in ALI vs. submerged conditions. In this study, we profiled the proteome and transcriptome of Calu-3 cells from submerged (non-polarized, NP) to ALI (polarized, P) culture conditions and in the omics data we observed an increase in cell replication in the non-polarized condition while polarized Calu-3 cells presented higher activation of cellular energy production, protein maturation and recycle and expression of immune active molecules. Moreover, the omics findings showed upregulation of different biological processes related to protein quality control system and antigen processing presentation in polarized Calu-3 cells. Immunoblot and fluorescence microscopy confirmed increased expression of bronchial epithelium integrity components like mucus and tight junctions in polarized Calu-3 and revealed a characteristic protein expression and cellular organization found in normal lung epithelial tissue. Furthermore, SARS-CoV-2 infection of polarized cells revealed higher cell death due to higher viral entry associated with higher apical membrane expression of ACE2 receptor. The differences observed in this study give us a better understanding of how ALI can mimic the human bronchial-epithelial cells and its applications in different contexts of lung diseases.
2026-02-23 | PXD056869 | Pride
Project description:Rationale: Ulcerative colitis (UC) is characterized by colonic mucosal inflammation and barrier dysfunction. We hypothesize that UC causes persistent defects in mucosal homeostasis, evident even in the absence of inflammation, contributing to disease chronicity. Objective: To test this, we grew patient biopsy-derived sigmoid colonoids into air-liquid interface (ALI) monolayers, characterizing them through microscopy, proteomics, bulk RNAseq, and their susceptibility to UC patient-isolated Escherichia coli pathobiont p19A. Findings: Non-IBD ALI monolayers formed uniform crypt-like structures, mature goblet cells and a thick mucus layer containing all epithelial-derived proteins previously identified in human colonic mucus. In contrast, ALI monolayers from UC patients displayed a range of impairments, from distorted crypt-like structures and a thinner and more permeable mucus layer to severe defects in cellular differentiation and crypt development. Transcriptome analysis identified activated pathways associated with extracellular matrix formation and cell signaling, including numerous cancer-associated genes in UC ALI monolayers, which also proved significantly more susceptible to E. coli p19A. Conclusions: The culturing of patient biopsies into ALI colonoid monolayers provides a powerful model to assess human mucosal development, healing, homeostasis and mucus barrier function, revealing that UC-derived colonoids display a range of developmental and functional defects that persist in the absence of inflammation.
2026-01-29 | PXD064643 | Pride
Project description:Background: The Inflammatory Bowel Disease (IBD) ulcerative colitis (UC) is characterized by colonic mucosal inflammation and barrier dysfunction. We hypothesize that UC causes persistent defects in mucosal homeostasis, evident even in the absence of active inflammation, contributing to disease chronicity. Methods: To test this, we grew patient biopsy-derived sigmoid colonoids into air-liquid interface (ALI) monolayers, characterizing them through microscopy, proteomics, bulk RNAseq, and their susceptibility to UC patient-isolated Escherichia coli pathobiont p19A. Results: Non-IBD ALI monolayers formed uniform crypt-like structures and a thick mucus layer containing all epithelial-derived proteins previously identified in human colonic mucus. In contrast, ALI monolayers from UC patients displayed a range of impairments, classified as a mild phenotype with distorted architecture and a thinner, more permeable mucus layer to a severe phenotype with defects in cellular differentiation and an inability to produce a mucus layer. Transcriptome analysis identified activated pathways associated with extracellular matrix formation and cell signaling, including numerous cancer-associated genes in UC ALI monolayers, which also proved significantly more susceptible to E. coli p19A. Conclusions: Taken together, the culturing of patient biopsies into ALI colonoid monolayers provides a powerful model to assess human colonic mucosal development, healing, homeostasis, and mucus barrier function, revealing that UC-derived colonoid monolayers display a range of developmental and functional defects that persist in the absence of inflammation.
2026-01-29 | GSE299477 | GEO
Project description:To identify differentially expressed genes and key biological pathways that define toxicity following nanomaterial exposure, we performed microarray analyses on NR8383 macrophages: here is the control for Air Liquid Interface (ALI) in DMEM culture medium supplemented with fetal bovine serum (FBS). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement N°. 686098
2023-08-18 | GSE156458 | GEO
Project description:Purpose: The goal of this study was to identify transcriptional changes that occur in mouse ileal stem cell-derived epithelium plated on transwells after the establishment of an air-liquid interface (ALI). Methods: Mouse ileal stem cell spheroids were plated on transwells and grown in L-WRN conditioned medium (top and bottom compartment) for 7 days, at which point the top medium was removed to establish ALI. Samples were collected for sequencing on the day of ALI initiation (non-ALI Day 0) and three days post top medium removal (ALI Day 3). Control samples were also collected from transwells submerged for all 10 days of the experiment (non-ALI Day 3) and from the initial stem cell spheroid cultures. Results: Non-ALI Day 0 and non-ALI Day 3 samples had similar transcriptional profiles, whereas ALI transwells showed upregulation of transcriptional factors that induce secretory cell lineages, as well as a general upregulation of metabolic genes involved in oxidative phosphorylation and downregulation of those involved in glycolysis. Conclusions: Removal of L-WRN conditioned medium from the top compartment of transwells plated with stem cell-derived intestinal epithelial cells establishes an air-liquid interface that changes the metabolic profile of the cultures and initiates a differentiation cascade for intestinal secretory cells such as goblet cells and paneth cells.
2019-07-29 | GSE124815 | GEO
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
Project description:Members of rhinovirus C (RV-C) species are more likely to cause wheezing illnesses and asthma exacerbations compared to other rhinoviruses. The cellular receptor for these viruses was heretofore unknown. We measured gene expression (Human Gene 1.0 ST Array, Affymetrix) in two series of experiments involving cells that were either susceptible or not susceptible to RV-C infection. In one experimental series, susceptible cells included whole sinus mucosal tissue specimens (n = 5), epithelial cell suspension from sinus tissue, and nasal epithelium obtained via brushing, while non-susceptible cells included monolayers of primary undifferentiated epithelial cells and transformed cell lines (n = 5). In a second experimental series, we compared three pairs of undifferentiated and fully differentiated (ALI) sinus epithelial cell cultures. We identified a total of 12 genes upregulated in RV-C susceptible cells (represented by 14 probe sets) encoding proteins localized to plasma membrane, and/or with predicted or functionally demonstrated receptor activity, including members of the Human MHC class II, stomatin, guanine nucleotide-binding, type I cytokine and atypical chemokine receptor and cadherin protein families. Sinus and bronchial epithelial tissue samples were obtained from residual surgical specimens. Primary airway epithelial cells were cultured submerged (undifferentiated monolayers) or at air-liquid interface (fully-differentiated). Established cell lines (HeLa, NCI-H358 and WisL) were cultured submerged. Epithelial tissue samples were placed in RNAlater solution (Life Technologies) to stabilize and protect cellular RNA; cultured cells were lysed directly and total RNAs were isolated using TRIzol reagent (Life Technologies). Gene expression was analyzed using the Human Genome 1.0 ST GeneChip arrays (Affymetrix, Santa Clara, CA).
2014-11-01 | E-GEOD-61396 | biostudies-arrayexpress
Project description:Rationale: Although epithelial-mesenchymal transition (EMT) is a common feature of fibrotic lung disease, its role in fibrogenesis is controversial. Recently, aberrant basaloid cells were identified in fibrotic lung tissue as a novel epithelial cell type displaying a partial EMT phenotype. The developmental origin of these cells remains unknown. Objectives: To elucidate the role of EMT in the development of aberrant basaloid cells from human bronchial epithelium by mapping EMT-induced transcriptional changes at the population and single-cell level. Methods: Human bronchial epithelial cells (HBECs) grown as submerged or air-liquid interface (ALI) cultures with or without EMT induction were analyzed by bulk and single-cell RNA-Sequencing. Measurements and Main Results: Comparison of submerged and ALI cultures revealed differential expression of 9,868—protein coding (PC) and long non-coding RNA (lncRNA)—genes and revealed epithelial cell-type-specific lncRNAs. Similarly, EMT induction in ALI cultures resulted in robust transcriptional reprogramming of 6,927—PC and lncRNA—genes. While there was no evidence for fibroblast/myofibroblast conversion, cells displayed a partial EMT gene signature and an aberrant basaloid-like cell phenotype. Conclusions: The substantial transcriptional differences between submerged and ALI cultures highlights that care must be taken when interpreting data from submerged cultures. This work supports that lung epithelial EMT does not generate fibroblasts/myofibroblasts and confirms ALI cultures provide a physiologically relevant system to study aberrant basaloid-like cells and mechanisms of EMT. We provide a catalog of PC and lncRNA genes and a data visualization package for further exploration for potential roles in the lung epithelium in health and lung disease.
2022-04-21 | GSE193682 | GEO