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Chronic hypoxic response for human bronchial epithelial culture [bulkRNA-Seq batch2]

ABSTRACT: Purpose: To identify the gene expression change under chronic hypoxia on HBE cells. Methods: bulk RNA-seq was performed on primary human bronchial epithelial cells (HBE) that were cultured on air-liquid interface (ALI) condition and treated under normoxia or hypoxia (1% O2) for 5days. Results: inflammatory cytokines, collagen degradation, and angiogenic genes were upregulated under chronic hypoxia.

ORGANISM(S): Homo sapiens

PROVIDER: GSE227501 | GEO | 2023/08/22

REPOSITORIES: GEO

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Hypoxic response for human bronchial epithelial culture [bulkRNA-Seq batch1]

Project description:Purpose: To identify the gene expression change under hypoxia on HBE cells. Methods: bulk RNA-seq was performed on primary human bronchial epithelial cells (HBE) that were cultured on air-liquid interface (ALI) condition and treated under normoxia or hypoxia (1% O2) for 6hr, 24hr, and 5days. Results: hypoxia-related genes were significantly upregulated under hypoxia including EGLN3.

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Project description:Purpose: To identify the cell types change and gene expression change under hypoxia on HBE cells. Methods: The primary human bronchial epithelial cells (HBE) were cultured on air-liquid interface (ALI) conditions. After 4 weeks, the cells were cultured under normoxic or hypoxic (1% O2) conditions for 6h or 5days. The cells were dissociated with Accutase solution and proceeded to scRNA-seq. Results: Hypoxia did not induce any hypoxia-specific cell types, however, all cell types upregulated hypoxia-related, and senescence-related genes and downregulated cell proliferation genes.

2023-08-22 | GSE227508 | GEO

Cellular response to hypoxia on human bronchial epithelial culture [scRNA-Seq CAP]

Project description:Purpose: To identify the cell types change and gene expression change under hypoxia on HBE cells. Methods: The primary human bronchial epithelial cells (HBE) were cultured on air-liquid interface (ALI) conditions. After 4 weeks, the cells were cultured under normoxic, symmetrical hypoxic (3.5% O2), or asymmetrical hypoxic (3.5% O2 basolateral with apical cap ~ 1% O2) conditions for 5 days. The cells were dissociated with Accutase solution and proceeded to scRNA-seq. Results: Asymmetrical hypoxic cells showed more hypoxia-related responses than symmetrical hypoxic cells.

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Chronic hypoxic response for human bronchial epithelial culture [bulkRNA-Seq batch2]

Project description:Chronic hypoxic response for human bronchial epithelial culture [bulkRNA-Seq batch2]

| PRJNA945403 | ENA

Bronchial epithelium epithelial-mesenchymal plasticity forms aberrant basaloid-like cells in vitro [bulkRNA-seq]

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.

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Gene expression data from primary human bronchial epithelial cells expressing EGFP or DN-GRHL2 for 48h

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Hypoxic gene regulation on mice Quadriceps muscle

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Open chromatin and transcriptome analysis of iPSCs differentiated into lung epithelium at air-liquid interface reveals key transcriptional drivers and processes (ATAC-seq data)

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