RNA-seq of human primary epithelial nasal cells infected with SARS-CoV-2 (20A clade) and treated with long chain inorganic polyphosphates (polyP120) against vehicle-(saline solution)- treated controls
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ABSTRACT: Primary human nasal epithelial cells collected by nasal brushing of healthy donors (data deposited at: EVA- EMBL-EBI; project ID: PRJEB42411; analyses: ERZ1700617) were plated (3x105 cells) and infected with SARS-CoV-2 viral particles 20A (EPI_ISL_514432-S66; MOI, 0.03). After 24 hours, the infected cells were treated with 18.5 microMolar long chain inorganic polyphosphates (polyP120) or vehicle (saline solution) as the negative control for the treatment. After 36 hours, the cells were lysed, and their RNA were extracted for RNAseq.
Project description:HEK-293T cells were plated (1x106 cells) and treated with a nutraceutical formula (solution-3) at 0.01x concentration or with vehicle (saline solution) as the negative control for the treatment. After 24 hours, the cells were lysed, and their RNA was extracted for RNAseq.
Project description:Caco-2 cells were plated (5x105 cells), treated with a nutraceutical formula (solution-3) at 0.01x concentration or with vehicle (saline solution) as the negative control for the treatment. After 1 hour, the cells were infected with SARS-CoV-2 viral particles (EG.5; MOI, 3). After 48 hours, the cells were lysed, and their RNA were extracted for RNAseq.
Project description:Caco-2 cells were plated (1000000 cells) and treated with a nutraceutical formula (Solution-3) at 0.01x concentration or with vehicle (saline solution) as the negative control for the treatment. After 24 hours, the cells were lysed, and their RNA was extracted for RNAseq.
Project description:mRNA expression was assayed from bronchial epithelial cells collected via bronchoscopy and nasal epithelial cells collected by brushing the inferior turbinate from healthy current and never smoker volunteers in order to determine the relationship between smoking-related gene expression changes in bronchial and nasal epithelium within the same individual. Bronchial epithelial cells were collected from current and never smokers via bronchoscopy, and nasal epithelial cells were collected by brushing the inferior turbinate during the same clinic visit. 1ug of RNA was isolated and hybridized to Affymetrix Human Exon 1.0 ST microarrays to obtain mRNA expression. The genome build upon which transcript assignments are based is hg18 (HuEx-1_0-st-v2.na27.hg18.transcript.csv).
Project description:Smoking is the leading cause of lung cancer death, although only a small percentage of smokers develop the disease. Cigarette smoke exposure is known to cause a field of injury in cells throughout the respiratory tract, and while these airway epithelial cells are morphologically normal, they can undergo genetic alterations in response to cigarette smoke exposure. We used microarrays to analyze the gene expression of epithelial cells in the extrathoracic epithelium, specifically nasal and buccal epithelium, to see if these cells underwent similar genetic alterations in response to tobacco exposure as seen in bronchial epithelial cells as has been previously reported. Experiment Overall Design: Buccal and nasal epithelial cell samples were collected from healthy current and never smokers. RNA was isolated from these samples and hybridized to Affymetrix microarrays. Gene expression from never smokers was compared to never smoker gene expression from bronchial epithelium as well as expression data from other tissues to determine commonalities in expression patterns in normal extra- and intra-thoracic samples. In addition, gene expression from smokers and nonsmokers was compared in bronchial, nasal, and buccal epithelium to determine similarities in gene expression in these tissues in response to cigarette smoker exposure.
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).
Project description:Changes occur in the lung epithelium after allergen challenge that may give insight into asthma pathogenesis and we sought to identify novelepithelial genes induced by allergen exposure. We used microarrays to identify up-regulated genes induced by allergen challenge in lung epithelium. Epithelal brushing of the large airways in mouse lungs was performed 24 hours after Alternaria allergen or PBS control challenge 24. Collected epithelial cells underwent RNA extraction and hybridization on Affymetrix microarrays. There are a total of 6 samples, 3 allergen and 3 control samples.
Project description:NSAID-exacerbated respiratory disease (N-ERD) represents a particularly severe endotype of chronic rhinosinusitis with nasal polyps (CRSwNP), which affects around 10-16% of CRSwNP patients. N-ERD is characterized by severe and refractory nasal polyposis, bronchial asthma and intolerance to non-steroidal anti-inflammatory drugs (NSAIDs), including aspirin. Today, the pathogenesis of N-ERD remains incompletely understood and curative treatments are lacking. Using a global transcriptomic approach, we identified local changes between the mucosa of N-ERD nasal polyps and healthy control inferior turbinates. Nasal brushing samples were collected from inferior turbinates of healthy controls and nasal polyps of N-ERD patients under anterior rhinoscopy and stored at -80°C in RNAprotect until RNA isolation and RNAseq.
Project description:A comparative gene expression analysis was performed using cDNA microarray technology in passage-2 normal human nasal epithelial cells to identify the differentially expressed genes between influenza A virus infected and uninfected cells. Two samples were analyzed. RNA was extracted from normal human nasal epithelial cells, which were further divided as H1N1 PI 0 day and H1N1 PI 2 day (influenza A virus infection for 48 hr).
Project description:We are investigating the methylation profiles associated with cigarette smoke exposure. We used arrays to compare the DNA methylation profiles in healthy human smokers and nonsmokers. Nasal epithelial cells were extracted from 12 volunteers (6 smokers, 6 nonsmokers), and grown until fully differentiated. DNA was extracted from samples, and bisulfite converted, hybridized, and scanned to IlluminaMethylation27 BeadChip arrays.