Expression data from peripheral blood - blood draws at Pre and Post time points of Allergen inhalation challenge (ER and DR)
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE40240 | GEO | 2013/09/20
SECONDARY ACCESSION(S): PRJNA173271
REPOSITORIES: GEO
Similar Datasets
Project description:To determine differential gene expression in peripheral blood of asthmatic individuals undergoing allergen inhalation challenge between early responders (ERs) and dual responders (DRs) following allergen inhalation challenge Blood was collected immediately prior to, and two hours after challenge The change in gene expression (post expression minus pre expression) in ERs was compared with the change in gene expression in DRs using age and sex as covariates Preprocessing and probeset filtering were applied to the entire dataset (28 CEL files) using the Factor Analysis for Robust MicroArray Summarization (farms) package in R The Linear Models for MicroArrays (limma) package was used to determine differential gene expression using a Benjamini Hochberg FDR of 10%.
2013-09-20 | E-GEOD-40240 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE34158: Expression data from peripheral blood - blood draws at Pre and Post time points of Allergen inhalation challenge (PAX.GR) GSE34159: Expression data from peripheral blood - blood draws at Pre and Post time points of Allergen inhalation challenge (PAX.NGR) GSE34160: Expression data from peripheral blood - blood draws at Pre and Post time points of Allergen inhalation challenge (PAX.NGR and EDTA) Refer to individual Series
2012-01-26 | E-GEOD-34172 | biostudies-arrayexpress
Project description:To determine differential gene expression in peripheral blood of asthmatic individuals undergoing allergen inhalation challenge, post-challenge compared to pre-challenge
2012-01-26 | GSE34160 | GEO
Project description:To determine differential gene expression in peripheral blood of asthmatic individuals undergoing allergen inhalation challenge, post-challenge compared to pre-challenge Blood was collected immediately prior to, and two hours after challenge The 8 PAXgene non-globin reduced (PAX.NGR) samples were combined with 10 EDTA samples (n=9) for one analysis (PAX.NGR+EDTA) comparing gene expression in whole blood between pre and post challenge using the following covariates: tube type, sex, age, PC20 at pre-challenge, and FEV1 after onset and 2h post challenge and the RNA integrity number. Preprocessing and filtering were applied to the PAX.NGR+EDTA dataset using the Factor Analysis for Robust MicroArray Summarization (farms) package in R The Linear Models for MicroArrays (limma) package was used to determine differential gene expression using a Benjamini Hochberg FDR of 5%.
2012-01-26 | E-GEOD-34160 | biostudies-arrayexpress
Project description:Background: Allergen inhalation challenge in mild asthmatics induces airflow obstruction, airway hyperresponsiveness and inflammation, providing a model for hypothesis-generating experiments to understand regulation of these responses. We have sought to evaluate the peripheral whole blood transcriptome, post-challenge compared to pre-challenge, and to determine the effect of globin mRNA reduction methodology. Methods: Asthmatic subjects (20-60 years of age, with stable, mild allergic asthma, n=17) underwent allergen inhalation challenges. All subjects had an early asthmatic response of ≥ 20% fall in FEV1; most had a late phase response of ≥ 15% fall in FEV1. Blood was collected immediately prior to, and two hours after allergen challenge. Transcriptome analysis was performed using Affymetrix GeneChip® Human Gene 1.0 ST arrays, with and without globin mRNA reduction (PAX-GR and PAX-NGR, respectively) in 4 subjects. Replication studies for expression of nine genes contributing to the top canonical pathway, Nrf2-mediated oxidative stress response pathway, were performed with 5 independent subjects with microarray data, also with the same 4 subjects had microarray results and 8 other independent subjects with QPCR. Data were analyzed using paired t-test and Partek® Genomics Suite™. Results: The number of differentially expressed probe sets from PAX-NGR samples was twice that of PAX-GR samples. Paired analysis of each subjects' pre- and post-sample additionally demonstrated twice the power to detect differentially expressed probe sets. The Nrf2-mediated oxidative stress response pathway was identified as the top canonical pathway in the PAX-NGR samples. ATP-binding cassette sub-family C member 1 (ABCC1) gene was significantly reduced two hours after allergen challenge in the 5 subjects’ microarray dataset and the 2 QPCR replication datasets with P < 0.05. Conclusions: Globin mRNA reduction does not provide benefits to detect differentially expressed genes during allergen inhalation challenge. Allergen inhalation challenge is associated with decreased peripheral blood cell transcript level of ABCC1 gene. 26 array were analyzed. We first identified differentially expreed genes between post- and pre-challenge samples from 4 asthmatic subjects by using globin reduction samples and non-globin reduction samples (16 arrays). Then we replicated our findings using 10 arrays from 5 asthmatic subjects challenged with allergen. Includes 4 normal blood samples.
2012-10-15 | E-GEOD-24745 | biostudies-arrayexpress
Project description:Background: Allergen inhalation challenge in mild asthmatics induces airflow obstruction, airway hyperresponsiveness and inflammation, providing a model for hypothesis-generating experiments to understand regulation of these responses. We have sought to evaluate the peripheral whole blood transcriptome, post-challenge compared to pre-challenge, and to determine the effect of globin mRNA reduction methodology. Methods: Asthmatic subjects (20-60 years of age, with stable, mild allergic asthma, n=17) underwent allergen inhalation challenges. All subjects had an early asthmatic response of ≥ 20% fall in FEV1; most had a late phase response of ≥ 15% fall in FEV1. Blood was collected immediately prior to, and two hours after allergen challenge. Transcriptome analysis was performed using Affymetrix GeneChip® Human Gene 1.0 ST arrays, with and without globin mRNA reduction (PAX-GR and PAX-NGR, respectively) in 4 subjects. Replication studies for expression of nine genes contributing to the top canonical pathway, Nrf2-mediated oxidative stress response pathway, were performed with 5 independent subjects with microarray data, also with the same 4 subjects had microarray results and 8 other independent subjects with QPCR. Data were analyzed using paired t-test and Partek® Genomics Suite™. Results: The number of differentially expressed probe sets from PAX-NGR samples was twice that of PAX-GR samples. Paired analysis of each subjects' pre- and post-sample additionally demonstrated twice the power to detect differentially expressed probe sets. The Nrf2-mediated oxidative stress response pathway was identified as the top canonical pathway in the PAX-NGR samples. ATP-binding cassette sub-family C member 1 (ABCC1) gene was significantly reduced two hours after allergen challenge in the 5 subjects’ microarray dataset and the 2 QPCR replication datasets with P < 0.05. Conclusions: Globin mRNA reduction does not provide benefits to detect differentially expressed genes during allergen inhalation challenge. Allergen inhalation challenge is associated with decreased peripheral blood cell transcript level of ABCC1 gene.
2012-10-15 | GSE24745 | GEO
Project description:Ozone and allergen inhalation causes pulmonary inflammation and impairs lung function in mice. These effects are heightened in the absence of the immunosuppressive surfactant protein-D. Increased expression of inflammatory mediators is critical for the initiation of inflammation and impairment of lung function following ozone and allergen inhalation. An Affymetrix microarray was used to understand global changes in gene expression that occurred after ozone inhalation and/or allergen sensitization and challenge in the abscence of surfactant protein-D. Identification of the set of genes up and down regulated in response to ozone and/or allergen led us to study specific cellular inflammatory pathways. This study has important implications for the study of lung diseases like asthma.
2019-04-30 | GSE111155 | GEO
Project description:This study investigated temporal transcriptomic changes in response to nasal allergen challenge of titrated timothy grass pollen. This is an open single-center observational study conducted outside the pollen season. Twelve participants with seasonal allergic rhinitis underwent a control (diluent) challenge followed by nasal allergen challenge after an interval of 14 days. On each challenge day, nasal challenge with control or titrated timothy grass pollen (Aquagen, phleum pratense; ALK) was administered. Peripheral blood was collected before nasal challenge (baseline) and at 3, 6 and 24 hours following challenge. RNA was extracted from whole blood and CD4 cells for microarray experiment using Affymetrix Human Gene 1.0 ST arrays.
2013-01-16 | E-GEOD-43497 | biostudies-arrayexpress
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.
2011-12-30 | E-GEOD-34764 | biostudies-arrayexpress
Project description:Detecting differential changes in the peripheral whole-blood transcriptome, post-challenge compared to pre-challenge; using non-globin reduced PAXgene (PAX.NGR) tubes Blood was collected immediately prior to, and two hours after challenge
2012-01-26 | GSE34159 | GEO