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Series GSE38994 Query DataSets for GSE38994
Status Public on Jan 18, 2013
Title Next-Generation Transcriptome Sequencing (RNA-Seq) of Human Endobronchial Biopsies: Asthma vs Controls
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Rationale: The cellular and molecular pathways in asthma are highly complex. Increased understanding can be obtained by unbiased transcriptomic analysis (RNA-Seq).
Hypothesis and Aims: We hypothesized that the transcriptomic profile of whole human endobronchial biopsies differs between patients with asthma and controls. First, we investigated the feasibility to obtain RNA from whole endobronchial biopsies suitable for RNA-Seq. Second, we examined the difference in transcriptomic profiles between asthma and controls.
Methods: This cross-sectional study compared 4 steroid-free atopic asthma patients and 5 healthy non-atopic controls. RNA of ASM from 4 endobronchial biopsies per subject was isolated and sequenced (GS FLX+, 454/Roche). Ingenuity Pathway Analysis was used to identify gene networks. Comparison of the numbers of reads per gene in asthma and controls was based on the Poisson distribution. At the current sample size the estimated false discovery rate was 4%.
Results: Yield of isolated RNA was 900-9,300ng. We identified 10,167 and 11,006 unique genes for asthma and controls, respectively. Forty-six genes were differentially expressed between asthma and controls, including pendrin, periostin, and BCL2. Ten gene networks involved in cellular morphology, movement, and development had an IPA network score ≥2.
Conclusion:RNA isolated from whole human endobronchial biopsies is suitable for RNA-Seq, showing different transcriptomic profiles between asthma and controls. Novel and confirmative genes were found to be linked to asthma. These results indicate that biological processes in the airways of asthma patients are differently regulated compared to healthy controls, which may be relevant for the pathogenesis and treatment of the disease.
 
Overall design This cross-sectional transcriptomics study consisted of 2 visits. At visit 1, atopic asthma patients (n=4), and healthy non-atopic controls (n=5) were screened for eligibility to participate according to the in- and exclusion criteria. Spirometry and a methacholine bronchoprovocation test were performed. At visit 2, FEV1 reversibility was measured and 4 endobronchial biopsies per subject were collected during a bronchoscopy. Total RNA from whole endobronchial biopsies was collected. cDNA was prepared using the Ovation RNA-Seq System (NuGEN). RNA-Seq was performed using the GS FLX+ instrument (454/Roche). Sequence reads were mapped against the human genome (hg19; UCSC). Comparison of the numbers of reads per gene between asthma and healthy controls was based on the Poisson distribution.
 
Contributor(s) Yick CY
Citation(s) 23314903
Submission date Jun 28, 2012
Last update date May 15, 2019
Contact name Ching Yong Yick
E-mail(s) c.y.yick@amc.uva.nl
Phone +31-20-5661660
Organization name Academic Medical Center
Department Respiratory Medicine
Street address Meibergdreef 9
City Amsterdam
ZIP/Postal code 1105AZ
Country Netherlands
 
Platforms (1)
GPL14603 454 GS FLX Titanium (Homo sapiens)
Samples (2)
GSM953385 Asthma
GSM953386 Control
Relations
SRA SRP014005
BioProject PRJNA170182

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE38994_RAW.tar 110.0 Kb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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