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| Status |
Public on Jan 26, 2012 |
| Title |
Expression data from peripheral blood - blood draws at Pre and Post time points of Allergen inhalation challenge (PAX.NGR and EDTA) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
To determine differential gene expression in peripheral blood of asthmatic individuals undergoing allergen inhalation challenge, post-challenge compared to pre-challenge
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| Overall design |
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%.
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| Contributor(s) |
Kam SH, Singh A, He J, Ruan J, Gauvreau GM, O'Byrne PM, FitzGerald JM, Tebbutt SJ |
| Citation(s) |
22316092 |
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| Submission date |
Dec 05, 2011 |
| Last update date |
Jul 26, 2018 |
| Contact name |
Scott Tebbutt |
| E-mail(s) |
[email protected]
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| Organization name |
University of British Columbia
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| Department |
Medicine
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| Lab |
James Hogg Research Centre
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| Street address |
Room 166, 1081 Burrard Street
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| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6Z 1Y6 |
| Country |
Canada |
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| Platforms (1) |
| GPL6244 |
[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] |
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| Samples (18)
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| GSM843272 |
Subject 004 PAX.NGR (reanalysis), biological rep1 |
| GSM843273 |
Subject 004 PAX.NGR (reanalysis), biological rep2 |
| GSM843274 |
Subject 005 PAX.NGR (reanalysis), biological rep1 |
| GSM843275 |
Subject 005 PAX.NGR (reanalysis), biological rep2 |
| GSM843276 |
Subject 006 PAX.NGR (reanalysis), biological rep1 |
| GSM843277 |
Subject 006 PAX.NGR (reanalysis), biological rep2 |
| GSM843278 |
Subject 026 PAX.NGR (reanalysis), biological rep1 |
| GSM843279 |
Subject 026 PAX.NGR (reanalysis), biological rep2 |
| GSM843280 |
Subject 012 EDTA, biological rep1 |
| GSM843281 |
Subject 012 EDTA, biological rep2 |
| GSM843282 |
Subject 102 EDTA, biological rep1 |
| GSM843283 |
Subject 102 EDTA, biological rep2 |
| GSM843284 |
Subject 105 EDTA, biological rep1 |
| GSM843285 |
Subject 105 EDTA, biological rep2 |
| GSM843286 |
Subject AKA EDTA, biological rep1 |
| GSM843287 |
Subject AKA EDTA, biological rep2 |
| GSM843288 |
Subject THG EDTA, biological rep1 |
| GSM843289 |
Subject THG EDTA, biological rep2 |
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| This SubSeries is part of SuperSeries: |
| GSE34172 |
Expression data from peripheral blood - blood draws at Pre and Post time points of Allergen inhalation challenge |
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| Relations |
| BioProject |
PRJNA156471 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE34160_RAW.tar |
71.6 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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