|
| Status |
Public on Jan 26, 2012 |
| Title |
Subject 006 PAX.NGR, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Post
|
| Organism |
Homo sapiens |
| Characteristics |
gender: M
age: 47
site: Van
allergen: Orchard Grass
mch pc20 (mg/ml) at pre-challenge: 0.28
mch pc20 (mg/ml) at post-challenge: NA
% fall in fev1 (early): -23
% fall in fev1 (late): -17
rna integrity number: 8.9
tissue: whole blood
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The samples collected pre- and post-challenge were frozen and transported to the laboratory on dry ice, where they were stored at –80°C until RNA extraction.
From 8 PAXgene Blood RNA tubes (PreAnalytiX – Qiagen / BD, Valencia, CA, USA), total intracellular RNA was purified from 2.5 mL of whole-blood according to manufacturer protocols using the RNeasy mini kit (Qiagen, Chatsworth, CA, USA).
The yield and quality of RNA was assessed by NanoDrop 8000 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
|
| Label |
biotin
|
| Label protocol |
standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
Affymetrix Human Gene 1.0 ST array (Affymetrix, Santa Clara, CA)
|
| Scan protocol |
standard Affymetrix protocol
|
| Data processing |
Raw data normalization using the 'farms' package consisted of quantile normalization and summarization of probe-level data.
Data filtering was also performed using the Informative vs. Non-Informative Calls function in the 'farms' package. Differential gene expression was determined using moderated t-tests in limma using an FDR cut-off of 5%.
All statistical analyses were performed in the statistical computing program R.
|
| |
|
| Submission date |
Dec 05, 2011 |
| Last update date |
Jan 28, 2012 |
| Contact name |
Scott Tebbutt |
| E-mail(s) |
scott.tebbutt@hli.ubc.ca
|
| Organization name |
University of British Columbia
|
| Department |
Medicine
|
| Lab |
James Hogg Research Centre
|
| Street address |
Room 166, 1081 Burrard Street
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6Z 1Y6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE34159 |
Expression data from peripheral blood - blood draws at Pre and Post time points of Allergen inhalation challenge (PAX.NGR) |
| GSE34172 |
Expression data from peripheral blood - blood draws at Pre and Post time points of Allergen inhalation challenge |
|
| Relations |
| Reanalyzed by |
GSM843277 |
