|
| Status |
Public on Jan 26, 2012 |
| Title |
Subject 004 PAX.GR, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
whole blood Pre-challenged
|
| Organism |
Homo sapiens |
| Characteristics |
gender: M
age: 36
site: Van
allergen: Timothy Grass
mch pc20 (mg/ml) at pre-challenge: 3.2
mch pc20 (mg/ml) at post-challenge: NA
% fall in fev1 (early): -61
% fall in fev1 (late): -38
rna integrity number: 8.3
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).
Aliquots of RNA isolated from PAXgene tube samples taken from the 4 individuals were subjected to globin transcript reduction processes using the GLOBINclear™ - Human kit (Ambion – AB, Austin, TX, 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 using factor analysis 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) |
| GSE34158 |
Expression data from peripheral blood - blood draws at Pre and Post time points of Allergen inhalation challenge (PAX.GR) |
| GSE34172 |
Expression data from peripheral blood - blood draws at Pre and Post time points of Allergen inhalation challenge |
|
