|
| Status |
Public on Jan 26, 2012 |
| Title |
Subject 004 PAX.NGR (reanalysis), biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Post
|
| 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: 8.7
tissue: whole blood
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were stored at -80⁰C until RNA extraction
From PAXgene tube samples, total RNA was purified from 2.5 mL of whole blood using Rneasy mini kit (Qiagen, Chatsworth, CA, USA)
From EDTA tube samples, total RNA was purified from 3.0 mL of whole blood following modified TRIzol-based extraction method.
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 |
standand Affymetrix protocol
|
| |
|
| Hybridization protocol |
Affymetrix Human Gene 1.0 ST array (Affymetrix, Santa Clara, CA)
|
| Scan protocol |
standand 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) |
| GSE34160 |
Expression data from peripheral blood - blood draws at Pre and Post time points of Allergen inhalation challenge (PAX.NGR and EDTA) |
| GSE34172 |
Expression data from peripheral blood - blood draws at Pre and Post time points of Allergen inhalation challenge |
|
| Relations |
| Reanalysis of |
GSM843265 |
