|
| Status |
Public on Sep 20, 2013 |
| Title |
Subject STS007, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Pre
|
| Organism |
Homo sapiens |
| Characteristics |
response: ER
site: VGH
allergen: Cat
Sex: M
ethnicity: Caucasian
age: 42
mch pc20 (mg/ml) at pre-challenge: 0.13
mch pc20 (mg/ml) at post-challenge: NA
% fall in fev1 (early): -23
% fall in fev1 (late): -9
erythrocytes (x10^12/l): 4.64
hemoglobin (g/l): 140
hematocrit (l/l): 0.377
mean cell volume (fl): 81.2
mean cell hb (pg): 30.1
mean cell hb conc. (g/l): 371
red cell distr. width (%): 14.5
platelets (x10^9/l): 184
leukocytes (x10^9/l): 3.91
neutrophils (x10^9/l): 2.27
lymphocytes (x10^9/l): 1.21
monocytes (x10^9/l): 0.278
eosinophils (x10^9/l): 0.14
basophils (x10^9/l): 0.008
relative.neutrophils: 0.582
relative.lymphocytes: 0.309
relative.monocytes: 0.071
relative.eosinophils: 0.0358
relative.basophils: 0.0021
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 |
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 RMA background correction, quantile normalization and summarization of probe-level data using Factor Analysis for Robust Microarray Summarization
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 10%.
All statistical analyses were performed in the statistical computing program R.
|
| |
|
| Submission date |
Aug 20, 2012 |
| Last update date |
Sep 20, 2013 |
| Contact name |
Scott Tebbutt |
| E-mail(s) |
[email protected]
|
| 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 (1) |
| GSE40240 |
Expression data from peripheral blood - blood draws at Pre and Post time points of Allergen inhalation challenge (ER and DR) |
|
