|
| Status |
Public on Jul 31, 2007 |
| Title |
KELH0033_P-25_46F18 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Universal RNA
|
| Organism |
Homo sapiens |
| Characteristics |
Tissue:Universal RNA
|
| Biomaterial provider |
Stratagene
|
| Treatment protocol |
none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Universal human reference RNA was purchased from Stratagene and was amplified using MessageAMP aRNA kits (Ambion) as per manufacturer's instructions prior to labeling
|
| Label |
Cy3
|
| Label protocol |
Universal RNA probes was prepared by direct labeling of universal aRNA with Cy-3 fluorescent dye
|
| |
|
| Channel 2 |
| Source name |
PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
Tissue:Blood, Patient id:P-25, Age:46, Sex:F, DSO:18, Status:post-pO2 nadir
|
| Biomaterial provider |
Dr. David Kelvin
|
| Treatment protocol |
none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Paxgene blood collection tubes then amplified using the MessageAmp aRNA kit (Ambion) as per the manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
Sample probes were prepared by direct labeling with Cy-5 fluorescent dye
|
| |
|
| |
| Hybridization protocol |
similar to direct labelling protocol listed at UHN Microarray facility web site.
|
| Scan protocol |
Scanned at 16 bits using the Genepix Axon Scanner at 10micro-meter resolution at 635 nm (Cy5) and 532 nm (Cy3) using Genepix Pro 6.0 analysis software (Molecular Devices Corporation)
|
| Description |
Peripheral blood was collected longitudinally from SARS patients during hospitalization into heparinized tubes and processed for further analysis within 2-3 hours of collection. RNA was stabilized and purified using Paxgene Blood Collection Tubes and Paxgene RNA kits (Qiagen, Mississauga, ON, Canada).
|
| Data processing |
Each quantified output file was run though the following pre-processing steps using R (URL: www.r-project.org)and the Limma package. For Minimum Intensity filtering, R and G values were treated with a surrogate replacement policy for estimating sub-threshold values. The raw merged R and G channels were lowess-normalized (grouped by print-tip), normalized between chips using quantile normalization and transformed to log2 ratios (70).
|
| |
|
| Submission date |
Oct 05, 2006 |
| Last update date |
Jul 31, 2007 |
| Contact name |
Mark J Cameron |
| E-mail(s) |
mcameron@uhnres.utoronto.ca
|
| Organization name |
UHN
|
| Street address |
3-913 TMDT, MaRS Centre, 101 College St.
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G1L7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL4387 |
| Series (1) |
| GSE5972 |
Gene expression profiling of patients with severe acute respiratory syndrome (SARS) |
|
