|
| Status |
Public on Jun 20, 2011 |
| Title |
WB_flare_PFAPA_Patient3 |
| Sample type |
RNA |
| |
|
| Source name |
whole blood, flare, PFAPA, Patient3
|
| Organism |
Homo sapiens |
| Characteristics |
patient identifier: Patient3
gender: male
age: 4.9 years
disease: PFAPA
disease state: flare
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from whole peripheral blood collected in PAXgene tubes (Qiagen) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA was prepared from 20 ng total RNA using the Ovation Whole Blood Solution (NuGen).
|
| |
|
| Hybridization protocol |
cDNA was hybridized for 18 hours at 45C on Affymetrix GeneChip Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
Gene Chips were scanned using an Affymetrix GeneChip Scanner 3000.
|
| Description |
PFAPA patient3 during flare
|
| Data processing |
Raw intensity data were converted to .CEL and Metrics files, respectively, using Affymetrix GeneChip Operating Software (GCOS v1.4). To control for chip-to-chip variation, gene expression values were generated using the RMA algorithm as implemented in Microarray Data Management and Analysis System (MDMAS), a proprietary software from NIAMS, Bethesda, USA. Only transcripts identified as present by MAS 5.0 in at least 4 of the 6 samples of each group were analyzed to filter for reliable intensity measurements from each individual chip.
|
| |
|
| Submission date |
Aug 20, 2009 |
| Last update date |
Jun 20, 2011 |
| Contact name |
Silvia Stojanov |
| E-mail(s) |
[email protected]
|
| Organization name |
NIH/NIAMS
|
| Street address |
10 Center Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (1) |
| GSE17732 |
Whole blood gene expression data from PFAPA syndrome |
|
