|
| Status |
Public on Jul 02, 2014 |
| Title |
Peripheral blood sample from anaphylaxis patient # 2 at timepoint 0 |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral blood sample from anaphylaxis patient # 2 at timepoint 0
|
| Organism |
Homo sapiens |
| Characteristics |
phenotype: Anaphylaxis patient
timepoint: at arrival
|
| Treatment protocol |
Blood samples were colected and stabilized in PAXgene tubes. The PAXgene tubes were placed immediately at 4°C then transferred to -20°C within 72 hours, before final storage at -80°C.
|
| Growth protocol |
Patients presented to the Emergency Department (ED) at Royal Perth Hospital with acute, moderately severe anaphylaxis. Samples were collected at ED arrival (T0), 1 hour later (T1), and 3 hours post arrival (T2).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the PAXgene Blood RNA Extraction Kits (PreAnalytiX GmbH, Switzerland) by automation with the Qiacube instrument (Qiagen, Australia).
|
| Label |
biotin
|
| Label protocol |
250ng of total RNA was amplified (Ambion WT kit), labeled with biotin (Affymetrix terminal labelling kit) and fragmented according to manufacturer’s instructions. This was performed by the Ramaciotti Centre for Gene Function Analysis (University of New South Wales).
|
| |
|
| Hybridization protocol |
5.5 μg of fragmented, biotin labeled ssDNA was hybridized to each Human Gene 1.0ST microarras according to manufacturer’s instructions. This was performed by the Ramaciotti Centre for Gene Function Analysis (University of New South Wales).
|
| Scan protocol |
The samples were scanned on a GeneChip® Scanner 3000 7G (Affymetrix).
|
| Data processing |
The microarray data was preprocessed in R employing the qFarms algorithm (laplacian prior). A custom CDF file was used (hugene10sthsentrezg, version 16). The data was filtered using the Informative/non-informative (I/NI) calls algorithm.
|
| |
|
| Submission date |
Jun 05, 2013 |
| Last update date |
Jul 03, 2014 |
| Contact name |
Anthony Bosco |
| E-mail(s) |
Anthony.Bosco@telethonkids.org.au
|
| Organization name |
Telethon Kids Institute
|
| Street address |
100 Roberts Road
|
| City |
Subiaco |
| State/province |
WA |
| ZIP/Postal code |
6008 |
| Country |
Australia |
| |
|
| Platform ID |
GPL17244 |
| Series (1) |
| GSE47655 |
Genomic responses in blood during acute human anaphylaxis |
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