|
| Status |
Public on Sep 01, 2015 |
| Title |
CD4 T cell sample from subject # 3 after allergen challenge. |
| Sample type |
RNA |
| |
|
| Source name |
CD4 T cell sample from subject # 3 after allergen challenge.
|
| Organism |
Homo sapiens |
| Characteristics |
phenotype: Allergic rhinitis patient
cell type: CD4 T cell
individual: subject # 3
treatment: after allergen challenge
|
| Treatment protocol |
The biopsy specimens were immediately digested for 60 min at 37°C in DMEM medium containing 2 mg/ml Liberase TL. The samples were washed, filtered, stained with a panel of antibodies, and CD4 T cells and CD45+ HLA-DR+ cells were isolated by FACS sorting.
|
| Growth protocol |
A mucosal biopsy was obtained on day 0 (prior to nasal challenge) from the lower turbinate of one nostril. The other untouched nasal cavity was then challenged daily for 8 days with a solution of birch pollen extract. A mucosal biopsy was obtained on day 9 from the challenge site.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol followed by RNeasy.
|
| Label |
biotin
|
| Label protocol |
The samples were processed using the NuGEN Ovation Pico WTA with the WT-Ovation Exon Module and the Encore Biotin Module at the Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Australia).
|
| |
|
| Hybridization protocol |
CD4 T cell samples were hybridized to Human Gene 1.0 ST microarrays and CD45+ HLA-DR+ samples were hybridized to Human Gene 1.1 ST microarrays at the Ramaciotti Centre for Gene Function Analysis (University of New South Wales).
|
| Scan protocol |
The samples were scanned on an Affymetrix GeneChip® Scanner 3000 7G (CD4 T cell samples) or on an Affymetrix GeneTitan system (CD45+HLA-DR+ cells).
|
| Data processing |
The raw microarray data was preprocessed in R software using the Single Channel Array Normalization (SCAN) algorithm and a custom chip description file (CD4 T cell samples, hugene10sthsentrezgprobe, version 17; CD45+HLA-DR+ samples, hugene11sthsentrezgprobe, version 17)
|
| |
|
| Submission date |
Aug 11, 2013 |
| Last update date |
Sep 01, 2015 |
| 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 |
GPL17556 |
| Series (1) |
| GSE49782 |
Gene expression profiles of CD4 T cells and CD45+ HLA-DR+ cells during experimental allergic rhinitis in humans. |
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