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Status |
Public on Sep 01, 2015 |
Title |
CD4 T cell sample from subject # 5 at baseline. |
Sample type |
RNA |
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Source name |
CD4 T cell sample from subject # 5 at baseline.
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Organism |
Homo sapiens |
Characteristics |
phenotype: Allergic rhinitis patient cell type: CD4 T cell individual: subject # 5 treatment: baseline
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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.
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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.
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted with TRIzol followed by RNeasy.
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Label |
biotin
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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).
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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).
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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).
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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)
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Submission date |
Aug 11, 2013 |
Last update date |
Sep 01, 2015 |
Contact name |
Anthony Bosco |
E-mail(s) |
Anthony.Bosco@telethonkids.org.au
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Organization name |
Telethon Kids Institute
|
Street address |
100 Roberts Road
|
City |
Subiaco |
State/province |
WA |
ZIP/Postal code |
6008 |
Country |
Australia |
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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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