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Sample GSM1206928 Query DataSets for GSM1206928
Status Public on Sep 01, 2015
Title CD45+ HLA-DR+ sample from subject # 3 at baseline.
Sample type RNA
 
Source name CD45+ HLA-DR+ sample from subject # 3 at baseline.
Organism Homo sapiens
Characteristics phenotype: Allergic rhinitis patient
cell type: CD45+ HLA-DR+
individual: subject # 3
treatment: baseline
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 GPL17555
Series (1)
GSE49782 Gene expression profiles of CD4 T cells and CD45+ HLA-DR+ cells during experimental allergic rhinitis in humans.

Data table header descriptions
ID_REF
VALUE Gene expression values were calculated by the Single Channel Array Normalization (SCAN) algorithm.

Data table
ID_REF VALUE
1_at 0.30475788
10_at -0.122003281
100_at 0.525911067
1000_at -0.018350661
10000_at 1.038587429
100009676_at 0.047429286
10001_at 1.27925551
10002_at -0.128281938
10003_at -0.122052284
100033413_at 0.229187622
100033414_at 2.782357456
100033416_at 0.516740864
100033418_at 2.805683253
100033420_at 1.779355472
100033422_at -0.071969155
100033423_at -0.017760143
100033424_at -0.051733449
100033425_at -0.172230192
100033426_at -0.078301115
100033427_at 0.466870784

Total number of rows: 19715

Table truncated, full table size 407 Kbytes.




Supplementary file Size Download File type/resource
GSM1206928_HLA_DR_3a.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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