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Sample GSM1206920 Query DataSets for GSM1206920
Status Public on Sep 01, 2015
Title CD4 T cell sample from subject # 5 at baseline.
Sample type RNA
 
Source name CD4 T cell sample from subject # 5 at baseline.
Organism Homo sapiens
Characteristics phenotype: Allergic rhinitis patient
cell type: CD4 T cell
individual: subject # 5
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 GPL17556
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 0.102796887
10_at -0.116184877
100_at 0.068918276
1000_at 0.052760823
10000_at 2.046076301
100009676_at -0.156966992
10001_at 1.444824012
10002_at -0.081998724
10003_at -0.002766718
100033413_at -0.001421287
100033414_at 1.265327255
100033416_at 0.443016757
100033418_at 1.729118466
100033420_at 0.302713618
100033422_at -0.011961658
100033423_at -0.224841805
100033424_at -0.131515802
100033425_at -0.147952507
100033426_at 0.840346066
100033427_at 0.844384666

Total number of rows: 19715

Table truncated, full table size 407 Kbytes.




Supplementary file Size Download File type/resource
GSM1206920_CD4_5a.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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