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Sample GSM1882163 Query DataSets for GSM1882163
Status Public on Jun 22, 2016
Title H1N1 DEE3 Subject 22, Hour 5
Sample type RNA
 
Source name peripheral blood of H1N1 DEE3 subject 22, hour 5
Organism Homo sapiens
Characteristics tissue: peripheral blood
virus: H1N1
time point: hour 5
subject: H1N1 DEE3 subject 22
Treatment protocol 148 human volunteer subjects under 4 different inoculation regimes (HRV, RSV, H1N1, H3N2). During each challenge study, subjects had peripheral blood taken prior to inoculation with virus (baseline), immediately prior to inoculation (pre-challenge) and at set intervals following challenge.
Extracted molecule total RNA
Extraction protocol RNA was extracted at Expression Analysis (Durham, NC) from whole blood using the PAXgene™ 96 Blood RNA Kit (PreAnalytiX, Valencia, CA) employing the manufacturer's recommended protocol. While whole blood RNA is initially extracted, a secondary procedure (B-globin reduction) was then employed to remove the contribution of red blood cell (RBC) RNA to the total RNA. A set of four peptide nucleic acid (PNA) oligomers whose sequences are complementary to the 3' portions of the alpha and beta hemoglobin RNA transcripts were added to reduce globin RNA transcription due to RBC. The inhibition of globin cDNA synthesis dramatically reduces the relative amount of anti-sense, biotin-labeled cRNA corresponding to the hemoglobin transcripts.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, cRNA were hybridized on GeneChip Human Genome U133A 2.0 Array.
Scan protocol GeneChips were scanned using the Affymetrix GeneArray Scanner.
Description H1N1_DEE3_SAMPLE_420
Gene expression profile from peripheral blood of H1N1 DEE3 subject 22, hour 5.
Data processing The data were analyzed with robust multi-array average (RMA) normalization using default background adjustment and quantile normalization settings. Then possible batch effect was removed by the parametric and nonparametric empirical Bayes frameworks.
Affymetrix GeneChip Human Genome U133A 2.0 Array [CDF: Brainarray Version 10, Hs133Av2_Hs_ENTREZG].
 
Submission date Sep 15, 2015
Last update date Jun 22, 2016
Contact name Alfred Hero
E-mail(s) hero@eecs.umich.edu
Organization name University of Michigan
Street address 1301 Beal Avenue
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platform ID GPL14604
Series (1)
GSE73072 Host gene expression signatures of H1N1, H3N2, HRV, RSV virus infection in adults

Data table header descriptions
ID_REF
VALUE RMA signal intensity after parametric and nonparametric empirical Bayes frameworks (ComBat) applied.

Data table
ID_REF VALUE
10_at 4.0828
100_at 8.6652
1000_at 4.4413
10000_at 4.4313
10001_at 7.8588
10002_at 4.635
10003_at 3.5232
10004_at 6.2667
10005_at 8.2151
10006_at 8.8914
10007_at 8.2702
10009_at 3.1932
1001_at 5.254
10010_at 7.9904
10013_at 7.6809
10014_at 8.5869
10015_at 10.637
10016_at 9.1053
10017_at 4.9772
10018_at 4.5514

Total number of rows: 12023

Table truncated, full table size 180 Kbytes.




Supplementary file Size Download File type/resource
GSM1882163_2011_93255_H133A2_23157_DU09-06S06729.CEL.gz 1.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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