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Sample GSM1881971 Query DataSets for GSM1881971
Status Public on Jun 22, 2016
Title H1N1 DEE3 Subject 12, Hour 45
Sample type RNA
 
Source name peripheral blood of H1N1 DEE3 subject 12, hour 45
Organism Homo sapiens
Characteristics tissue: peripheral blood
virus: H1N1
time point: hour 45
subject: H1N1 DEE3 subject 12
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_228
Gene expression profile from peripheral blood of H1N1 DEE3 subject 12, hour 45.
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 4.159
100_at 7.5614
1000_at 4.6727
10000_at 4.4213
10001_at 7.776
10002_at 4.8462
10003_at 3.5904
10004_at 5.1957
10005_at 7.8789
10006_at 9.9671
10007_at 7.6632
10009_at 3.4726
1001_at 5.4638
10010_at 10.735
10013_at 7.7757
10014_at 7.5211
10015_at 9.6338
10016_at 9.0949
10017_at 5.0694
10018_at 5.1095

Total number of rows: 12023

Table truncated, full table size 180 Kbytes.




Supplementary file Size Download File type/resource
GSM1881971_2011_93143_H133A2_23002_DU09-06S13353.CEL.gz 1.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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