|
| Status |
Public on Jun 22, 2016 |
| Title |
H1N1 DEE3 Subject 2, Hour 60 |
| Sample type |
RNA |
| |
|
| Source name |
peripheral blood of H1N1 DEE3 subject 2, hour 60
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood
virus: H1N1
time point: hour 60
subject: H1N1 DEE3 subject 2
|
| 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_30
Gene expression profile from peripheral blood of H1N1 DEE3 subject 2, hour 60.
|
| 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 |
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