|
| Status |
Public on Apr 10, 2014 |
| Title |
PBMC_260_day7 |
| Sample type |
RNA |
| |
|
| Source name |
Individual 260 at day7
|
| Organism |
Homo sapiens |
| Characteristics |
mn_mfc_class: 1
mn_adjmfc_class: 1
individual id: 260
tissue: peripheral blood mononuclear cells (PBMC)
gender: female
age: 51
ethnicty: Asain
sample collection time: 7 days post vaccination (day7)
mn_a_ca_07_swine: 2560
mn_a_brisbane_59_2007: 160
mn_a_uruguay_716_2007: 2560
mn_b_brisbane_60_2001: 320
elispot_effector_total_igg: 1500
elispot_effector_h1n1_igg: 1595
elispot_effector_seasonal_igg: 225
elispot_memory_total_igg: NA
elispot_memory_h1n1_igg: NA
elispot_memory_seasonal_igg: NA
|
| Treatment protocol |
Individuals were vaccinated with the 2009 Fluvirin seasonal influenza (Novartis), and H1N1 pandemic (Sanofi-Aventis) vaccines, both without adjuvant.
|
| Growth protocol |
Blood specimens were collected in heparinized syringes and peripheral blood mononuclear cells (PBMC) were isolated using Leucosep tubes with Ficoll-Paque Plus density gradient media and centrifugation. Fresh isolated PBMC were directly lysed in 700ul of Qiazol and stored at -80C till isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 1e7 freshly isolated PBMC using miRNeasy kit (Qiagen) according to the manufacturer’s instructions and eluted in 40ul of elution buffer with the addition of 1ul of RNase inhibitor (Invitrogen).
|
| Label |
biotin
|
| Label protocol |
Fragmented single-stranded sense cDNA were terminally labeled with biotin according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Labeled cDNA were hybridized to Human 1.0 ST GeneChip arrays (Affymetrix) and stained on a Genechip Fluidics Station 450 (Affymetrix), according to the respective manufacturers' instructions.
|
| Scan protocol |
Arrays were scanned on a GeneChip Scanner 3000 7G (Affymetrix).
|
| Description |
260_day7
Gene expression data from PBMC extracted from individual 260 7 days post vaccination
MN_MFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC). For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
MN_adjMFC_class: low (0), middle (1) and high (2) responders based on day 70 microneutralization titer change as Maximum Fold Change (MFC) adjusted for day 0 titer. For details, see "Titer Definitions" section in Extended Experimental Procedures (Supplemental) in the publication.
|
| Data processing |
The raw intensities of gene probesets in the CEL files were processed using Affymetrix Power Tools. The apt-probeset_summarize script was used for background correction and normalization (RMA with sketch, quantile normalization). The Bioconductor package arrayQualityMetrics was used to assess the quality of the microarray data.
|
| |
|
| Submission date |
May 24, 2013 |
| Last update date |
May 22, 2014 |
| Contact name |
Yuri Kotliarov |
| E-mail(s) |
kotliary@mail.nih.gov
|
| Organization name |
NHLBI
|
| Department |
CHI
|
| Street address |
4 Memorial Dr., room 134
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE47353 |
Global Analyses of Human Immune Variation Reveal Baseline Predictors of Postvaccination Responses |
|
