NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1147912 Query DataSets for GSM1147912
Status Public on Apr 10, 2014
Title PBMC_245_day-7
Sample type RNA
 
Source name Individual 245 at day-7
Organism Homo sapiens
Characteristics mn_mfc_class: 1
mn_adjmfc_class: 2
individual id: 245
tissue: peripheral blood mononuclear cells (PBMC)
gender: female
age: 45
ethnicty: White
sample collection time: 7 days prior to vaccination (day-7)
mn_a_ca_07_swine: NA
mn_a_brisbane_59_2007: NA
mn_a_uruguay_716_2007: NA
mn_b_brisbane_60_2001: NA
elispot_effector_total_igg: NA
elispot_effector_h1n1_igg: NA
elispot_effector_seasonal_igg: NA
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 245_day-7
Gene expression data from PBMC extracted from individual 245 7 days prior to 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

Data table header descriptions
ID_REF
VALUE log2 RMA

Data table
ID_REF VALUE
7892501 7.63224
7892502 6.53157
7892503 5.79067
7892504 9.0848
7892505 4.04876
7892506 7.56961
7892507 5.66523
7892508 7.90127
7892509 10.49287
7892510 4.9666
7892511 4.53542
7892512 7.41463
7892513 6.61506
7892514 10.57512
7892515 9.69621
7892516 4.56995
7892517 6.99429
7892518 3.87785
7892519 5.9582
7892520 9.25259

Total number of rows: 33297

Table truncated, full table size 519 Kbytes.




Supplementary file Size Download File type/resource
GSM1147912_245_day-7.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap