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Sample GSM1147953 Query DataSets for GSM1147953
Status Public on Apr 10, 2014
Title PBMC_256_day7
Sample type RNA
 
Source name Individual 256 at day7
Organism Homo sapiens
Characteristics mn_mfc_class: 1
mn_adjmfc_class: 2
individual id: 256
tissue: peripheral blood mononuclear cells (PBMC)
gender: female
age: 21
ethnicty: African American
sample collection time: 7 days post vaccination (day7)
mn_a_ca_07_swine: 40
mn_a_brisbane_59_2007: 20480
mn_a_uruguay_716_2007: 2560
mn_b_brisbane_60_2001: 160
elispot_effector_total_igg: 8133.5
elispot_effector_h1n1_igg: 1335
elispot_effector_seasonal_igg: 6348.5
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 256_day7
Gene expression data from PBMC extracted from individual 256 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

Data table header descriptions
ID_REF
VALUE log2 RMA

Data table
ID_REF VALUE
7892501 5.63929
7892502 6.20722
7892503 3.61503
7892504 8.62139
7892505 3.97854
7892506 7.16006
7892507 5.95407
7892508 7.89192
7892509 9.9993
7892510 5.47272
7892511 4.4518
7892512 7.75348
7892513 5.87929
7892514 9.8913
7892515 9.67684
7892516 3.56829
7892517 7.02263
7892518 4.84665
7892519 5.7341
7892520 9.51499

Total number of rows: 33297

Table truncated, full table size 518 Kbytes.




Supplementary file Size Download File type/resource
GSM1147953_256_day7.CEL.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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