Comment[ArrayExpressAccession]	E-GEOD-30101
MAGE-TAB Version	1.1								
Public Release Date	2013-04-19
Investigation Title	Genome-wide profiling of whole blood from healthy adult volunteers before and after receiving non-live vaccines including seasonal influenza or pneumococcal vaccine or placebo (saline) injections.								
Comment[Submitted Name]	Genome-wide profiling of whole blood from healthy adult volunteers before and after receiving non-live vaccines including seasonal influenza or pneumococcal vaccine or placebo (saline) injections.
Experiment Description	The objective of this study is to: 1) Characterize the immune responsiveness to administration of non-live vaccines in three cohorts of healthy adult subjects through the analysis of blood leukocytes transcriptional profiles. 2) Validate whole blood transcriptional profiles generated from standard 3mL blood draws versus 200uL blood draws obtained by finger stick. 3) Discover potential biomarkers for immune-responsiveness to non-live vaccines. A total of 621 blood samples were collected either by venipuncture (387) or finger prick (234) from four groups of healthy adults receiving either, 2009/10 seasonal influenza or 23-valent pneumococcal vaccine or placebo (saline) injections. Subjects were recruited in 3 cohorts with 4-7 individuals per group; cohort 3 was recruited for validation of the systemic day 1 immune signature in response to seasonal influenza and pneumococcal vaccination.  From each subject, peripheral blood was drawn into Tempus tubes (Applied Biosystems) or obtained by finger prick into micro capillaries and then transferred into tempus reagent to lyse blood cells and stabilize RNA before storing at -80ºC until mRNA extraction.  The training set for transcriptional profiling of blood obtained by venipuncture was performed in cohort 1 which included 6 healthy adult individuals receiving seasonal influenza vaccine, 6 healthy adult individuals receiving pneumococcal vaccine, and 6 healthy adult individuals receiving placebo (saline injections). The test set for transcriptional profiling of blood obtained by venipuncture was performed in cohort 2 which included 6 healthy adult individuals receiving seasonal influenza vaccine, 6 healthy adult individuals receiving pneumococcal vaccine, and 6 healthy adult individuals receiving placebo (saline injections). The validation set for confirming systemic day 1 transcriptome immune signature in response to seasonal influenza and pneumococcal vaccination was performed in cohort 3 which included 6 healthy adult individuals receiving seasonal influenza vaccine and 4 healthy adult individuals receiving pneumococcal vaccine.  The training set for transcriptional profiling of blood obtained by finger prick was performed in cohort 2 and the test set in cohort 1.								
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl							
Person Last Name	Chaussabel								
Person First Name	Damien								
Person Email	DChaussabel@benaroyaresearch.org								
Person Affiliation	Baylor Institute for Immunology Research								
Person Address	Baylor Institute for Immunology Research, 3434 Live Oak, Dallas, TX, USA								
Person Roles	submitter								
Protocol Name	P-GSE30101-1	P-GSE30101-3	P-GSE30101-4	P-GSE30101-2	P-GSE30101-5				
Protocol Description	Following background subtraction, the raw signal intensities extracted with Illumina Genome Studio v2010.1 Gene Expression 1.6.0 software were scaled to the mean intensity of the dataset. ID_REF =  VALUE = background subtracted, mean intensity-scaled signal	Biotinylated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion	Hybridization to HumanHT-12 v3 Expression BeadChip as per Illumina protocol	RNA was isolated using the MagMAX™-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer's instructions	Illumina BeadStation 500 SentrixScanVersion 2.3.0.13				
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol				
Experimental Factor Name	AGE	ETHNICITY	SEX	SUBJECT ID	SAMPLE SET	VACCINE	DAY	RACE	BLOOD SOURCE
Experimental Factor Type	age	ethnicity	sex	subject id	sample set	vaccine	day	race	blood source
Publication Title	Systems scale interactive exploration reveals quantitative and qualitative differences in response to influenza and pneumococcal vaccines.								
Publication Author List	Obermoser G, Presnell S, Domico K, Xu H, Wang Y, Anguiano E, Thompson-Snipes L, Ranganathan R, Zeitner B, Bjork A, Anderson D, Speake C, Ruchaud E, Skinner J, Alsina L, Sharma M, Dutartre H, Cepika A, Israelsson E, Nguyen P, Nguyen QA, Harrod AC, Zurawski SM, Pascual V, Ueno H, Nepom GT, Quinn C, Blankenship D, Palucka K, Banchereau J, Chaussabel D								
PubMed ID	23601689								
Publication DOI	10.1016/j.immuni.2012.12.008								
Comment[SecondaryAccession]	GSE30101								
Comment[GEOReleaseDate]	2013-04-19								
Comment[ArrayExpressSubmissionDate]	2011-06-20								
Comment[GEOLastUpdateDate]	2013-04-23								
Comment[AEExperimentType]	transcription profiling by array								
SDRF File	E-GEOD-30101.sdrf.txt