Comment[ArrayExpressAccession]	E-GEOD-49663
MAGE-TAB Version	1.1					
Public Release Date	2013-08-09
Investigation Title	Gene expression in the blood of Live Attenuated Rev-Independent Nef¯SIV  infected Rhesus macaques during acute infection					
Comment[Submitted Name]	Gene expression in the blood of Live Attenuated Rev-Independent Nef¯SIV  infected Rhesus macaques during acute infection
Experiment Description	Rhesus macaques (RMs) inoculated with live-attenuated Rev-Independent Nef¯ simian immunodeficiency virus (Rev-Ind Nef¯SIV) as adults or neonates controlled viremia to undetectable levels and showed no signs of immunodeficiency over 6-8 years of follow-up.  We tested the capacity of this live-attenuated virus to protect RMs against pathogenic, heterologous SIVsmE660 challenges Blood PBMC Time after SIV infection: 2 weeks post SIV infection Infection:Rev-Ind Nef¯SIV					
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	Byrareddy	Byrareddy	Ruprecht			
Person First Name	Siddappa	Siddappa	Ruth			
Person Email	geo@ncbi.nlm.nih.gov					
Person Affiliation	Emory Univeristy					
Person Address	Pathology & Laboratory Medicine, Emory Univeristy, 101 Woodruff circle, Atlanta, USA					
Person Roles	submitter					
Protocol Name	P-GSE49663-1	P-GSE49663-4	P-GSE49663-5	P-GSE49663-2	P-GSE49663-3	P-GSE49663-6
Protocol Description	The data from gene chips was processed with GeneChip Operating Software (GCOS) 1.4 CEL files were processed and normalized using the robust multiarray average (RMA) algorithm. To identify genes correlating with the phenotypic groups, the data were fitted to a linear model using the limma package and tested for differential gene expression Genes with statistically significant differences between the naive vs. Rev-Ind Nef¯SIV infected were determined using a false-discovery-rate cutoff of <5% and a log fold-change cutoff of >1.  Expression values of significant probe sets were loaded into the MultiExperiment Viewer (MeV) and analyzed using average-linkage hierarchical clustering with a Pearson correlation coefficient distance metric. Affymetrix CEL files were processed and normalized using the robust multiarray average (RMA) algorithm.  Principal component analysis (PCA) was performed on the normalized expression values to identify phenotypically similar groups by visualizing the top three principal components. To identify genes correlating with the phenotypic groups, the data were fitted to a linear model using the limma package and tested for differential gene expression. ID_REF =  VALUE = RMA normalized signal intensity	Biotinylated complementary RNAs (cRNAs) were synthesized in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix by in vitro transcription (IVT) reaction.	Hybridization and post-hybridization processing were performed following the Affymetrix GeneChip Expression Analysis standard protocols (Affymetrix inc.)	Rhesus macaques were infected intravenously with Rev-Ind Nef¯SIV. The naïve rhesus PBMC were obtained from same animals before infection	RNA was extracted with Rneasy mini kit (Qiagen)	The gene chips were scanned on Affymetrix scanner 3000
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	INFECTION STATUS					
Experimental Factor Type	infection status					
Comment[SecondaryAccession]	GSE49663					
Comment[GEOReleaseDate]	2013-08-09					
Comment[ArrayExpressSubmissionDate]	2013-08-08					
Comment[GEOLastUpdateDate]	2013-08-11					
Comment[AEExperimentType]	transcription profiling by array					
Comment[AdditionalFile:Data1]	GSE49663_fold_change.txt					
SDRF File	E-GEOD-49663.sdrf.txt