Comment[ArrayExpressAccession]	E-GEOD-35460
Public Release Date	2012-07-09								
Investigation Title	Gene expression profiling data from sooty mangabeys treated with interferon alpha								
Comment[Submitted Name]	Gene expression profiling data from sooty mangabeys treated with interferon alpha
Experiment Description	In contrast to pathogenic HIV and SIV infection of humans and macaques, SIV infection of sooty mangabeys (SMs) is typically non-pathogenic despite high virus replication. A key feature of primary SIV infection of SMs is a strong type I interferon (IFN-I) response, characterized by massive up-regulation of interferon-stimulated genes (ISG), followed by rapid resolution during the acute-to-chronic phase transition and establishment of an immune quiescent state that persists throughout the chronic infection. Based on these observations we hypothesized that low levels of IFN-I signaling may be instrumental in preventing chronic immune activation and disease progression in SIV-infected SMs. We used microarrays to characterize gene expression changes induced by IFNalpha treatment. To directly assess the effects of an experimentally-induced augmentation of IFN-I signaling in chronically SIV-infected SMs, we administered recombinant rhesus macaque IFNalpha2-IgFc (rmIFNα2) to eight naturally SIV-infected SMs weekly for 16 weeks and longitudinally monitored viral load, lymphocyte counts, immune activation, SIV-specific CD8+ T-cell responses, and gene expression profile. Administration of rmIFNα2 was bioactive in vivo with gene expression profiling revealing a strong upregulation of numerous ISGs in the blood of treated animals.								
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Term Source Name	EFO
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Term Source File	http://www.ebi.ac.uk/efo/efo.owl								
Person Last Name	Tharp	Vanderford	Silvestri	Bosinger	Villinger	Schlicter	Lawson	Rend	Tharp
Person First Name	Gregory	Thomas	Guido	Steven	Francois	Chloe	Benton	Obaede	Greg
Person Mid Initials	K	H		E			O		K
Person Email	gktharp@emory.edu								
Person Affiliation	Yerkes National Primate Research Center								
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Person Address	Developmental and Cognitive Neuroscience, Yerkes National Primate Research Center, 954 Gatewood Dr, Atlanta, GA, USA								
Person Roles	submitter								
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Protocol Name	P-GSE35460-1	P-GSE35460-6	P-GSE35460-3	P-GSE35460-8	P-GSE35460-7	P-GSE35460-2	P-GSE35460-4	P-GSE35460-5	
Protocol Description	ID_REF = <br>VALUE = Log2 scale of signal intensity after RMA normalization and summarization.	Following fragmentation, 20 micrograms of cRNA were diluted into 300 microlitres of hybridization cocktail, with 200 microlitres hybridized for 16 hr at 45 C on GeneChip Rhesus Macaque Genome Array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.	N/A	Data from .CEL files were uploaded to the RACE Bioconductor utility to perform RMA normalization. RACE normalized files were uploaded and analyzed using Partek Genomics Suite.	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.	SIV+ Sooty mangabey monkeys were injected with 500,000 units subcutaneously with recombinant rhesus macaque IFNalpha2-IGFC fusion protein every week for 16 weeks.	Whole blood was drawn into PAXgene tubes and stored at -80, samples were purified using standard Paxgene purification with QIAshredder columns and on-column DNAse digestion.	0.5 micrograms of total RNA was labeled using a modified version of the Affymetrix IVT Express protocol, incorporating blocking PNA oligos specific for rhesus & mangabey hemoglobin into the initial reverse transcription step, as reported in Taaffe et al. 2009 J Med Primatol and Bosinger et al. J Clin Invest 2009.	
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Protocol Type	bioassay_data_transformation	hybridization	grow	feature_extraction	image_aquisition	specified_biomaterial_action	nucleic_acid_extraction	labeling	
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Experimental Factor Name	TREATMENT	SUBJECT	TIME						
Experimental Factor Type	treatment	subject	time						
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Publication Title	Treatment of SIV-infected sooty mangabeys with a type-I IFN agonist results in decreased virus replication without inducing hyperimmune activation.								
Publication Author List	Vanderford TH, Slichter C, Rogers KA, Lawson BO, Obaede R, Else J, Villinger F, Bosinger SE, Silvestri G								
PubMed ID	22550346								
Publication DOI	10.1182/blood-2012-02-411496								
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Comment[SecondaryAccession]	GSE35460								
Comment[GEOLastUpdateDate]	2012-07-09
Comment[AEExperimentType]	transcription profiling by array								
Comment[GEOReleaseDate]	2012-07-08
Comment[ArrayExpressSubmissionDate]	2012-01-31
SDRF File	E-GEOD-35460.sdrf.txt