Comment[ArrayExpressAccession]	E-GEOD-40012
Public Release Date	2012-08-14					
Investigation Title	Blood transcriptome of human bacterial and influenza A pneumonia					
Comment[Submitted Name]	Blood transcriptome of human bacterial and influenza A pneumonia
Experiment Description	Introduction: Diagnosis of severe influenza pneumonia remains challenging because of the lack of correlation between presence of influenza virus and patient’s clinical status. We conducted gene expression profiling in the whole blood of critically ill patients to identify a gene signature that would allow clinicians to distinguish influenza infection from other causes of severe respiratory failure (e.g. bacterial pneumonia, non-infective systemic inflammatory response syndrome).   Methods: Whole blood samples were collected from critically ill individuals and assayed on Illumina HT-12 gene expression beadarrays. Differentially expressed genes were determined by linear mixed model analysis and over-represented biological pathways determined using GeneGo MetaCore.   Results: The gene expression profile of H1N1 influenza A pneumonia was distinctly different from bacterial pneumonia and systemic inflammatory response syndrome. The influenza gene expression profile is characterized by up-regulation of genes from cell cycle regulation, apoptosis and DNA-damage response pathways. In contrast, no distinctive gene-expression signature was found in patients with bacterial pneumonia or systemic inflammatory response syndrome. The gene expression profile of influenza infection persisted through five days of follow-up. Furthermore, in patients with primary H1N1 influenza A infection who subsequently developed bacterial co-infection, the influenza gene-expression signature remained unaltered, despite the presence of a super-imposed bacterial infection.   Conclusions: The whole blood expression profiling data indicates that the host response to influenza pneumonia is distinctly different from that caused by bacterial pathogens. This information may speed up identification of the cause of infection in patients presenting with severe respiratory failure, allowing appropriate patient care to be undertaken more rapidly. Daily PAXgene samples for up to 5 days for; influenza A pneumonia patients (n=8),  bacterial pneumonia patients (n=16), mixed bacterial and influenza A pneumonia patients (n=3), systemic inflammatory response patients (SIRS, n=13). Days 1 and 5 PAXgene samples for healthy control individuals					
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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	Parnell	Parnell	Tang			
Person First Name	Grant	Grant	Benjamin			
Person Mid Initials		P	M			
Person Email	gpar3109@uni.sydney.edu.au					
Person Affiliation	University of Sydney					
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Person Address	Nepean Clinical School, University of Sydney, Nepean Hospital, Kingswood, NSW, Australia					
Person Roles	submitter					
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Protocol Name	P-GSE40012-1	P-GSE40012-5	P-GSE40012-4	P-GSE40012-2	P-GSE40012-3	P-GSE40012-6
Protocol Description	ID_REF = <br>VALUE = GenomeStudio quantile normalised average signal intensity<br>Detection Pval = 	Scanned using default parameters on Illumina BeadArray Reader	Hyb protocol as per Illumina Whole-Genome Gene Expression Direct Hybridization Experienced User Guide	RNA extracted using PAXgene blood RNA kit v2 (PreAnalytixs)	cRNA prepared using Ambion Illumina TotalPrep RNA Amplification Kit	Data were processed in GenomeStudio. Quantile normalisation was applied without background adjustment
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Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	nucleic_acid_extraction	labeling	feature_extraction
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Comment[SecondaryAccession]	GSE40012					
Comment[AdditionalFile:Data1]	GSE40012_non-normalized.txt					
Comment[GEOLastUpdateDate]	2012-08-15
Comment[AEExperimentType]	transcription profiling by array					
Comment[GEOReleaseDate]	2012-08-13
Comment[ArrayExpressSubmissionDate]	2012-08-08
SDRF File	E-GEOD-40012.sdrf.txt