Comment[ArrayExpressAccession]	E-GEOD-51526
MAGE-TAB Version	1.1					
Public Release Date	2014-04-02
Investigation Title	IM015 - Influenza infection of C57BL6 and RIPK3 knock-out mice					
Comment[Submitted Name]	IM015 - Influenza infection of C57BL6 and RIPK3 knock-out mice
Experiment Description	This purpose of this experiment was to investigate the transcriptional differences between C57BL6, RIPK3 knock-out mice infected with influenza strain A/CA/04/2009 (H1N1) virus. Overview of Experiment: Groups of 6-8 week-old C57BL6 and RIPK3 knock-out mice were infected with influenza A/CA/04/2009 virus. Infections were done at 10^5 PFU or time-matched mock infected. Time points were 2 and 4 d.p.i.  There were 2-3 animals/dose/time point. Lung samples were collected for virus load and transcriptional analysis. Weight loss and animal survival were also monitored.					
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	Katze	Katze	Kawaoka	Law	Eisfeld	Chang
Person First Name	Michael	Michael	Yoshiro	Lynn	Amie	Jean
Person Email	data@viromics.washington.edu					
Person Affiliation	University of Washington					
Person Address	Microbiology, University of Washington, Rosen Building 960 Republican St., Seattle, WA, USA					
Person Roles	submitter					
Protocol Name	P-GSE51526-1	P-GSE51526-4	P-GSE51526-5	P-GSE51526-2	P-GSE51526-3	P-GSE51526-6
Protocol Description	Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages. ID_REF =  VALUE = Normalized log2 expression values for probes passing Agilent QC flags	The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.	The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K mouse array.	Lung tissue from each animal were harvested and briefly rinsed in cold (4M-:C) PBS. Following the RNALater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNALater. After a 4M-:C incubation overnight, samples were stored at -80M-:C until processing. Lung tissue was removed from RNALater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) Trizol and stored at -80M-0C until RNA isolation.	All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturerM-bM-^@M-^Ys recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.	Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	MOUSE STRAIN	INFECTION				
Experimental Factor Type	mouse strain	infection				
Comment[SecondaryAccession]	GSE51526					
Comment[GEOReleaseDate]	2014-04-02					
Comment[ArrayExpressSubmissionDate]	2013-10-22					
Comment[GEOLastUpdateDate]	2014-04-02					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-51526.sdrf.txt