Comment[ArrayExpressAccession]	E-GEOD-46087
MAGE-TAB Version	1.1					
Public Release Date	2013-04-17
Investigation Title	Differential microRNA expression profiles of mouse lungs infected with 2009 pandemic H1N1 influenza virus and seasonal H1N1 virus					
Comment[Submitted Name]	Differential microRNA expression profiles of mouse lungs infected with 2009 pandemic H1N1 influenza virus and seasonal H1N1 virus
Experiment Description	To further understand the molecular pathogenesis of the 2009 pandemic H1N1 influenza virus infection, we profiled cellular miRNAs of lung tissue from BALB/c mice infected with influenza virus BJ501 and a mouse-adapted influenza virus A/Puerto Rico/8/34 (H1N1)(PR8) as a comparison. Five groups of mice were selected, and three of each group were used to profile the miRNA, two were in case for unqualified RNA extraction. Whole lungs from mice infected by BJ501 or PR8  were harvested on 2,5 days post infection (dpi), and compared with lung samples from 5 uninfected mice.					
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	Li	Wu	Zhang	Li	Zhang	Song
Person First Name	Peng	Zhihao	Chuanfu	Peng	Xiaoai	Hongbin
Person Email	jiekenlee@gmail.com					
Person Affiliation	Institute of Disease Control and Prevention					
Person Address	Department of Infectious Disease Control, Institute of Disease Control and Prevention, Dongda street 20# Fengtai District, Beijing, China					
Person Roles	submitter					
Protocol Name	P-GSE46087-1	P-GSE46087-4	P-GSE46087-5	P-GSE46087-2	P-GSE46087-3	P-GSE46087-6
Protocol Description	The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.The extracted data were then normalized with Agilent GeneSpring 12.0 by three main steps. First,a filtering step is done wherein both flag (gIsGeneDetected column) and error (gTotalProbeError column) is taken into account. Only those rows are used that have a flag value of 1. For each miRNA, if all flags are 0 then the signal value is taken as 0.1. Or GeneSpring uses only those rows for summarization which have value of 1. Then if the signal value passes the filter(greater than 3 times the error value), it is used and assigned with a value of 0 for error. Second,the multiple probes that map to a given systematic name are first summed up. The signal value is computed as the SUM of all values and not average. Summarization is based on the systematic name as explained above and is done before thresholding of signal values. Last,the data was then normalizes to 90th percentile with Percnetile Shift algorithms. ID_REF =  VALUE = Normalized signal intensity	Cyanine-3 (Cy3) labeled RNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by Qiagen RNAeasy Mini Kit(QIAGEN 217004, Valencia, CA). Dye incorporation and RNA yield were checked with the NanoDrop ND-1000 Spectrophotometer (Thermo).	Cy3-labelled RNA was dried on the medium-high heat setting with a vacuum concentrator according to the manufacture's protocol. On completion of sample dryness, 22.5 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized for 20 hours at 55M-0C in a rotating Agilent hybridization oven at 20 rpm. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37M-0C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.	Specific pathogen-free 6- to 8-week-old male BALB/c mice were intranasally inoculated with 10^4 TCID50 (25 M-5l) of BJ501 or PR8 virus respectively. In addition, a normal control group were set up and given i.n. phosphate buffered saline (PBS)	Whole mouse lung tissues were homogenized in QIAzol lysis regant (Qigen). Total RNA was extracted from mouse lung using miRvana miRNA isolation kit (Ambion) according to the manufacturerM-bM-^@M-^Ys protocol. The concentration of RNA was determined by a Nanodrop ND-1000 Spectrophotometer (Thermo)	Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	TIME	INFECTED WITH				
Experimental Factor Type	time	infected with				
Comment[SecondaryAccession]	GSE46087					
Comment[GEOReleaseDate]	2013-04-17					
Comment[ArrayExpressSubmissionDate]	2013-04-16					
Comment[GEOLastUpdateDate]	2013-04-18					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-46087.sdrf.txt