Comment[ArrayExpressAccession]	E-GEOD-50855
MAGE-TAB Version	1.1									
Public Release Date	2014-05-22
Investigation Title	Gene Expression Analysis of Host Immune Responses in CD11b positive cells isolated from lungs of the UV inactivated SARS-CoV-immunized mice following Lethal SARS-CoV Infection									
Comment[Submitted Name]	Gene Expression Analysis of Host Immune Responses in CD11b positive cells isolated from lungs of the UV inactivated SARS-CoV-immunized mice following Lethal SARS-CoV Infection
Experiment Description	To better understand the biological pathways by which UV inactivated SARS-CoV-induced pulmonary eosinophilia occurs, we examined global transcriptional changes in macrophages from the lungs of mouse. Female BALB/c mice were used at 21 weeks of age.  Mice were subcutaneously immunized with UV inactivated SARS-CoV (UV-V) or UV-V and Toll like receptor (TLR) ligands at 6 and 1 weeks prior to mouse-adapted SARS-CoV (n=6 per group).   Mice were intranasally challenged with 1E+6 TCID50 in 30M-NM-<L.  MEM was challenged in six mice as control infection.  Mice were sacrificed and collected lungs at 1 days after challenge, then CD11b positive cells were isolated from the lungs of these mice. These cells were used for the analysis of microarray.									
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	Iwata-Yoshikawa	Iwata-Yoshikawa	Uda	Sato	Tsunetsugu-Yokota	Morikawa	Tashiro	Sata	Hasegawa	Nagata
Person First Name	Naoko	N	A	Y	Y	S	M	T	H	N
Person Email	inok@nih.go.jp									
Person Affiliation	National institute of infectious diseases									
Person Address	Pathology, National institute of infectious diseases, 1-23-1 Toyama, Shinnjuku-ku, Tokyo, Japan									
Person Roles	submitter									
Protocol Name	P-GSE50855-1	P-GSE50855-4	P-GSE50855-5	P-GSE50855-2	P-GSE50855-3	P-GSE50855-6				
Protocol Description	The image files were analyzed by using of Feature Extraction software (Agilent) and automatically exported with flag information. GeneSpring GX 12.1(Agilent) was used for data analysis. The raw data were normalized per chip to the 75th percentile expression level and per gene to the median expression intensity of all samples. ID_REF =  VALUE = Normalized signal intensity	Twenty five nanogram of total RNA and spike-in control was amplified and labeled using Low RNA Input Linear Amplification Kit (Agilent). RNA was denatured and reverse transcribed to cDNA. cDNA was transcribed from 25 ng of total RNA using a poly-T nucleotide primer containing a T7 RNA polymerase promoter. cRNA was subsequently synthesized and labeled with cyanine-3 (Cy3) by T7 RNA polymerase.	After the purification of labeled cRNA, 1.65 mg labeled samples were fragmented by the incubation with Fragmentation Buffer (Agilent) at 60M-0C for 30 min. These samples were hybridized onto the Whole Mouse Genome Microarray 60k probes M-CM-^W 8 arrays/ slide (Agilent) at 65M-0C for 16 h in a rotating hyb oven at a speed of 10 rounds per min (RPM). Microarrays slides were washed in the order of Wash Solution 1 (Agilent), Wash Solution 2 (Agilent) and acetonitrile (Wako).	CD11b positive cells were isolated from mouse lungs treated with lysis buffer of RNeasy mini kit (Qiagen) were stored at -80M-0C until use.	Total RNA was purified from the samples using RNeasy mini kit (Qiagen) according to the manufacturerM-bM-^@M-^Ys protocol. The concentrations and qualities of total RNA were measured by Spectrophotometer ND-100 (Nanodrop Technologies) and Agilent 2100 bioanalyzer (Agilent), respectively.	Microarrays slides were scanned at 5 micrometer resolution on a microarray scanner (Agilent) with excitation of the fluorophores Cy3.				
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol				
Publication Title	Effects of Toll-like Receptor Stimulation on Eosinophilic Infiltration in Lungs of BALB/c Mice Immunized with UV-inactivated Severe Acute Respiratory Syndrome-related Coronavirus Vaccine.									
Publication Author List	Iwata-Yoshikawa N, Uda A, Suzuki T, Tsunetsugu-Yokota Y, Sato Y, Morikawa S, Tashiro M, Sata T, Hasegawa H, Nagata N									
PubMed ID	24850731									
Publication DOI	10.1128/JVI.00983-14									
Comment[SecondaryAccession]	GSE50855									
Comment[GEOReleaseDate]	2014-05-22									
Comment[ArrayExpressSubmissionDate]	2013-09-13									
Comment[GEOLastUpdateDate]	2014-05-23									
Comment[AEExperimentType]	transcription profiling by array									
SDRF File	E-GEOD-50855.sdrf.txt