Comment[GEAAccession]	E-GEAD-331
MAGE-TAB Version	1.1
Investigation Title	Measles Virus Induces Cell-Type Specific Changes In Gene Expression
Experiment Description	Measles virus (MV) causes various responses including the induction of immune responses, transient immunosuppression and establishment of long-lasting immunity. To obtain a comprehensive view of the effects of MV infection on target cells, DNA microarray analyses of two different cell types were performed. An epithelial (293SLAM; a 293 cell line stably expressing SLAM) and lymphoid (COBL-a) cell line were inoculated with purified wild-type MV. Microarray analyses revealed significant differences in the regulation of cellular gene expression between these two different cells. In 293SLAM cells, upregulation of genes involved in the antiviral response was rapidly induced; in the later stages of infection, this was followed by regulation of many genes across a broad range of functional categories. On the other hand, in COBL-a cells, only a limited set of gene expression profiles was modulated after MV infection. Since it was reported that V protein of MV inhibited the IFN signaling pathway, we performed a microarray analysis using V knockout MV to evaluate V protein?fs effect on cellular gene expression. The V knockout MV displayed a similar profile to that of parental MV. In particular, in COBL-a cells infected with the virus, no alteration of cellular gene expression, including IFN signalling, was observed. Furthermore, IFN signaling analyzed in vitro was completely suppressed by MV infection in the COBL-a cells. These results reveal that MV induces different cellular responses in a cell-type specific manner. Microarray analyses will provide us useful information about potential mechanisms of MV pathogenesis.
Experimental Design	cell type comparison design	time series design	dye swap design
Experimental Factor Name	cell_line	treatment	time
Experimental Factor Type	cell_line	treatment	time
Person Last Name	Kai	Honma	Yoneda	Miura	Tsukiyama-Kohara	Ikeda	Seki	Watanabe	Sato
Person First Name	Chieko	Reiko	Misako	Ryuichi	Kyoko	Fusako	Takahiro	Shinya	Hiroki
Person Affiliation	Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo								
Person Roles	submitter	submitter	submitter	submitter	submitter	submitter	submitter	submitter	submitter
Public Release Date	2019-10-07
PubMed ID	18374960
Protocol Name	P-GEAD-295	P-GEAD-296	P-GEAD-297	P-GEAD-298	P-GEAD-299	P-GEAD-300	P-GEAD-301	P-GEAD-302
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning and feature extraction protocol	normalization data transformation protocol	growth protocol	treatment protocol
Protocol Description	COBL-a cells were grown in RPMI1640 medium with 100 U penicillin per ml, 100 microg streptomycin per ml, and 10% fetal calf serum (FCS), at 37degree C in a 5% CO2 incubator. Human embryonic kidney 293 cells and their derivatives were grown in Dulbecco minimal essential medium with 10% FCS, penicillin, and streptomycin at 37degree C in a 5% CO2 incubator.	The medium was removed and 10 ml ISOGEN (NIPPON GENE) was immediately pipetted into a 10-cm dish. To prepare total RNA, lysates were further processed according to the manufacturer's instructions. Poly (A)+ RNA was prepared by using the MicroPoly(A) Purist kit (Ambion, Carlsbad, CA, USA).	Poly (A)+ RNA (2 microgram) was labeled with SuperScript II (Invitrogen) and Cyanine 3-dUTP (PerkinElmer, MA, USA). Labeling, hybridization, and subsequent washes of microarrays were performed with a Labeling & Hybridization Kit (MicroDiagnostic), in accordance with the manufacturer's instructions. Poly (A)+ RNA (2 microgram) was labeled with SuperScript II (Invitrogen) and Cyanine 5-dUTP (PerkinElmer, MA, USA). Labeling, hybridization, and subsequent washes of microarrays were performed with a Labeling & Hybridization Kit (MicroDiagnostic), in accordance with the manufacturer's instructions.	A pair of the Cyanine 5- and Cyanine 3-labeled samples was hybridized onto a single microarray. Hybridization and subsequent washes of microarrays were performed with a Labeling & Hybridization Kit (MicroDiagnostic), in accordance with the manufacturer's instructions.	Hybridization signals were measured with a GenePix 4000A scanner (Axon Instruments, CA, USA) and then processed into primary expression ratios ([Cyanine 5-intensity obtained from each target or control sample]/[Cyanine 3-intensity obtained from each control or target sample], which are indicated as 'median of ratios' in GenePix Pro 3.0 software (Axon Instruments)).	All pairs of target and control samples were labeled and hybridized to microarrays twice along with color flip of Cyanine 5 and Cyanine 3. Normalization was performed for the median of ratios (primary expression ratios) by multiplying normalization factors calculated for each feature on a microarray by the GenePix Pro 3.0 software (designated normalized ratios). Data processing and subsequent hierarchical clustering analysis were performed with an Excel program (Microsoft, WA, USA) and an MDI gene expression analysis software package (MicroDiagnostic). The primary expression ratios were converted into log2 values (log2 Cyanine 5- intensity/Cyanine 3- intensity)(designated log ratios). After conversion of the normalized ratios into log2 values, log ratios derived from pairs of Cyanine 3-labeled target and Cyanine 5-labeled control samples were converted into reciprocals. Eventually, log ratios derived from pairs of Cyanine 5-labeled target and Cyanine 3-labeled control samples and the reciprocal log ratios derived from pairs of Cyanine 3-labeled target and Cyanine 5-labeled control samples were subjected to calculation of mean averages for individual genes (designated mean log ratios).	COBL-a cells were grown in RPMI1640 medium with 100 U penicillin per ml, 100 microg streptomycin per ml, and 10% fetal calf serum (FCS), at 37degree C in a 5% CO2 incubator. Human embryonic kidney 293 cells and their derivatives were grown in Dulbecco minimal essential medium with 10% FCS, penicillin, and streptomycin at 37degree C in a 5% CO2 incubator.	COBL-a cells and 293SLAM cells (3 x 107) were infected with MV-HL or V knockout MV at an MOI of 2. After 1 h of adsorption at 37degree C, the inocula were replaced with warm spent medium. Alternatively, both cells were treated with 1,000 IU/ml of human universal type I IFN (PBL Biomedical Laboratories).
SDRF File	E-GEAD-331.sdrf.txt
Comment[Number of channel]	dual-channel
Comment[Array Design REF]	A-GEAD-9
Comment[AEExperimentType]	transcription profiling by array
Comment[SecondaryAccession]	CBX32
Comment[BioProject]	PRJDB8854
Comment[CIBEX Accept Date]	2010-01-01
Comment[CIBEX Public Release Date]	2009-06-19
Comment[Last Update Date]	2019-10-09