Comment[ArrayExpressAccession]	E-MTAB-2164
MAGE-TAB Version	1.1																							
Investigation Title	Eum2																							
Comment[Submitted Name]	Eum2
Experiment Description	The low immunogenicity of many cancer cells and the immunosuppression by various cancers and anti-cancer therapies have been an obstacle in the development of efficacious immunotherapies. Our goal was to test if TLR agonists and anti-cancer chemotherapeutic agents synergize in rendering tumor cells more immunogenic.																							
Experimental Design	compound treatment design	in_vitro_design	co-expression_design																					
Comment[AEExperimentType]	transcription profiling by array																							
Comment[AEExperimentDisplayName]	Transcription profiling by array of mouse pre-B cells treated with Ara-C, Pam3CSK4, or a combination of both to test whether the compounds synergize in rendering tumor cells more immunogenic																							
Experimental Factor Name	compound																							
Experimental Factor Type	compound																							
Quality Control Type	Biological replicate																							
Quality Control Term Source REF	EFO																							
Public Release Date	2014-03-01																							
Person Last Name	Gasser																							
Person First Name	Stephan																							
Person Mid Initials																								
Person Email	micsg@nus.edu.sg																							
Person Phone	6565167209																							
Person Address	28 Medical Drive, Singapore, 117495, Singapore																							
Person Affiliation	National University of Singapore																							
Person Roles	submitter																							
Protocol Name	P-MTAB-37287	P-MTAB-37288	P-MTAB-37289	P-MTAB-37290	P-MTAB-37291	P-MTAB-37292	P-MTAB-37293
Protocol Type	Growth	treatment protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning protocol	normalization data transformation protocol																	
Protocol Description	EuM2 cells were maintained in RPMI 1640 medium containing 20 mM HEPES buffer, 10% heat-inactivated fetal bovine serum (Gibco/Invitrogen), 50 uM 2-mercaptoethanol, 200 uM asparagine, and 100 U/mL penicillin-streptomycin.	EuM2 or BC2 cells (1.6 x 105/ml) were treated with 0.1% DMSO or 1 uM Ara-C (Sigma) for 16 hrs. For the combination treatment, the cells were treated with 1 ug/ml Pam3CSK4 (Invivogen) or endotoxin-free water used for dissolving Pam3CSK4 for 16 hrs followed by 1 uM Ara-C or DMSO for 16 hrs. 	Total RNA of treated EuM2 cells was extracted using RNeasy kit (Qiagen) according to the manufacturer's instructions. The quality of total RNA was evaluated using Agilent Bioanalyzer (Agilent Technologies, USA); only samples with RNA integrity number >7.5 were analyzed. RNA of four different treatments were hybridized to two microarrays each.          	Labeling was conducted as per the manufacturer's instructions (Illumina).          	EuM2_Ara-C_Pam3CSK4.txt	Scanning were conducted as per the manufacturer's instructions (Illumina).          	Expression levels were extracted with Affymetrix GeneChip Command Console (AGCC). Arrays were normalized to DMSO samples using the robust multi-array average method and filtered to remove non-informative probes. 																	
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO	EFO																	
Term Source Name	EFO	ArrayExpress
Term Source File	http://www.ebi.ac.uk/efo	http://www.ebi.ac.uk/arrayexpress																						
SDRF File	E-MTAB-2164.sdrf.txt