Comment[ArrayExpressAccession]	E-GEOD-51414
MAGE-TAB Version	1.1					
Public Release Date	2013-12-03
Investigation Title	Expression data from oxaliplatin-treated tumors from mice pre-treated or not with antibiotics cocktail					
Comment[Submitted Name]	Expression data from oxaliplatin-treated tumors from mice pre-treated or not with antibiotics cocktail
Experiment Description	The gut microbiota influences both local and systemic inflammation. Inflammation contributes to development, progression and treatment of cancer, but it remains unclear whether commensal bacteria affect inflammation in the sterile tumor microenvironment. Here we show that disruption of the microbiota impairs the response of subcutaneous tumors to CpG-oligonucleotide immunotherapy and platinum chemotherapy. In antibiotic-treated or germ-free mice, tumor-infiltrating myeloid-derived cells responded poorly to therapy, resulting in lower cytokine production and tumor necrosis after CpG-oligonucleotide treatment, and deficient production of reactive oxygen species and cytotoxicity following chemotherapy.  Thus, optimal responses to cancer therapy require an intact commensal microbiota that mediates its effects by modulating myeloid-derived cell functions in the tumor microenvironment. These findings underscore the importance of the microbiota in the outcome of disease treatment. Oxaliplatin treatment induces expression of pro-inflammatory genes, which are inhibited by antibiotic pretreatment. Our goal was to ascertain the effect of antibiotic on the tumor gene expression profile prior to treatment and early on after the treatment with chemotherapy (oxaliplatin). The time points were selected t					
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	Dzutsev	Dzutsev	Trinchieri			
Person First Name	Amiran	Amiran	Giorgio			
Person Email	dzutsev@pop.nci.nih.gov					
Person Affiliation	NCI, NIH					
Person Address	CIP, NCI, NIH, 1050 Boyles Str, Frederick, MD, USA					
Person Roles	submitter					
Protocol Name	P-GSE51414-1	P-GSE51414-4	P-GSE51414-5	P-GSE51414-2	P-GSE51414-3	P-GSE51414-6
Protocol Description	The data was analyzed with Partek Genomics Suite 6.6 ID_REF =  VALUE = Signal intensity (Log2 of RMA processed data)	300ng of total RNA was amplified into complement-strand RNA (cRNA) using WT expression kit according to the Invitrogen protocol. Sense DNA was converted via RT reaction and labeled with biotin using Affymetrix labeling kits	cRNA was hybridized overnight in a hybridization oven on to MouseGene 1.0 ST array according to manual factory protocol. Posthybridization arrays were stained with florescence on a Genechip Fluidics Station 450 (Affymetrix) according to the respective manufacturers' instructions.	Mice that were either pre-treated for 3 weeks with antibiotics cocktail or left untreated were injected in the flank subcutaneously with 5 x10^5 EL4 cells. Seven days after the tumor inoculation the mice were treated with intraperitoneal oxaliplatin injection (10 mg per kg body weight). Tumors were collected after 0, 6 and 18 hours post-oxaliplatin injection.	Total RNA was extracted using RNAeasy kit (QIAGEN) according to the manufacturer's instructions.	Arrays were then scanned on a GeneChip Scanner 3000 7G (Affymetrix).
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	TIME POST-OXALIPLATIN	ABX TREATMENT				
Experimental Factor Type	time post-oxaliplatin	abx treatment				
Publication Title	Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment.					
Publication Author List	Iida N, Dzutsev A, Stewart CA, Smith L, Bouladoux N, Weingarten RA, Molina DA, Salcedo R, Back T, Cramer S, Dai RM, Kiu H, Cardone M, Naik S, Patri AK, Wang E, Marincola FM, Frank KM, Belkaid Y, Trinchieri G, Goldszmid RS					
PubMed ID	24264989					
Publication DOI	10.1126/science.1240527					
Comment[SecondaryAccession]	GSE51414					
Comment[GEOReleaseDate]	2013-12-03					
Comment[ArrayExpressSubmissionDate]	2013-10-18					
Comment[GEOLastUpdateDate]	2013-12-04					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-51414.sdrf.txt