Comment[ArrayExpressAccession]	E-GEOD-45682
MAGE-TAB Version	1.1					
Public Release Date	2013-06-01
Investigation Title	Microarray analysis of C. rodentium infected colons					
Comment[Submitted Name]	Microarray analysis of C. rodentium infected colons
Experiment Description	Defense against attaching and effacing (A/E) bacteria requires the sequential generation of IL-23 and IL-22 to induce protective mucosal responses. While the critical source of IL-22 has been identified as CD4+ and Nkp46+ innate lymphoid cells (ILCs), the precise source of IL-23 is unclear. Here, we use genetic techniques to deplete specific classical dendritic cell (cDC) subsets and analyze immunity to the A/E pathogen Citrobacter rodentium. We find that Zbtb46+ cDCs, and specifically Notch2-dependent intestinal CD11b+ cDCs, but not Batf3-dependent CD103+ cDCs, are required for IL-23 production and immunity against C. rodentium. Notch2 controls cDC differentiation at a terminal step mediated by lymphotoxin signaling. Importantly, these results provide the first demonstration of a non-redundant function of CD11b+ cDCs in vivo. Analysis of genes differentially expressed between WT, Batf3 KO and Notch2 KO colons following C. rodentium infection. Mice were infected with 2 x 10^9 C. rodentium and colons harvested at either Day 4 or Day 9.					
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	Satpathy	Satpathy	Murphy			
Person First Name	Ansuman	Ansuman	Kenneth			
Person Email	satpathya@wusm.wustl.edu					
Person Affiliation	Washington University in St. Louis					
Person Phone	314-362-2004					
Person Address	Pathology and Immunology, Washington University in St. Louis, 660 S. Euclid Ave., Saint Louis, MO, USA					
Person Roles	submitter					
Protocol Name	P-GSE45682-1	P-GSE45682-4	P-GSE45682-5	P-GSE45682-2	P-GSE45682-3	P-GSE45682-6
Protocol Description	Data were processed using RMA Quantile Normalization with DNASTAR Arraystar software. ID_REF =  VALUE = Linear expression value	Ambion WT Expression kit, Genechip WT Terminal Labeling and Controls Kit	Hybed onto Mouse Gene 1.0 ST Arrays (Affymetrix)	Mice were analyzed following infection with 2 x 10^9 C. rodentium strain DBS100 (American Type Culture Collection).	The distal colon (2nd 1cm segment) was harvested and RNA prepared using the Qiagen Rneasy Mini Kit.	Scanner model: M10, Core software/version: AGCC ScanCom
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	TIME	GENOTYPE				
Experimental Factor Type	time	genotype				
Comment[SecondaryAccession]	GSE45682					
Comment[GEOReleaseDate]	2013-06-01					
Comment[ArrayExpressSubmissionDate]	2013-04-01					
Comment[GEOLastUpdateDate]	2013-06-02					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-45682.sdrf.txt