Comment[ArrayExpressAccession]	E-GEOD-43456
MAGE-TAB Version	1.1													
Public Release Date	2013-09-19
Investigation Title	Cytokine-dependent dendritic cell differentiation in the splenic microenvironment													
Comment[Submitted Name]	Cytokine-dependent dendritic cell differentiation in the splenic microenvironment
Experiment Description	The dendritic cell (DC)-derived chemokine CCL17, a ligand of CCR4, has been shown to promote various inflammatory diseases such as atopic dermatitis, atherosclerosis, and inflammatory bowel disease. Under steady state conditions, and even after systemic stimulation with lipopolysaccharide, CCL17 is not expressed in resident splenic DC as opposed to CD8-CD11b+ lymph node (LN) DC, which produce large amounts of CCL17, in particular after maturation. Upon systemic NKT cell activation through alpha-galactosylceramide stimulation, however, CCL17 can be upregulated in both CD8- and CD8+ splenic DC subsets and enhances cross-presentation of exogenous antigens. Based on genome wide expression profiling, we now show that splenic DC are susceptible to Interferon-gamma (IFNgamma) mediated suppression of CCL17, whereas LN DC are much less responsive to IFNgamma and downregulate the IFNgamma receptor. Under inflammatory conditions, particularly in the absence of IFNgamma signaling in IFNgamma receptor deficient mice, CCL17 expression is strongly induced in a major proportion of splenic DC by the action of granulocyte-macrophage colony stimulating factor (GM-CSF) in concert with interleukin (IL)-4. Our findings demonstrate that the local cytokine milieu and differential cytokine responsiveness of DC subsets regulate lymphoid organ specific immune responses at the level of chemokine expression. 15 h after pretreatment with 100 µg LPS, spleens and LN (MLN and PLN) from CCL17E/+ mice were harvested and DC-enriched cell suspensions of the respective organs were stained for NK1.1, CD8alpha, CD11c and CD11b. For isolation of LN DC, NK1.1-CD8alpha-CD11c+CD11b+ cells expressing CCL17/EGFP were sorted (FACSAria). Splenic DC were sorted in parallel from the same mice, but only CCL17/EGFP-negative cells expressing the same markers were selected. After the sort, cells were immediately lysed in Trizol (Invitrogen) before storage at -80°C for RNA isolation.													
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	Schultze	Globisch	Lukacs-Kornek	Degrandi	Dresing	Alferink	Lang	Pfeffer	Beyer	Weighardt	Kurts	Ulas	Schultze	Förster
Person First Name	Joachim	T	V	D	P	J	R	K	M	H	C	T	J	I
Person Mid Initials													L	
Person Email	j.schultze@uni-bonn.de													
Person Affiliation	LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)													
Person Address	Genomics and Immunoregulation, LIMES (Life and Medical Sciences Center Genomics and Immunoregulation), Carl-Troll-Strasse 31, Bonn, NRW, Germany													
Person Roles	submitter													
Protocol Name	P-GSE43456-1	P-GSE43456-3	P-GSE43456-4	P-GSE43456-2	P-GSE43456-5									
Protocol Description	The data were normalised using quantile normalisation in Partek Genomic Suite 6.6 (v.6.12.1227) ID_REF =  VALUE = quantile normalized Detection Pval = 	Biotinylated cRNA were prepared with the TargetAmpTM Nano-gTM Biotin-aRNA Labeling Kit	Standard Illumina hybridization protocol	Total RNA from all cell samples was isolated using TRIzol Reagent (Invitrogen).	Standard Illumina scanning protocol									
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol									
Experimental Factor Name	SORTED CELLS	CELL TYPE	ORGANISM PART											
Experimental Factor Type	sorted cells	cell type	organism part											
Comment[SecondaryAccession]	GSE43456													
Comment[GEOReleaseDate]	2013-09-19													
Comment[ArrayExpressSubmissionDate]	2013-01-11													
Comment[GEOLastUpdateDate]	2013-09-21													
Comment[AEExperimentType]	transcription profiling by array													
Comment[AdditionalFile:Data1]	GSE43456_non_normalized.txt													
SDRF File	E-GEOD-43456.sdrf.txt