Investigation Title	Maturation of myeloid dendritic cells through cognate interaction with invariant NKT cells	
Comment[Submitted Name]	Maturation of myeloid dendritic cells through cognate interaction with invariant NKT cells	
Experimental Design	co-expression_design	in_vitro_design	stimulated_design_type	transcription profiling by array	
Experimental Design Term Source REF	The MGED Ontology			EFO	
Comment[SecondaryAccession]		
Comment[ArrayExpressReleaseDate]	2010-10-08	
Comment[AEMIAMESCORE]	4	
Comment[ArrayExpressAccession]	E-MEXP-2938	
Comment[MAGETAB TimeStamp_Version]	2010-10-14 19:27:33 Last Changed Rev: 14677	
Experimental Factor Name	CELL_TYPE	
Experimental Factor Type	cell_type	
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Person Last Name	Falcone	
Person First Name	Marika	
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Public Release Date	2010-10-08	
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Experiment Description	Aim of the experiment was to characterize the gene activation profile<br><br>induced within immature myeloid DCs by cell-cell contact with activated<br><br>invariant NKT cells under steady-state conditions.	
Protocol Name	P-MTAB-17316	P-MTAB-17315	P-MTAB-17317	P-MTAB-17314	P-AFFY-2	Affymetrix:Protocol:Hybridization-Midi_Euk2v3	P-AFFY-6	
Protocol Type	nucleic_acid_extraction	grow	specified_biomaterial_action	pool	labeling	hybridization	feature_extraction	
Protocol Description	Total RNA was extracted from CD11c+ DCs with TRIzol reagent, cleaned by<br><br>Qiagen RNeasy® clean-up procedure and linearly amplified according to the Affymetrix GeneChip® Expression Analysis Technical Manual using the one cycle target labelling kit.<br>(Parameters: Extracted product = genomic_DNA, Amplification = RNA polymerases)	Bone marrow cells were cultured in complete RPMI plus 5% FBS supplemented with 10 ng/ml of recombinant murine GM-CSF and rmFlt3L. After 6 days the non-adherent cell fraction was removed and the adherent fraction containing > 90% CD11c+ was co-cultured with iNKT cells (DC: NKT cell ratio= 1:2) or left untreated (immature DCs).<br>(Parameters: time unit = seconds, temperature unit = C)	After 4 hours of iNKT-DC co-culture, the non-adherent cells were removed and the adherent cell fraction was collected with 30¹ incubation with PBS containing 0.05% EDTA at 4°C. Cells were washed with cold PBS, stained with bead-conjugated anti-CD11c mAb and passed throughout a magnetic column.	Immature or NKT-matured DCs from triplicate wells were pooled for RNA<br><br>extraction. The experiment was repeated three times and biological<br><br>triplicates of immature and NKT-cell matured DCs were analyzed by<br><br>microarrays.				
Protocol Parameters	
Protocol Hardware	
Protocol Software						MicroArraySuite 5.0	MicroArraySuite 5.0	
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Protocol Term Source REF	The MGED Ontology	The MGED Ontology	The MGED Ontology	The MGED Ontology		mo	
SDRF File	E-MEXP-2938.sdrf.txt	
Term Source Name	EFO		The MGED Ontology	ArrayExpress	The MGED Ontology	EFO	mo	
Term Source File	http://www.ebi.ac.uk/efo/		http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php	
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