Comment[ArrayExpressAccession]	E-MTAB-2298
Investigation Title	Monocyte to macrophage differentiation and loading/deloading with lipoproteins (eLDL, oxLDL, HDL3)																										
Comment[Submitted Name]	Monocyte to macrophage differentiation and loading/deloading with lipoproteins (eLDL, oxLDL, HDL3)
Experiment Description	Elutriated monocytes from 9 healthy donors with ApoE3/E3 genotype were differentiated for up to six days in vitro to macrophages using rhMCSF under serum-free conditions. Samples were taken on days 1, 4, 5 and 6 and analyzed for their transcriptomic profiles. After four days of differentiation cells were loaded for 24 hours with enzymatically modified LDL (eLDL, 40 µg/ml) or mildly oxidized LDL (oxLDL, 80 µg/ml). Finally on day five, lipid deloading was performed in serum free medium containing M-CSF and cells were incubated another 24 h with HDL3 (100 µg/mL).																										
Date of Experiment	2010-07-15																										
Public Release Date	2014-03-02																										
Comment[AEExperimentType]	transcription profiling by array																										
Comment[AEExperimentDisplayName]	Transcription profiling by array of monocyte to macrophage differentiation and loading/deloading with lipoproteins (eLDL, oxLDL, HDL3)																										
Experimental Design	cell type comparison design	development or differentiation design	in vitro design																								
Experimental Design Term Source REF	EFO	EFO	EFO																								
Experimental Factor Name	individual	growth condition	time	cell type																							
Experimental Factor Type	individual	growth condition	time	cell type																							
Person Last Name	Wallner	Schmitz	Sigrüner	Orsó	Peer																						
Person First Name	Stefan	Gerd	Alexander	Evelyn	Markus																						
Person Email	stefan.wallner@klinik.uni-regensburg.de	gerd.schmitz@klinik.uni-regensburg.de	alexander.sigruener@klinik.uni-regensburg.de	evelyn.orso@klinik.uni-regensburg.de																							
Person Phone	+49-941-944 6261	+49-941-944 6201																									
Person Address	Franz-Josef-Strauss-Allee 11; 93053 Regensburg	Franz-Josef-Strauss-Allee 11; 93053 Regensburg	Franz-Josef-Strauss-Allee 11; 93053 Regensburg	Franz-Josef-Strauss-Allee 11; 93053 Regensburg																							
Person Affiliation	Institute for Clinical Chemistry and Laboratory Medicine; University Hospital Regensburg	Institute for Clinical Chemistry and Laboratory Medicine; University Hospital Regensburg	Institute for Clinical Chemistry and Laboratory Medicine; University Hospital Regensburg	Institute for Clinical Chemistry and Laboratory Medicine; University Hospital Regensburg																							
Person Roles	submitter;investigator	investigator	investigator	investigator																							
Person Roles Term Source REF	EFO	EFO	EFO	EFO																							
Publication Author List	Stefan Wallner, Margot Grandl, Tatiana Konovalova, Alexander Sigrüner, Thomas Kopf, Markus Peer, Evelyn Orsó, Gerhard Liebisch, and Gerd Schmitz																										
Publication Title	Monocyte to macrophage differentiation goes along with modulation of the plasmalogen pattern through transcriptional regulation																										
Publication Status	submitted																										
Protocol Name	P-MTAB-37607	P-MTAB-37608	P-MTAB-37609	P-MTAB-37610	P-MTAB-37611	P-MTAB-37612
Protocol Type	growth protocol	treatment protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning and feature extraction protocol																					
Protocol Description	1x10^6 cells/mL in macrophage serum-free medium (Invitrogen, Germany) supplemented with 50 ng/mL recombinant human monocyte-colony stimulating factor (M-CSF; R&D Systems, USA)	Loading with eLDL, oxLDL and deloading with HDL3. Loading: eLDL (40 ug/mL) or oxLDL (80 ug/mL);deloading: HDL3 (100 ug/mL)	RNA isolated with RNeasy Mini Kit (Qiagen) according to manufacturer's instruction	300 ng of total RNA was labeled with Cy3 using the Agilent Quick-Amp Labeling Kit - 1 color according to the manufacturer´s instructions	Hybridization with Agilent Gene Expression Hybridisation Kit, incubated in Agilent SureHyb chambers for 17 hours at 65°C while rotating. Washing according to manufacturer’s instructions.	Agilent G2565CA Microarray Scanner System with Agilent Feature Extraction software (10.7)																					
Protocol Parameters																											
Protocol Hardware						Agilent G2565CA Microarray Scanner System																					
Protocol Software						Agilent Feature Extraction software (10.7)																					
Term Source Name	EFO	ArrayExpress
Term Source File	http://www.ebi.ac.uk/efo/efo.owl	http://www.ebi.ac.uk/arrayexpress																									
Term Source Version																											
SDRF File	E-MTAB-2298.sdrf.txt