Comment[ArrayExpressAccession]	E-GEOD-26950						
MAGE-TAB Version	1.1						
Public Release Date	2011-04-13						
Investigation Title	Expression data from human lupus EPCs/CACs						
Comment[Submitted Name]	Expression data from human lupus EPCs/CACs						
Experiment Description	Systemic lupus erythematosus (SLE) is characterized by increased vascular risk due to premature atherosclerosis independent of traditional risk factors. We previously proposed that interferon-α plays a crucial role in premature vascular damage in SLE. IFN-α alters the balance between endothelial cell apoptosis and vascular repair mediated by endothelial progenitor cells (EPCs) and myeloid circulating angiogenic cells (CACs). Here we demonstrate that IFN-α promotes an antiangiogenic signature in SLE and control EPCs/CACs, characterized by transcriptional repression of IL-1α and β, IL-1 receptor 1 and vascular endothelial growth factor A (VEGF-A) and upregulation of IL-1 receptor antagonist (IL-1RN) and the decoy receptor IL1-R2. IL-1β promotes significant improvement in the functional capacity of lupus EPCs/CACs, therefore abrogating the deleterious effects of IFN-α. We used microarrays to analyze the effect of IFNα on peripheral blood EPCs/CACs and on bone marrow EPCs exposed to proangiogenic stimulation. Human lupus EPCs and CACs from PBMCs were isolated and cultured under proangiogenic stimulation; after IFNa incubation or not, RNA was extracted and processed for hybridization on Affymetrix microarrays.						
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	Berthier	Thacker	Berthier	Mattinzoli	Rastaldi	Kretzler	Kaplan
Person First Name	Celine	Seth	Celine	Deborah	Maria	Matthias	Mariana
Person Mid Initials	C	G	C		P		J
Person Email	geo@ncbi.nlm.nih.gov						
Person Affiliation	University of Michigan						
Person Address	University of Michigan, 1150 W. Medical Center Dr, MSRB2, Ann Arbor, MI, USA						
Person Roles	submitter						
Protocol Name	P-GSE26950-1	P-GSE26950-5	P-GSE26950-6	P-GSE26950-2	P-GSE26950-3	P-GSE26950-4	P-GSE26950-7
Protocol Description	The data were analyzed using the GenePattern pipeline: the RMA method and Human Entrez Gene custom CDF annotation version 10 was used for the normalization. Healthy EPCs, lupus EPCs and healthy bone marrow EPCs were normalized separately. ID_REF =  VALUE = Log base 2 normalized expression value	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, Affymetrix).	Standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual).	Cells were incubated in the presence or absence of IFNa for 6 hours prior to RNA harvesting.	PBMCs containing EPCs and CACs were cultured in endothelial cell-specific enrichment medium on fibronectin-coated wells.	Total RNA was isolated with Tri-pure (Roche), and further purified and concentrated using an Rneasy kit (Qiagen).	GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	TREATMENT						
Experimental Factor Type	treatment						
Publication Title	Inflammasome activation of IL-18 results in endothelial progenitor cell dysfunction in systemic lupus erythematosus.						
Publication Author List	Kahlenberg JM, Thacker SG, Berthier CC, Cohen CD, Kretzler M, Kaplan MJ						
PubMed ID	22058412						
Publication DOI	10.4049/jimmunol.1101284						
Comment[SecondaryAccession]	GSE26950						
Comment[GEOReleaseDate]	2011-04-13						
Comment[ArrayExpressSubmissionDate]	2011-01-28						
Comment[GEOLastUpdateDate]	2012-11-29						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-26950.sdrf.txt