Comment[ArrayExpressAccession]	E-GEOD-43133						
MAGE-TAB Version	1.1						
Public Release Date	2013-07-10						
Investigation Title	CD47 Inhibits Self-renewal and Reprogramming by Regulating c-Myc and Other Stem Cell Transcription Factors						
Comment[Submitted Name]	CD47 Inhibits Self-renewal and Reprogramming by Regulating c-Myc and Other Stem Cell Transcription Factors						
Experiment Description	Signaling through the thrombospondin-1 receptor CD47 broadly limits cell and tissue survival of stress, but the molecular mechanisms are incompletely understood. We now show that loss of CD47 permits sustained proliferation of primary murine endothelial cells and enables these cells to spontaneously reprogram to form multipotent embryoid bodies.  c-Myc, Klf4, Oct4, and Sox2 expression is elevated in CD47-null endothelial cells, in several tissues of CD47- or thrombospondin-1-null mice, and in a human T cell line lacking CD47. CD47 knockdown acutely increases mRNA levels of c-Myc and other stem cell transcription factors in cells and in vivo, whereas CD47 ligation by thrombospondin-1 suppresses c-Myc expression. The inhibitory effects of increasing CD47 levels can be overcome by maintaining c-Myc expression and are absent in cells with dysregulated c-Myc. Thus, CD47 antagonists enable cell self-renewal and reprogramming by overcoming negative regulation of c-Myc and other stem cell transcription factors. To identify gene expression changes associated with CD47 null cells, we compared the gene expression profile of these cells with WT endothelial cell, CD47 null Embryoid bodies cells and an established Embryonic Stem cell line.						
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	elkahloun	Kaur	Elkahloun	Roberts			
Person First Name	abdel	Sukhbir	Abdel	David			
Person Mid Initials			G	D			
Person Email	abdel@mail.nih.gov						
Person Affiliation	nih						
Person Address	nih, 50 south dr, bethesda, MD, USA						
Person Roles	submitter						
Protocol Name	P-GSE43133-1	P-GSE43133-5	P-GSE43133-6	P-GSE43133-2	P-GSE43133-3	P-GSE43133-4	P-GSE43133-7
Protocol Description	Gene expression intensities were calculated using GeneChip Command Console Software (AGCC version 3.2.4). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software (version 1.2.1) to generate an RMA normalized, log2 transformed and gene summarized matrix table. ID_REF =  VALUE = RMA	Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human HuGene-1_0-st-v1 GeneChips (Affymetrix, Inc). Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. 300 ng of total RNA was used for labeling with theAmbion WT Expression Kit (Cat#4411974) and Affymetrix kit (Cat # 900652). After hybridization, the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).	The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Mouse GeneChip 1.0 ST microarrays. The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.	CD47 null mouse lung endothelial cells passaged for 6 months were seeded into 6-well tissue culture plates using basal Endothelial Basal Medium (Lonza) without serum. Embryoid bodies appeared after 24-36 h.	WT and CD47 null Mouse lung endothelial cells were cultured at 37 degreeC with 5% CO2 using Endothelial Growth Medium-2 (EGM2) (Lonza).V6.5 mES cells were cultured in DMEM medium containing 15% fetal bovine serum and 1000 IU/ml LIF (Leukemia Inhibitory Factor.	total RNA was extracted by TRIzol (Invitrogen) method.	An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.
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	cell line	cell type	genotype				
Experimental Factor Type	cell line	cell type	genotype				
Comment[SecondaryAccession]	GSE43133						
Comment[GEOReleaseDate]	2013-07-10						
Comment[ArrayExpressSubmissionDate]	2012-12-24						
Comment[GEOLastUpdateDate]	2013-07-11						
Comment[AEExperimentType]	transcription profiling by array						
Pubmed ID	23591719						
Publication DOI	10.1038/srep01673						
Publication Title	Thrombospondin-1 signaling through CD47 inhibits self-renewal by regulating c-Myc and other stem cell transcription factors						
Publication Author List	Kaur S, Soto-Pantoja DR, Stein EV, Liu C, Elkahloun AG, Pendrak ML, Nicolae A, Singh SP, Nie Z, Levens D, Isenberg JS, Roberts DD						
SDRF File	E-GEOD-43133.sdrf.txt