Investigation Title	Transcription profiling of mouse pooled embryonic humeri E14.5 from wild type and RUNX2-/- mutants detects novel skeletogenesis target genes	
Comment[Submitted Name]	Expression data from mouse E14.5 wt and RUNX2 -/- humeri	
Experimental Design	individual_genetic_characteristics_design	co-expression_design	transcription profiling by array	
Experimental Design Term Source REF		mo	EFO	
Comment[ArrayExpressReleaseDate]	2007-11-23	
Comment[SecondaryAccession]	GSE4911	
Comment[AEMIAMESCORE]	5	
Comment[SecondaryAccession]	GDS2186	
Comment[SecondaryAccession]	GDS2185	
Comment[SecondaryAccession]	GDS2184	
Comment[ArrayExpressAccession]	E-GEOD-4911	
Comment[MAGETAB TimeStamp_Version]	2011-01-22 20:33:41 Last Changed Rev: 14857	
Experimental Factor Name	Genotype	
Experimental Factor Type	genotype	
Experimental Factor Term Source REF	
Person Last Name	Hecht	
Person First Name	Jochen	
Person Mid Initials	
Person Email	hecht@molgen.mpg.de	
Person Phone	
Person Fax	
Person Address	Mundlos, Max Planck Institute for Molecular Genetics, Ihnestr. 73, Berlin, 14195, Germany	
Person Affiliation	Max Planck Institute for Molecular Genetics	
Person Roles	submitter	
Person Roles Term Source REF		
Quality Control Type	
Quality Control Term Source REF	
Replicate Type	
Replicate Term Source REF	
Normalization Type	
Normalization Term Source REF	
Date of Experiment	
Public Release Date	2007-11-23	
PubMed ID	16829211	
Publication DOI	16829211	
Publication Author List	J Hecht, V Seitz, M Urban, F Wagner, P N Robinson, A Stiege, C Dieterich, U Kornak, U Wilkening, N Brieske, C Zwingman, A Kidess, S Stricker, S Mundlos	
Publication Title	Detection of novel skeletogenesis target genes by comprehensive analysis of a Runx2(-/-) mouse model.	
Publication Status	journal_article	
Publication Status Term Source REF	The MGED Ontology	
Experiment Description	We used microarrays to identify genes differentially expressed between mouse RUNX2 -/- and wt embryonic humeri at stage E14.5 Experiment Overall Design: To minimize the effects of random biological variation, humeri from different preparations were pooled (approximately 75 wildtype and 60 Runx2-/- for each of the two biological replicates).	
Protocol Name	P-G4911-1	P-G4911-2	P-G4911-3	Affymetrix:Protocol:Hybridization-EukGE-WS2v4	Affymetrix:Protocol:Hybridization-EukGE-WS2v4_450	P-AFFY-6	
Protocol Type	specified_biomaterial_action	nucleic_acid_extraction	labeling	hybridization	hybridization	feature_extraction	
Protocol Description	humeri were disected in RNAlater (Qiagen) and stored in liquid nitrogen until RNA isolation. To minimize the effects of random biological variation, humeri from different preparations were pooled (approximately 75 wildtype and 60 Runx2-/- for each of the two biological replicates).	peqGOLD TriFast (peqLab) extraction of total RNA was performed according to the manufacturer's instructions followed by Qiagen RNeasy column purification including an on column Dnase digestion according to manufacturers instructions	10 Âμg of total RNA were first reverse transcribed into cDNA (cDNA Synthesis System, Roche). The cDNA was used for in vitro transcription (T7 Megascript Kit, Ambion) and labeling with Biotin-11-CTP and Biotin-16-UTP (Perkin-Elmer, Boston, USA)	Title: Fluidics Station Protocol. Description: 	Title: Affymetrix EukGE-WS2v4_450 Hybridization. Description: 	Title: Affymetrix CEL analysis. Description: 	
Protocol Parameters	
Protocol Hardware	
Protocol Software				MicroArraySuite 5.0		MicroArraySuite 5.0	
Protocol Contact	
Protocol Term Source REF					mo	
SDRF File	E-GEOD-4911.sdrf.txt	
Term Source Name	EFO		The MGED Ontology	NCI_thesaurus	ncbitax	ArrayExpress	mo	EFO	The MGED Ontology	
Term Source File	http://www.ebi.ac.uk/efo/		http://mged.sourceforge.net/ontologies/MGEDontology.php	ncithesaurus.obo.alt	http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html	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	
Term Source Version