Comment[ArrayExpressAccession]	E-GEOD-51686
MAGE-TAB Version	1.1									
Public Release Date	2013-10-25
Investigation Title	Fracture healing in osteoporotic mice									
Comment[Submitted Name]	Fracture healing in osteoporotic mice
Experiment Description	Genome-wide comparative gene expression analysis of callus tissue of osteoporotic mice (Col1a1-Krm2 and Lrp5-/-) and wild-type were performed to identify candidate genes that might be responsible for the impaired fracture healing observed in Col1a1-Krm2 and Lrp5-/- mice. To investigate bone healing in osteoporosis, we performed fracture healing studies in wild-type mice (C57BL/6 genetic background) and the low bone mass strains Col1a1-Krm2 and Lrp5-/- (Schulze et al., 2010; Kato et al., 2002). Osteotomy was set in femora of female mice and stabilized by a semi-rigid fixator to allow fast bone healing (RM-CM-6ntgen et al., 2010). 21 days post surgery we analyzed the fracture calli by biochemical/histological methods, as well as micro-computed tomography, and observed impaired fracture healing in Col1a1-Krm2 and Lrp5-/- mice in comparison to wild-type. To identify genes that may be responsible for the impaired healing in osteoporotic mice, we performed microarray analysis of three independent callus samples of each genotype. The callus tissue was taken 10 days after surgery, because extensive bone formation took place at this point.									
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	Ebert	Benisch	Ignatius	RM-CM-6ntgen	Liedert	Amling	Schinke	Jakob	Ebert	Klein-Hitpass
Person First Name	Regina	P	A	V	A	M	T	F	R	L
Person Email	r-ebert.klh@uni-wuerzburg.de									
Person Affiliation	University of Wuerzburg									
Person Address	Orthopedic Center for Musculoskeletal Research, University of Wuerzburg, Brettreichstrasse 11, Wuerzburg, Germany									
Person Roles	submitter									
Protocol Name	P-GSE51686-1	P-GSE51686-4	P-GSE51686-5	P-GSE51686-2	P-GSE51686-3	P-GSE51686-6				
Protocol Description	Global scaling was performed by Affymetrix Gene Chip Operating Software 1.4 using the MAS5 algorithm. ID_REF =  VALUE = MAS5 signal ABS_CALL = 	RNA was amplified and labeled according to the GeneChip 3M-bM-^@M-^YIVT Express Kit (Affymetrix, High Wycombe, United Kingdom).	Following fragmentation, 10 M-5g of cRNA were hybridized on Affymetrix Gene Chip MG 430 2.0 at 45M-0C for 16 h. Subsequently, GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit.	We generated Col1a1-Krm2 transgenic mice as previously described (Schulze et al., 2010), which express Krm2 under control of an osteoblast-specific Col1a1 promoter fragment. The Col1a1-Krm2 mice developed a severe osteoporosis due to disturbed bone formation and increased bone resorption. Lrp5 deficient mice (Lrp5-/-) were kindly provided by G. Karsenti (Columbio University, New York, USA). Deletion of Lrp5 resulted in low bone mass due to decreased bone formation, whereas bone resorption was unaffected (Kato et al., 2002). Osteotomy was set in femora of 26 weeks old female mice of each genotype and was stabilized by a semi-rigid fixator according to the previously described protocol (RM-CM-6ntgen et al., 2010). Animals were sacrificed 10 days after surgery.	Whole femur was dissected and immediately shock frozen in liquid nitrogen. Fracture callus was cut from frozen bone and crushed with manual pastel in 400 M-5l QIAzol Lysis Reagent (QIAgen GmbH, Hilden, Germany). For further homogenization we used a knife-rotor homogenizator (T 10 basic ULTRA-TURRAXM-., IKAM-.-Werke GmbH & Co. KG, Staufen, Germany). Total RNA was isolated with RNeasy Lipid Tissue Mini Kit (QIAgen) according to manufactureM-bM-^@M-^Ys instructions, including DNase digestion.	Hybridization signals were detected with Affymetrix GeneChip Scanner 3000.				
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol				
Experimental Factor Name	PHENOTYPE	GENOTYPE								
Experimental Factor Type	phenotype	genotype								
Comment[SecondaryAccession]	GSE51686									
Comment[GEOReleaseDate]	2013-10-25									
Comment[ArrayExpressSubmissionDate]	2013-10-24									
Comment[GEOLastUpdateDate]	2013-10-27									
Comment[AEExperimentType]	transcription profiling by array									
SDRF File	E-GEOD-51686.sdrf.txt