Comment[ArrayExpressAccession]	E-GEOD-50549
MAGE-TAB Version	1.1							
Public Release Date	2013-09-04
Investigation Title	Histone Deacetylase Inhibition Promotes Osteoblast Maturation by Altering the Histone 4 (H4) Epigenome (BeadChip)							
Comment[Submitted Name]	Histone Deacetylase Inhibition Promotes Osteoblast Maturation by Altering the Histone 4 (H4) Epigenome (BeadChip)
Experiment Description	Suberoylanilidehydroxamic acid (SAHA) significantly increased the expression levels of 127 transcripts and suppressed expression of 130 genes by more than 2-fold within 3 standard deviations of the mean in differentiating MC3T3 sc4 osteoblasts  Total RNA was obtained from differentiating MC3T3 sc4 cells treated with SAHA or vehicle (DMSO).							
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	Westendorf	Dudakovic	Evans	Li	Middha	McGee-Lawrence	van Wijnen	Westendorf
Person First Name	Jennifer	Amel	Jared	Ying	Sumit	Meghan	Andre	Jennifer
Person Mid Initials			M			E	J	J
Person Email	geo@ncbi.nlm.nih.gov							
Person Affiliation	Mayo Clinic							
Person Address	Mayo Clinic, 200 1st St SW, Rochester, USA							
Person Roles	submitter							
Protocol Name	P-GSE50549-1	P-GSE50549-5	P-GSE50549-6	P-GSE50549-2	P-GSE50549-3	P-GSE50549-4	P-GSE50549-7	
Protocol Description	The data were normalized with the fastlo R package ID_REF =  VALUE = fastlo normalized Detection Pval = 	The quality of total RNA samples was assessed by using the Agilent Bioanalyzer 2100 (Santa Clara, CA). Labeling of high quality samples was performed according to manufacturerM-bM-^@M-^Ys instructions for the Illumina Total Prep RNA Amplification Kit (Life Technologies, Grand Island, NY). Briefly, 200 ng of total RNA was reverse transcribed with T7 Oligo d(T) to create second strand cDNA. Subsequently, the products were column purified and then in vitro transcribed to generate biotin-labeled cRNA.	cRNA products were column purified and hybridized onto Illumina Mouse Whole Genome 6 Beadchips for 16 hours at 58M-: C.	MC3T3 sc4 cells were plated in 10cm plates in maintenance medium. At confluence, maintenance medium was replaced with osteogenic medium (M-NM-1-Minimal Essential Medium supplemented with 10% FBS, 100 U/ml penicillin, and 100 M-5g/ml streptomycin, 50 M-5g/ml ascorbic acid and 4 mM beta glycerol phosphate). Fresh differentiation medium was added three days later. On day four, fresh differeniation medium containing 20M-5M SAHA and/or its solvent (DMSO) were added for 2 hours. RNA was isolated and microarray analysis performed.	MC3T3 sc4 murine calvarial osteoblasts were maintained in M-NM-1-Minimal Essential Medium without ascorbic acid containing 10% FBS, 100 U/ml penicillin, and 100 M-5g/ml streptomycin (maintenance medium).	Collagenase digests were performed with 1 mg/ml type II collagenase and 1 mg/ml BSA (Sigma) in HankM-bM-^@M-^Ys balanced salt solution for 40 min (cells were exposed to SAHA or vehicle during this incubation). Cells were then harvested and RNA isolated with RNeasy kit.	Following hybridization, the arrays were washed, stained with streptavidin-cy3 conjugate, and then scanned in an Illumina BeadArray Reader. All quality assessment parameters were determined to be within normal ranges before proceeding to the final data reduction.	
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	TIME						
Experimental Factor Type	treatment	time						
Comment[SecondaryAccession]	GSE50549							
Comment[GEOReleaseDate]	2013-09-04							
Comment[ArrayExpressSubmissionDate]	2013-09-03							
Comment[GEOLastUpdateDate]	2013-09-04							
Comment[AEExperimentType]	transcription profiling by array							
Comment[AdditionalFile:Data1]	GSE50549_non-normalized.txt							
SDRF File	E-GEOD-50549.sdrf.txt