Comment[ArrayExpressAccession]	E-GEOD-50869
MAGE-TAB Version	1.1					
Public Release Date	2013-09-14
Investigation Title	Different developmental trajectories of ovaries in Siberian hamsters raised in long and short day lengths					
Comment[Submitted Name]	Different developmental trajectories of ovaries in Siberian hamsters raised in long and short day lengths
Experiment Description	A genome-wide association study was performed on ovaries from Siberian hamsters raised in either long or short photoperiod. Few differences between long and short photoperiod were noted at 3 wk of age, when ovarian histology was identical, whereas many differences in gene expression were noted at 8 wk of age, when ovarian histologies were markedly different. Hamsters were gestated and maintained in 16 or 10 hours of light per day, the latter short photoperiod delays sexual maturity and alters ovarian histology. Differences in gene expression were evaluated by microarray at 3 and 8 wk of age, as were changes between 3 and 8 wk of age in each photoperiod.					
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	Place	Place	Park			
Person First Name	Ned	Ned	Sung-Un			
Person Mid Initials		J				
Person Email	njp27@cornell.edu					
Person Affiliation	Cornell University					
Person Address	Population Medicine & Diagnostic Sciences, Cornell University, 240 Farrier Road, Ithaca, NY, USA					
Person Roles	submitter					
Protocol Name	P-GSE50869-1	P-GSE50869-4	P-GSE50869-5	P-GSE50869-2	P-GSE50869-3	P-GSE50869-6
Protocol Description	The Scanned images were analyzed with Agilent Feature Extraction software by obtaining fluorecent signal. ID_REF =  VALUE = Agielnt default normalized signal intensity	One ug of total RNA is amplified and labeled with Cyanine-3 (Cy3) using Ambion Amino Allyl MessageAmpM-bM-^DM-" II aRNA Amplification Kit.	Cy3-labelled cRNA was hybridized to 4X44K microarray and washed, according to manufacturer's protocols. Briefly, Cy3-labelled cRNA was fragmented at 60M-0C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse 44K custom high-definition whole-genome oligo array (G2519F-014868) for 17 hours at 65M-CM-^BM-0C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37M-CM-^BM-0C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.	Female hamsters from both LD and SD groups were euthanized by CO2 Chamber at the age of 3 week or 8 week, respectively. Ovaries were asecptically removed,snap-frozen on dry ice, and stored at -80 degree until RNA extraction.	Both ovaries from each hamster were homogenized with a Polytron, and total RNA was extracted with Trizol (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions. RNA was purified again with Rneasy Kit (Qiagen, Valencia, CA), examined its quantity and quality with and Agilent Bioanlyzer 2100 (Agilent Technologies,Palo Alto, CA).	Agilent microarray scanner was used to scan the microarry using one color scan setting.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	TREATMENT	AGE				
Experimental Factor Type	treatment	age				
Comment[SecondaryAccession]	GSE50869					
Comment[GEOReleaseDate]	2013-09-14					
Comment[ArrayExpressSubmissionDate]	2013-09-13					
Comment[GEOLastUpdateDate]	2013-09-15					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-50869.sdrf.txt