Comment[ArrayExpressAccession]	E-GEOD-46814
MAGE-TAB Version	1.1									
Public Release Date	2013-06-07
Investigation Title	Mouse Uterine Transcriptome in Estrus and Proestrus: whole uterine tissue and isolated lumenal epithelial cells									
Comment[Submitted Name]	Mouse Uterine Transcriptome in Estrus and Proestrus: whole uterine tissue and isolated lumenal epithelial cells
Experiment Description	This SuperSeries is composed of the SubSeries listed below. Refer to individual Series									
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	Waxman									
Person First Name	David									
Person Mid Initials	J.									
Person Email	djw@bu.edu									
Person Affiliation	Boston University									
Person Phone	617-353-7401									
Person Fax	617-353-7404									
Person Address	Department of Biology, Boston University, 5 Cummington Mall, Boston, MA, USA									
Person Roles	submitter									
Protocol Name	P-GSE46814-2	P-GSE46814-1	P-GSE46814-8	P-GSE46814-4	P-GSE46814-9	P-GSE46814-5	P-GSE46814-3	P-GSE46814-7	P-GSE46814-10	P-GSE46814-6
Protocol Description	Linear and LOWESS normalization and analysis using Rosetta Resolver pipeline (version 5.1). ID_REF =  VALUE = Normalized log2 ratio (estrus/proestrus) Estrus/Proestrus Ratio =  Estrus/Proestrus Fold Change =  Estrus Signal Intensity =  Proestrus Signal Intensity =  P-value = 	Linear and LOWESS normalization and analysis using Rosetta Resolver pipeline (version 5.1) ID_REF =  VALUE = Estrus/Proestrus Log2 Ratio	RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor's protocol (Epicentre, Madison, WI). Five M-5g of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature. Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA). Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.	RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendorM-bM-^@M-^Ys protocol (Epicentre, Madison, WI). Five M-5g of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature. Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA). Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.	Hybridization was performed using 0.825 M-5g of Alexa 555-labeled aRNA and 0.825 M-5g of Alexa 647-labeled aRNA. Agilent's SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65M-0 C at 10 rpm. After hybridization, the slides were washed per Agilent's SSPE wash protocol.	Hybridization was performed using 0.825 M-5g of Alexa 555-labeled aRNA and 0.825 M-5g of Alexa 647-labeled aRNA. AgilentM-bM-^@M-^Ys SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65M-0 C at 10 rpm. After hybridization, the slides were washed per AgilentM-bM-^@M-^Ys SSPE wash protocol.	Trizol extraction of RNA	Trizol extraction of RNA.	Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 um scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation. TIFF images were analyzed using Agilent's Feature Extraction software (version 10.7.1.1, protocol GE2_107_Sep09).	Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 um scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation. TIFF images were analyzed using AgilentM-bM-^@M-^Ys feature extraction software (version 10.7.1.1, protocol GE2_107_Sep09).
Protocol Type	normalization data transformation protocol	normalization data transformation protocol	labelling protocol	labelling protocol	hybridization protocol	hybridization protocol	nucleic acid extraction protocol	nucleic acid extraction protocol	array scanning protocol	array scanning protocol
Experimental Factor Name	ESTRUS CYCLE STAGE	AGE	ORGANISM PART							
Experimental Factor Type	estrus cycle stage	age	organism part							
Publication Title	Changes in Mouse Uterine Transcriptome in Estrus and Proestrus.									
Publication Author List	Stanley Yip K, Suvorov A, Connerney J, Lodato NJ, Waxman DJ									
PubMed ID	23740946									
Publication DOI	10.1095/biolreprod.112.107334									
Comment[SecondaryAccession]	GSE46814									
Comment[GEOReleaseDate]	2013-06-07									
Comment[ArrayExpressSubmissionDate]	2013-05-09									
Comment[GEOLastUpdateDate]	2013-06-09									
Comment[AEExperimentType]	transcription profiling by array									
SDRF File	E-GEOD-46814.sdrf.txt