Investigation Title	Transcription profiling of mouse WT and Nxf2 KO post-natal day 21 testes	
Comment[Submitted Name]	Transcript profiling of WT and Nxf2 KO post-natal day 21 testes	
Experimental Design	unknown_experiment_design_type	transcription profiling by array	
Experimental Design Term Source REF		EFO	
Comment[SecondaryAccession]	GSE13526	
Comment[ArrayExpressReleaseDate]	2009-11-14	
Comment[AEMIAMESCORE]	3	
Comment[ArrayExpressAccession]	E-GEOD-13526	
Comment[MAGETAB TimeStamp_Version]	2010-07-30 10:49:41 Last Changed Rev: 13058	
Experimental Factor Name	
Experimental Factor Type	
Experimental Factor Term Source REF	
Person Last Name	Pan	
Person First Name	Jieyan	
Person Mid Initials	
Person Email	jieyanpan@gmail.com	
Person Phone	
Person Fax	
Person Address	RM 200E, Department of Animal Biology, University of Pennsylvania, 3800 Spruce Street, Philadelphia, 19104, USA	
Person Affiliation	University of Pennsylvania	
Person Roles	submitter	
Person Roles Term Source REF	The MGED Ontology	
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Quality Control Term Source REF	
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Normalization Type	
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Date of Experiment	
Public Release Date	2009-11-14	
PubMed ID	
Publication DOI	
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Publication Title	
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Publication Status Term Source REF	
Experiment Description	In euakryotes, mRNAs must be exported from the nucleus to the cytsoplasm. NXF2 is highly expressed in the mouse male germ cells.  We are interested in its function in spermatogenesis, espically in the nuclear RNA export in the testis. To this end, we made Nxf2 mutant mice by gene targeting. In an attempt to identify the mRNA substrates of NXF2, we perform the microarray experiments on testes. We used microarrays to check the expression profiles of the Nxf2 WT and KO 21d testes on C57BL/6 background. Experiment Overall Design: To examine the expression difference between WT and Nxf2 KO testes, we collected testes from juvenile mice of three ages ( 21d, 26d, 28d). Testis weight was similar between WT and KO mice at post-natal day 21.  Three pairs of WT and KO 21d testes were chosen for microarray analysis.	
Protocol Name	P-G13526-1	P-G13526-2	P-G13526-5	P-G13526-3	P-AFFY-6	P-G13526-4	
Protocol Type	grow	specified_biomaterial_action	nucleic_acid_extraction	labeling	feature_extraction	bioassay_data_transformation	
Protocol Description	Mice were housed under normal barrier condition	Testes were collected from juvenile mice at post-natal day 21. The testes were weighted and stored at -80°C.	Total RNA was extracted using Trizol reagent followed by purification using an RNeasy kit.	Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP	Title: Affymetrix CEL analysis. Description: 	Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features.	
Protocol Parameters	
Protocol Hardware	
Protocol Software					MicroArraySuite 5.0	
Protocol Contact	
Protocol Term Source REF						The MGED Ontology	
SDRF File	E-GEOD-13526.sdrf.txt	
Term Source Name	NCBI Taxonomy		The MGED Ontology	ArrayExpress	EFO	The MGED Ontology	
Term Source File	http://www.ncbi.nlm.nih.gov/Taxonomy/		http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress	http://www.ebi.ac.uk/efo/	http://mged.sourceforge.net/ontologies/MGEDontology.php	
Term Source Version