Investigation Title Transcription profiling of mouse polysome vs RNP fractions from testis obtained from prepuberttal and adult animals to investigate post transcriptional control mechanisms in gametes Comment[Submitted Name] Developmental changes in RNP and Polysome associated mRNAs in Mouse testes Experimental Design development_or_differentiation_design co-expression_design transcription profiling by array Experimental Design Term Source REF mo:1.3.1.1 mo EFO Comment[ArrayExpressReleaseDate] 2007-11-23 Comment[SecondaryAccession] GSE4711 Comment[AEMIAMESCORE] 5 Comment[SecondaryAccession] GDS2277 Comment[ArrayExpressAccession] E-GEOD-4711 Comment[MAGETAB TimeStamp_Version] 2010-08-05 17:09:23 Last Changed Rev: 13058 Experimental Factor Name Age OrganismPart DevelopmentalStage Experimental Factor Type age organism_part developmental_stage Experimental Factor Term Source REF Person Last Name Hecht Person First Name Norman Person Mid Initials B. Person Email Person Phone Person Fax Person Address University of Pennsylvania, 421 Curie Blvd, Philadelphia, 19104, USA Person Affiliation University of Pennsylvania Person Roles submitter Person Roles Term Source REF The MGED Ontology Quality Control Type Quality Control Term Source REF Replicate Type Replicate Term Source REF Normalization Type Normalization Term Source REF Date of Experiment Public Release Date 2007-11-23 PubMed ID 16682651 Publication DOI 16682651 Publication Author List Naoko Iguchi, John W Tobias, Norman B Hecht Publication Title Expression profiling reveals meiotic male germ cell mRNAs that are translationally up- and down-regulated. Publication Status journal_article Publication Status Term Source REF The MGED Ontology Experiment Description Gametes rely heavily on post-transcriptional control mechanisms to regulate their differentiation. In eggs, the storage and selective temporal activation of maternal mRNAs is essential for normal development. In the male, transcription ceases during spermiogenesis necessitating the post-transcriptional regulation of many paternal mRNAs required for spermatid differentiation and spermatozoan function. Messenger RNAs that are being actively translated form polysomes. whereas translationally inactive mRNAs are often sequestered in ribonucleoproteins (RNPs). Here we combine polysome display and microarray analyses of RNP and polysome fractions of testes from prepubertal and adult mice to characterize the translation state of individual mRNAs as spermatogenesis proceeds.. Consistent with published reports, many post-meiotic mRNAs known to be translationally delayed shift from the RNPs into the polysomes, confirming the validity of this approach. In addition, based upon the criterion of movement from RNPs to polysomes, we detect another 742 mouse testicular genes showing dramatic shifts between RNPs and polysomes. One sub-group of 35 genes including the known translationally delayed Pgk2, are initially transcribed and translationally repressed in meiotic spermatocytes, and translated post-meiotically. This high-through-put approach defines the changing translation patterns of a large number of genes as male germ cells differentiate and identifies a new group of post-transcriptionally regulated meiotic transcripts for future study. Mouse testes from animals of 3 different ages were fractionated on a sucrose gradient and transcripts were quantified in the RNP and Polysome fractions. Transcripts were identified that changed their RNP/Polysome representation at the different developmental time points. Protocol Name P-G4711-1 P-G4711-2 P-G4711-3 P-G4711-4 P-G4711-5 P-AFFY-6 Protocol Type specified_biomaterial_action specified_biomaterial_action nucleic_acid_extraction labeling hybridization feature_extraction Protocol Description cytoplasmic extract of mouse testes were subjected to 10-30% sucrose gradient centrifugation.Total RNAs were extracted from fractions 11-17 from total 17 as polysome-associated fraction by Trizol. cytoplasmic extract of mouse testes were subjected to 10-30% sucrose gradient centrifugation.Total RNAs were extracted from fractions 2-8 from total 17 as RNP-associated fraction by Trizol. Trizol extraction of total RNA was performed according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix). Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip MOE 430A Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Title: Affymetrix CEL analysis. Description: Protocol Parameters Protocol Hardware Protocol Software MicroArraySuite 5.0 Protocol Contact Protocol Term Source REF SDRF File E-GEOD-4711.sdrf.txt Term Source Name ncbitax NCI_thesaurus The MGED Ontology ArrayExpress mo:1.3.1.1 mo EFO The MGED Ontology Term Source File http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html ncithesaurus.obo.alt http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress http://mged.sourceforge.net/ontologies/MGEDontology.php http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/efo/ http://mged.sourceforge.net/ontologies/MGEDontology.php Term Source Version 1.3.1.1