Investigation Title Transcription profiling of human hGRbeta in the absence of hGR alpha Comment[Submitted Name] hGRβ: Elucidation of its Role in Transcriptional Regulation and Identification of a Ligand Experimental Design unknown_experiment_design_type transcription profiling by array Experimental Design Term Source REF EFO Comment[ArrayExpressReleaseDate] 2008-06-13 Comment[SecondaryAccession] GSE5310 Comment[AEMIAMESCORE] 3 Comment[ArrayExpressAccession] E-GEOD-5310 Comment[MAGETAB TimeStamp_Version] 2010-08-06 16:50:20 Last Changed Rev: 13058 Experimental Factor Name Experimental Factor Type Experimental Factor Term Source REF Person Last Name Group Person First Name NIEHS Microarray Person Mid Initials Person Email microarray@niehs.nih.gov Person Phone Person Fax Person Address NMG, DIR, NIEHS, 111 T.W. Alexander Drive, RTP, 27709, USA Person Affiliation NIEHS Person Roles submitter Person Roles Term Source REF 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 2008-06-13 PubMed ID 17242213 Publication DOI 17242213 Publication Author List Laura J Lewis-Tuffin, Christine M Jewell, Rachelle J Bienstock, Jennifer B Collins, John A Cidlowski Publication Title Human glucocorticoid receptor beta binds RU-486 and is transcriptionally active. Publication Status journal_article Publication Status Term Source REF The MGED Ontology Experiment Description The human glucocorticoid receptor (GR) is expressed as two alternately spliced Cterminal isoforms: α and β. In contrast to the canonical hGRα, hGRβ is constitutively nuclear, is not thought to bind ligand, and is believed to affect gene transcription only by acting as a dominant negative to hGRα. Microarray analysis indicated that hGRβ, expressed in the absence of hGRα, can regulate gene expression, and furthermore, occupation of hGRβ with the antagonist RU-486 diminishes that capacity. Experiment Overall Design: RNA preparation: Total RNA was extracted from 5x10 6 U-OFF or U-2 Experiment Overall Design: OSβ cells treated with either ethanol vehicle or 1μM RU-486 for 6 hours using the RNAqueous Total RNA Isolation Kit (Ambion Inc. Austin, TX) according to manufacturer’s instructions. RNA was treated with DNase using the DNA-Free DNase Treatment and Removal Reagents (Ambion Inc.) according to manufacturer’s instructions prior to use with the microarray. Four pairs of RNA (vehicle vs. RU-486 treated) were harvested for each cell type to yield four biological replicates for gene expression analysis. Experiment Overall Design: Linear Amplification Label Protocol and Feature Extraction: Gene expression analysis was conducted using Agilent Human1Av2 arrays (Agilent Technologies, Palo Alto, CA). Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer’s protocol. For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol. Slides were washed as indicated in this protocol Experiment Overall Design: and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software (v7.5), using defaults for all parameters. Protocol Name P-G5310-2 P-G5310-1 Protocol Type bioassay_data_transformation bioassay_data_transformation Protocol Description Data heading descriptions from GEO:
#ID_REF =
#rProcessedSignal =
#gProcessSignal =
#VALUE = Log10(Ratio of hGRB:U-off) Data heading descriptions from GEO:
#ID_REF =
#rProcessedSignal =
#gProcessSignal =
#VALUE = Log10(Ratio of Treated:Control) Protocol Parameters Protocol Hardware Protocol Software Protocol Contact Protocol Term Source REF SDRF File E-GEOD-5310.sdrf.txt Term Source Name mo The MGED Ontology ArrayExpress EFO The MGED Ontology Term Source File http://mged.sourceforge.net/ontologies/MGEDontology.php 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