Investigation Title Transcription profiling of mouse embryonic stem cell differentiation following treatment with DKK1 Comment[Submitted Name] Murphy M. musculus DKK1-treated ES cell differentiation Experimental Design time_series_design compound_treatment_design development_or_differentiation_design transcription profiling by array Experimental Design Term Source REF mo mo mo:1.3.1.1 EFO Comment[ArrayExpressReleaseDate] 2006-12-31 Comment[AEMIAMESCORE] 5 Comment[ArrayExpressAccession] E-MEXP-759 Comment[MAGETAB TimeStamp_Version] 2010-08-11 15:56:21 Last Changed Rev: 13058 Experimental Factor Name time compound Experimental Factor Type time compound_treatment_design Experimental Factor Term Source REF Person Last Name Lindsley Murphy Gill Murphy Person First Name R. Coleman Kenneth Jennifer Ken Person Mid Initials M G M Person Email murphy@pathology.wustl.edu Person Phone (314) 362-2009 Person Fax Person Address BOX 8118, 660 S. Euclid Ave. Person Affiliation Washington University School of Medicine Washington University School of Medicine Washington University School of Medicine Pathology and Immunology 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 2006-12-31 PubMed ID 19805038 Publication DOI 19805038 Publication Author List Jenner, Richard G.; Townsend, Michael J.; Jackson, Ian; Sun, Kaiming; Bouwman, Russell D.; Young, Richard A.; Glimcher, Laurie H.; Lord, Graham M. Publication Title The transcription factors T-bet and GATA-3 control alternative pathways of T-cell differentiation through a shared set of target genes Publication Status journal_article Publication Status Term Source REF Experiment Description Assessed effect of DKK1 treatment on gene expression during the first four days of ES cell differentiation in serum containing medium. Protocol Name P-MEXP-23954 P-MEXP-23953 P-MEXP-23955 P-AFFY-2 Affymetrix:Protocol:Hybridization-Unknown P-AFFY-6 P-MEXP-23958 Protocol Type grow specified_biomaterial_action nucleic_acid_extraction labeling hybridization feature_extraction bioassay_data_transformation Protocol Description ES cells were maintained on irradiated mouse embryonic fibroblasts in IMDM supplemented with 15% FCS, NEAA (0.1 mM each), L-glutamine (2 mM), Na Pyruvate (1 mM), Pen/Strep (1000 U/mL), 2-mercaptoethanol (55 μM) and LIF (EsGro, Chemicon International; 1000 U/mL). For differentiation, ES cells were plated in suspension at 1.5 x 104 cells/mL in serum-containing medium (SCM: IMDM supplemented with 10% FCS, NEAA, L-glutamine, Na Pyruvate, Pen/Strep, and 2-mercaptoethanol) Recombinant murine Dkk1 treatment added at initiation of differentiation (1X concentration). Specific activity determined by functional titration, defined as the concentration required to inhibit generation of Flk1+ mesoderm from ES cells. RNA purified using RNeasy Mini kit (Qiagen). Title: Affymetrix in vitro transcription. Description: Title: Affymetrix Generic Hybridization. Description: Title: Affymetrix CEL analysis. Description: Model Based Expression values determined using DNA-Chip Analyzer (dChip) (Li and Hung, 2001; Li and Wong, 2001). Protocol Parameters media;stop time;start time; Extracted product;Amplification; Protocol Hardware Protocol Software MicroArraySuite 5.0 MicroArraySuite 5.0 Protocol Contact Protocol Term Source REF mo mo The MGED Ontology SDRF File E-MEXP-759.sdrf.txt Term Source Name mo ncbitax The MGED Ontology ArrayExpress mo mo:1.3.1.1 EFO The MGED Ontology Term Source File http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html 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