Investigation Title Transcription profiling of human mesenchymal stem cells treated for 8 hours with BMP6 Comment[Submitted Name] 8 hours BMP6 treated vs untreated human mesenchymal stem cells (hMSC) Experimental Design unknown_experiment_design_type transcription profiling by array Experimental Design Term Source REF EFO Comment[AEMIAMESCORE] 4 Comment[SecondaryAccession] GSE13604 Comment[ArrayExpressReleaseDate] 2009-06-08 Comment[ArrayExpressAccession] E-GEOD-13604 Comment[MAGETAB TimeStamp_Version] 2010-07-30 11:21:55 Last Changed Rev: 13058 Experimental Factor Name Experimental Factor Type Experimental Factor Term Source REF Person Last Name Luo Person First Name Weijun Person Mid Initials Person Email luo@cshl.edu Person Phone Person Fax Person Address Cold Spring Harbor Lab, 1 Bungtown Rd, Cold Spring Harbor, 11724, USA Person Affiliation Cold Spring Harbor Lab 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 2009-06-08 PubMed ID Publication DOI Publication Author List Publication Title Publication Status Publication Status Term Source REF Experiment Description We have established that BMP6 is an important endogenous regulator of human osteoblast differentiation. Our preliminary experiment showed that 8 hour BMP6 treatment induced early osteoblast markers in hMSC. In this study, we used microarrays to profile the global gene expression program in hMSC induced by BMP6 treatment and further identify the early osteogenic responses to BMP6 stimulation. Experiment Overall Design: The dataset contains a total of 4 gene chip measurements from duplicate experiments each with paired measurements of human MSC with or without 8 hours BMP6 treatment. Protocol Name P-G13604-2 P-G13604-1 P-G13604-4 P-G13604-3 P-AFFY-6 Protocol Type specified_biomaterial_action grow nucleic_acid_extraction labeling feature_extraction Protocol Description 20 nM BMP6 (R&D Systems) was then added for the pre-designed time periods and then removed. To remove BMP6, cells were rinsed 2 times and fresh media without BMP was added. Passage 5 human MSC (5x105) were plated in 24-well dishes and cultured for 3 days. The cells were subsequently placed in serum free media supplemented with ITS for 24 hours. Qiagen extraction of total RNA was performed according to the manufacturer's instructions. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Title: Affymetrix CEL analysis. Description: Protocol Parameters Protocol Hardware Protocol Software MicroArraySuite 5.0 Protocol Contact Protocol Term Source REF SDRF File E-GEOD-13604.sdrf.txt Term Source Name ncbitax The MGED Ontology ArrayExpress EFO The MGED Ontology Term Source File http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html 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