Investigation Title Transcription profiling of human MDA-MB-231 breast cancer cells in vitro and in vivo as xenografts to assess the effect of ectopic expression of sFRP1 Comment[Submitted Name] Effect of ectopic expression of sFRP1 on MDA-MB-231 human breast cancer cells in vitro and in vivo as xenograft Experimental Design unknown_experiment_design_type transcription profiling by array Experimental Design Term Source REF EFO Comment[SecondaryAccession] GSE13806 Comment[ArrayExpressReleaseDate] 2009-05-11 Comment[AEMIAMESCORE] 3 Comment[ArrayExpressAccession] E-GEOD-13806 Comment[MAGETAB TimeStamp_Version] 2010-07-30 13:09:52 Last Changed Rev: 13058 Experimental Factor Name Experimental Factor Type Experimental Factor Term Source REF Person Last Name Oakeley Person First Name Edward Person Mid Initials Person Email Person Phone Person Fax Person Address FMI, Maulbeerstrasse 66, Basel, 4058, Switzerland Person Affiliation FMI 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 2009-05-11 PubMed ID Publication DOI Publication Author List Publication Title Publication Status Publication Status Term Source REF Experiment Description RNA was isolated from ectopically sFRP1-expressing MDA-MB-231 cells and control MDA-MB-231 cells and as well from tumor lysates arising from these cells as nude mouse xenograft. Gene expression profiles for these samples were investigated using Affymetrix arrays. Experiment Overall Design: MDA-MB-231 human breast cancer cells were stably transfected with human sFRP1 encoding vector or empty vector as control. After the selection with antibiotics, three clones of MDA-MB-231/sFRP1 and three clones of MDA-MB-231/control were selected. These six clones were cultured individually in DMEM 10% FCS with 1mg/ml G-418. When cells reached 70-80% confluence, RNA was isolated from the cells. In parallel, the three clones of MDA-MB-231/sFRP1 and the three clones of MDA-MB-231/control were pooled respectively. One million of cells from each pool were suspended in 100ul PBS and injected to fat pads of female balb/c nude mice (6 mice were injected with MDA-MB-231/sFRP1 and 5 mice were injected with MDA-MB-231/control) to do a xenograft experiment. A few - several weeks after, mice were sacrificed when tumor reached a certain size, tumors were taken and RNA was isolated using trizol reagent. Protocol Name P-G13806-1 P-G13806-2 P-G13806-4 P-G13806-3 P-AFFY-6 Protocol Type grow specified_biomaterial_action nucleic_acid_extraction labeling feature_extraction Protocol Description Three MDA-MB-231/sFRP1 clones and three MDA-MB-231/control clones were cultured in DMEM 10% FCS with 1mg/ml G-418. In parallel, the three sFRP1+ clones and the three control clones were pooled and injected to fat pads of nude mice. A few – several weeks after, mice were sacrificed and tumors arising from these cells were taken to isolate RNA. RNA was taken from cell lysates and tumor lysates Cultured cells were collected when plates were 70-80% confluent and RNA was extracted using RNeasy Mini kit (Qiagen, Venlo, The Netherlands). To extract the RNA from tumours, dissected tumours were put in RNAlater (Qiagen) over night at 4°C, followed by RNA extraction using TRIzol reagent (Invitrogen) and washing using the RNAeasy Mini kit according to manufacturer’s instructions. Affymetrix protocol Title: Affymetrix CEL analysis. Description: Protocol Parameters Protocol Hardware Protocol Software MicroArraySuite 5.0 Protocol Contact Protocol Term Source REF SDRF File E-GEOD-13806.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