Investigation Title Human colorectal cancer cell lines treated with several inhibitors of PI3Kinase AKT signaling pathway Comment[Submitted Name] Human colorectal cancer cell lines treated with several inhibitors of PI3Kinase AKT signaling pathway Experimental Design transcription profiling by array Experimental Design Term Source REF EFO Comment[AEMIAMESCORE] 5 Comment[SecondaryAccession] Comment[SecondaryAccession] GSE18005 Comment[AEExperimentType] transcription profiling by array Comment[ArrayExpressReleaseDate] 2010-06-23 Comment[ArrayExpressAccession] E-GEOD-18005 Comment[MAGETAB TimeStamp_Version] 2010-08-03 13:34:56 Last Changed Rev: 13058 Experimental Factor Name compound dose Experimental Factor Type compound dose Experimental Factor Term Source REF Person Last Name Jurchott Schafer Krech Person First Name Karsten Reinhold Till Person Mid Initials Person Email karsten.juerchott@charite.de Person Phone Person Fax Person Address Institute of Theoretical Biology, Charite - Universitatsmedizin Berlin, Invalidenstr. 43, Berlin, Germany Person Affiliation Charite - Universitatsmedizin Berlin 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 2010-06-23 PubMed ID 20546605 Publication DOI 10.1186/1471-2407-10-287 Publication Author List Krech T, Thiede M, Hilgenberg E, Schafer R, Jurchott K Publication Title Characterization of AKT independent effects of the synthetic AKT inhibitors SH-5 and SH-6 using an integrated approach combining transcriptomic profiling and signaling pathway perturbations Publication Status Publication Status Term Source REF Experiment Description Signal transduction processes mediated by phosphatidyl inositol phosphates affect a broad range of cellular processes such as cell cycle progression, migration and cell survival. The protein kinase AKT is one of the major effectors in this signaling network. Chronic AKT activation contributes to oncogenic transformation and tumor development. Therefore, new small drugs were designed to block AKT activity for cancer treatment. Here we characterize the biological effects of the phosphatidyl inositol phosphate analogs SH-5 and SH-6 in colorectal cancer cell lines. We demonstrate that the two compounds did not reduce AKT phosphorylation significantly in the presence of growth factors, but induce a broad range of morphological and transcriptional alterations. Transcriptomic profiling in inhibitor-treated SW480 cells revealed a cluster of down- regulated genes associated with mitosis. Moreover, the treatment of SW480 cells with either SH-5 or SH-6 caused the formation of binucleated cells as a result of a specific abscission defect. The cells were treated with certain inhibitors for 48 hours. We used one sample per cell line treated with DMSO as a control, and one sample for each of the treatments. Protocol Name P-GSE18005-4 P-GSE18005-3 P-GSE18005-2 P-GSE18005-5 P-GSE18005-6 P-GSE18005-7 P-GSE18005-8 P-GSE18005-1 Protocol Type nucleic_acid_extraction grow specified_biomaterial_action labeling hybridization image_acquisition feature_extraction bioassay_data_transformation Protocol Description Trizol extraction of total RNA was performed according to the manufacturer's instructions. SW480, HT29 and HCT116 cells were cultured in complete L-15 medium at 37 degreeC and 5% CO2 in a humidified incubator. After 24 hours, the cells were treated once with the indicated inhibitors for 48 hours. Labelling of RNA targets were performed according to protocols provided by Affymetrix. Hybridization and post-hybridization procedures were performed according to protocols provided by Affymetrix. Arrays were scanned twice at 3 um resolution using a confocal argon laser scanner (Hewlett-Packard, Santa Clara, CA), controlled by Microarray Suite 5.0 software (Affymetrix). Photoemission was detected by a photomultiplier tube through a 570-nm long-pass filter. Computer-generated array images were overlayed with a virtual grid, controlled by Microarray Suite 5.0 software. About 40 pixels within each feature were averaged after discarding outliers and pixels close to feature boundaries. ID_REF =
VALUE = Gene expression levels were calculated according to the average hybridization intensities of perfectly matched versus mismatched oligonucleotide probes. Arrays were scaled by Microarray Suite 5.0 software to an average hybridization intensity of 2,500 per gene and analyzed independently.
ABS_CALL =
DETECTION P-VALUE = Protocol Parameters Protocol Hardware Protocol Software Protocol Contact Protocol Term Source REF The MGED Ontology The MGED Ontology The MGED Ontology The MGED Ontology The MGED Ontology The MGED Ontology The MGED Ontology SDRF File E-GEOD-18005.sdrf.txt Term Source Name The MGED Ontology ArrayExpress EFO The MGED Ontology Term Source File 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