ONTOLOGY SOURCE REFERENCE Term Source Name "CHEBI" "CLO" "NCBITAXON" "XCO" Term Source File "http://data.bioontology.org/ontologies/CHEBI" "http://data.bioontology.org/ontologies/CLO" "http://data.bioontology.org/ontologies/NCBITAXON" "http://data.bioontology.org/ontologies/XCO" Term Source Version "78" "39" "2" "33" Term Source Description "Chemical Entities of Biological Interest Ontology" "Cell Line Ontology" "National Center for Biotechnology Information (NCBI) Organismal Classification" "Experimental Conditions Ontology" INVESTIGATION Investigation Identifier "" Investigation Title "" Investigation Description "" Investigation Submission Date "" Investigation Public Release Date "" Comment [Created with configuration] "" Comment [Last Opened With Configuration] "" Comment[Created With Configuration] "" Comment[Last Opened With Configuration] "" INVESTIGATION PUBLICATIONS Investigation PubMed ID "" Investigation Publication DOI "" Investigation Publication Author List "" Investigation Publication Title "" Investigation Publication Status "" Investigation Publication Status Term Accession Number "" Investigation Publication Status Term Source REF "" INVESTIGATION CONTACTS Investigation Person Last Name "" Investigation Person First Name "" Investigation Person Mid Initials "" Investigation Person Email "" Investigation Person Phone "" Investigation Person Fax "" Investigation Person Address "" Investigation Person Affiliation "" Investigation Person Roles "" Investigation Person Roles Term Accession Number "" Investigation Person Roles Term Source REF "" STUDY Study Identifier "E-GEOD-14538" Study Title "Transcriptional profiling of human Caco2 cells treated with the NSAID mesalazine" Study Description "Expression profiling of Caco-2 cells, treated vs. untreated, 1 sample each. [original description: Several reports indicate that mesalazine (5-aminosalicylic acid or 5-ASA) is a promising candidate for the chemoprevention of Colo-Rectal Cancer (CRC) due to its ability to reach the purpose, yet avoiding at the same time the side effects that are usually determined by prolonged administrations of Non Steroidal Anti-Inflammatory Drugs. This activity of 5-ASA is probably the consequence of a number of effects determined on colon cancer cells and consisting of reduced proliferation, increased apoptosis and activation of cell cycle checkpoints. A recent observation has suggested that these effects could be mediated by the capacity of 5-ASA to interfere with the nuclear translocation of beta-catenin, in turn responsible for the inhibition of its transcription activity. The aim of our study was to better characterize the molecular mechanism by which 5-ASA inhibits the beta-catenin signaling pathway. To address this issue we assessed, by means of the Affymetrix microarray methodology, the transcriptome changes determined on Caco2 cells by a 96 h treatment with 20 mM mesalazine. Experiment Overall Design: We used the Affymetrix microarray methodology to assess the transcriptome changes determined on Caco2 cells by a 96 h treatment with 20 mM mesalazine. One sample was treated with mesalazine, and one sample was left untreated.]" Comment[Study Grant Number] "" Comment[Study Funding Agency] "" Study Submission Date "" Study Public Release Date "2010-02-17" Study File Name "s_E-GEOD-14538_study_samples.txt" STUDY DESIGN DESCRIPTORS Study Design Type "unknown_experiment_design_type" "transcription profiling by array" Study Design Type Term Accession Number "" "" Study Design Type Term Source REF "" "" STUDY PUBLICATIONS Study PubMed ID "19785626" Study Publication DOI "10.1111/j.1365-2036.2009.04149.x" Study Publication Author List "Parenti S, Ferrarini F, Zini R, Montanari M, Losi L, Canovi B, Ferrari S, Grande A." Study Publication Title "Mesalazine inhibits the beta-catenin signalling pathway acting through the upregulation of mu-protocadherin gene in colo-rectal cancer cells." Study Publication Status "Published" Study Publication Status Term Accession Number "" Study Publication Status Term Source REF "" STUDY FACTORS Study Factor Name "Treatment with compound" Study Factor Type "Mesalazine" Study Factor Type Term Accession Number "" Study Factor Type Term Source REF "" STUDY ASSAYS Study Assay File Name "a_E-GEOD-14538_GeneChip_assay.txt" Study Assay Measurement Type "transcription profiling" Study Assay Measurement Type Term Accession Number "" Study Assay Measurement Type Term Source REF "" Study Assay Technology Type "DNA microarray" Study Assay Technology Type Term Accession Number "" Study Assay Technology Type Term Source REF "" Study Assay Technology Platform "" STUDY PROTOCOLS Study Protocol Name "P-G14538-6" "P-G14538-2" "P-G14538-1" "P-G14538-5" "P-G14538-3" "P-AFFY-6" "P-G14538-4" Study Protocol Type "specified_biomaterial_action" "specified_biomaterial_action" "grow" "nucleic_acid_extraction" "labeling" "feature_extraction" "bioassay_data_transformation" Study Protocol Type Term Accession Number "" "" "" "" "" "" "" Study Protocol Type Term Source REF "" "" "" "" "" "" "" Study Protocol Description "5-ASA (SofarFarm S.p.A., Milano, Italy) was dissolved in cell culture medium at concentrations 20 mM. Caco2 cell line was treated with 5-ASA 20mM for 96h." "Untreated cells." "The Caco2 cell line was obtained from ATCC (Rockville, MD) and cultured in DMEM medium (Euroclone, Devon, UK), supplemented with 10% heat inactivated fetal bovine serum (Lonza, Walkersvillle, MD) and 1mM L-Glutamine (Euroclone)." "Total cellular RNA was extracted from 5-10x10^5 cells of each sample using RNeasy Mini Kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer." "Total RNA (3 µg) of Caco2 cells untreated and treated for 96 hours with 20 mM 5-ASA were converted in biotinylated cRNA according to the one-cycle target labeling protocol advised by Affymetrix (Affymetrix, Santa Clara,CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation." "Title: Affymetrix CEL analysis. Description: " "Scaling to TGT value=150. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples." Study Protocol URI "" "" "" "" "" "" "" Study Protocol Version "" "" "" "" "" "" "" Study Protocol Parameters Name "" "" "" "" "" "" "" Study Protocol Parameters Name Term Accession Number "" "" "" "" "" "" "" Study Protocol Parameters Name Term Source REF "" "" "" "" "" "" "" Study Protocol Components Name "" "" "" "" "" "MicroArraySuite 5.0" "" Study Protocol Components Type "" "" "" "" "" "" "" Study Protocol Components Type Term Accession Number "" "" "" "" "" "" "" Study Protocol Components Type Term Source REF "" "" "" "" "" "" "" STUDY CONTACTS Study Person Last Name "Grande" Study Person First Name "Alexis" Study Person Mid Initials "" Study Person Email "alexis.grande@unimore.it" Study Person Phone "" Study Person Fax "" Study Person Address "Biological Chemistry Section, Department of Biomedical Sciences, University of Modena and Reggio Emilia, via Campi n 287, MODENA, 41100, ITALY" Study Person Affiliation "University of Modena and Reggio Emilia" Study Person Roles "submitter" Study Person Roles Term Accession Number "" Study Person Roles Term Source REF "" Comment[Study Person REF] ""