ONTOLOGY SOURCE REFERENCE
Term Source Name	"CHEBI"	"EFO"	"BTO"	"NCBITAXON"	
Term Source File	"http://data.bioontology.org/ontologies/CHEBI"	"http://data.bioontology.org/ontologies/EFO"	"http://data.bioontology.org/ontologies/BTO"	"http://data.bioontology.org/ontologies/NCBITAXON"	
Term Source Version	"78"	"111"	"20"	"2"	
Term Source Description	"Chemical Entities of Biological Interest Ontology"	"Experimental Factor Ontology"	"BRENDA Tissue and Enzyme Source Ontology"	"National Center for Biotechnology Information (NCBI) Organismal Classification"	
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-19232"
Study Title	"Human mesenchymal stem cells induced to differentiate by treatment with the NSAID indomethacin and/or other drugs. [original title: miR-335 regulates cell migration and differentiation in human mesenchymal stem cells]"
Study Description	"Total RNA was collected, and miRNA expression was compared from mesenchymal stem cells (MSCs) induced to differentiate along adipogenic or osteogenic pathways or transduced with miR-335. Controls: uninduced MSCs, skin fibroblasts, and MSCs transduced with a control vector. [original description: Human mesenchymal stem cells (hMSC) have an extensive potential for clinical applications in cell therapy. However, very little is known of the specific molecular regulatory mechanisms that control the therapeutical properties of these cells. We aimed to identify microRNAs (miRNAs) that could be involved in controlling the transition between the self-renewing (undifferentiated) and the reparative (differentiated) phenotypes of hMSCs. MicroRNA microarrays were used to identify miRNAs that are upregulated in undifferentiated hMSCs. For that, we compared the miRNA expression profiles of undifferentiated bone marrow-derived hMSCs with the same primary cell lines after 9 days of in vitro adipogenic or osteogenic induction. We also compared the miRNA expression profiles of undifferentiated hMSCs with skin fibroblasts (a mesenchymal cell lineage with a more restricted differentiation potential). These experiments allowed us to identify miR-335 as the only miRNA downregulated upon MSC differentiation as well as in MSCs in comparison with skin fibroblasts. Gene expression microarrays were used to identify genes that are downregulated in hMSCs overexpressing miR-335. We compared the miRNA expression profiles of hMSCs transduced with a lentiviral vector encoding miR-335 with MSCs transduced with a control lentiviral vector. Our results suggest miR-335 downregulation could be one of the triggers for the initiation of MSCs activities involved in tissue repair and remodeling, including cell migration and differentiation. We compared the miRNA expression profiles of undifferentiated bone marrow-derived hMSCs with the same primary cell lines after 9 days of adipogenic or osteogenic induction, as well as with skin fibroblasts. A total of four independent samples were used for each condition. For the adipogenic/osteogenic vs. undifferentiated MSC comparison, the RNA samples were pooled (two independent samples/pool) before labeling. We also compared the miRNA expression profiles of hMSCs transduced with the lentiviral vector pLV-EmGFP-MIRN335 with MSCs transduced with the control vector pLV-EmGFP-Mock. For the gene expression microarrays, a total of three independent samples were used for each condition.]"
Comment[Study Grant Number]	""
Comment[Study Funding Agency]	""
Study Submission Date	""
Study Public Release Date	"2010-05-06"
Study File Name	"s_E-GEOD-19232_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"transcription profiling by array"
Study Design Type Term Accession Number	""
Study Design Type Term Source REF	""
STUDY PUBLICATIONS
Study PubMed ID	"21164520"
Study Publication DOI	"10.1038/cdd.2010.167"
Study Publication Author List	"Tomé M, López-Romero P, Albo C, Sepúlveda JC, Fernández-Gutiérrez B, Dopazo A, Bernad A, González MA."
Study Publication Title	"miR-335 orchestrates cell proliferation, migration and differentiation in human mesenchymal stem cells."
Study Publication Status	"Published"
Study Publication Status Term Accession Number	""
Study Publication Status Term Source REF	""
STUDY FACTORS
Study Factor Name	"condition"	"tissue"	"cell type"	"NSAID"	"NSAID conc"	"drug 1"	"drug 1 conc"	"drug 2 "	"drug 2 conc"	"chemical 1"	"chemical 1 conc"	"chemical 2"	"chemical 2 conc"
Study Factor Type	"condition"	"tissue"	"cell type"	"chemical compound"	"concentration"	"chemical compound"	"concentration"	"chemical compound"	"concentration"	"chemical compound"	"concentration"	"chemical compound"	"concentration"
Study Factor Type Term Accession Number	""	""	""	"http://purl.obolibrary.org/obo/CHEBI_37577"	""	"http://purl.obolibrary.org/obo/CHEBI_37577"	""	"http://purl.obolibrary.org/obo/CHEBI_37577"	""	"http://purl.obolibrary.org/obo/CHEBI_37577"	""	"http://purl.obolibrary.org/obo/CHEBI_37577"	""
Study Factor Type Term Source REF	""	""	""	"EFO"	""	"EFO"	""	"EFO"	""	"EFO"	""	"EFO"	""
STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-19232_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-GSE19232-3"	"P-GSE19232-2"	"P-GSE19232-10"	"P-GSE19232-9"	"P-GSE19232-4"	"P-GSE19232-5"	"P-GSE19232-11"	"P-GSE19232-6"	"P-GSE19232-12"	"P-GSE19232-7"	"P-GSE19232-13"	"P-GSE19232-8"	"P-GSE19232-14"	"P-GSE19232-1"
Study Protocol Type	"grow"	"specified_biomaterial_action"	"specified_biomaterial_action"	"specified_biomaterial_action"	"nucleic_acid_extraction"	"labeling"	"labeling"	"hybridization"	"hybridization"	"image_aquisition"	"image_aquisition"	"feature_extraction"	"feature_extraction"	"bioassay_data_transformation"
Study Protocol Type Term Accession Number	""	""	""	""	""	""	""	""	""	""	""	""	""	""
Study Protocol Type Term Source REF	""	""	""	""	""	""	""	""	""	""	""	""	""	""
Study Protocol Description	"Human bone-marrow and skin biopsies were obtained from healthy donors. Mesenchymal stem cells (from bone marrow) and skin fibroblasts were isolated as described. All cells were cultured in expansion medium (Dulbecco's modified Eagle's medium (DMEM), with 4.5 g/l D-glucose supplemented with 10% heat-inactivated fetal calf serum (FCS), 2 mM L-glutamine, and 50 ug/ml gentamicin; all culture reagents from Invitrogen, Carlsbad, CA)."	"Cells grown in expansion medium."	"Cells grown in osteogenic medium (expansion medium plus 10 mM beta-glycerophosphate, 0.1 uM dexamethasone, 0.2 mM ascorbic acid)."	"Cells grown in adipogenic medium (expansion medium plus 0.01 uM dexamethasone, 0.5 mM IBMX, 60 uM indomethacin)."	"Total RNA was isolated by using the miRNeasy Mini Kit (Qiagen, Valencia, CA), according to manufacturer's instructions."	"miRNA Microarray System Protocol (Agilent Technologies) was used to label RNA. Basically, 100 ng of total RNA were dephosphorylated and Cyanine 3-pCp molecule was ligated to the 3' end of each RNA molecule by using T4 RNA ligase."	"1 ug of total RNA was reverse transcribed using T7 promoter Primer and MMLV-RT. Then cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP."	"100 ng of Cy3 labelled RNA were hybridized to Human miRNA V2 Microarray 8x15K (G4470B, Agilent Technologies) for 20 hours at 55°C in a hybridization oven (G2545A, Agilent) set to 15 rpm in a final concentration of 1X GE Blocking Agent and 1X Hi-RPM Hybridization Buffer, according to manufacturer's instructions (miRNA Microarray System Protocol, Agilent Technologies)."	"Samples were hybridized to Whole Human Genome Microarray 4 x 44K (G4112F, Agilent Technologies). 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65°C in a hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). Arrays were washed according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). Arrays were dried out using a centrifuge."	"Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for miRNA Microarray v2.0 (miRNA Microarray System Protocol, Agilent Technologies). Images provided by the scanner were analyzed using Agilent's software Feature Extraction version 9.5.3.1."	"Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format one-color arrays. Images provided by the scanner were analyzed using Feature Extraction software version 9.5.3.1 (Agilent Technologies)"	"Data pre-processing and differential expression analysis were done using the Bioconductor package AgiMicroRna. The Total Gene Signal provided by the Agilent Feature Extracion image analysis software was used for the data analysis. Data were normalized between arrays using the quantile method. The image analysis software attach to each feature a flag that identifies different quantification errors of the signal that can be used to filter out the microRNAs that do not reach a minimum of quality. This filtering was done after the normalization of the Total Gene Signal. We kept for the analysis those microRNA genes flagged by Agilent Feature Extraction software as detected (gIsGeneDetected=1) in at least one experimental condition. Basically, the gIsGeneDetected filtering removes microRNAs that are not expressed in any experimental condition."	"Data pre-processing was done using the Bioconductor package Agi4x44PreProcess. The data were background corrected and normalized between arrays in order to compensate for systematic technical differences between chips. We selected the MeanSignal and the BGMedianSignal for the foreground and background signals, respectively, from the collection of signals provided by the Agilent Feature Extraction image analysis software. These signals were used for the background correction and normalization of the data. First, we produced a Background Subtracted Signal using the half option in Agi4x44Preprocess. According to this method, background signal is subtracted from the foreground signal and any intensity which is less than 0.5 is reset to be equal to 0.5 to produce positive corrected intensities. After background correction, data were normalized between arrays using quantile method. An offset equals 50 were added to the intensities before log-transforming, so that the log ratios are shrunk towards zero at the lower intensities. The AFE software attaches to each feature a flag that identifies different quantification errors of the signal. These quantification flags can be used to filter out signals that don't reach a minimum arbitrary criterion of quality. The data were filtered trying to 1) keeping features within the dynamic range of the scanner and 2) keeping features that are of good quality. To keep features within the dynamic range, for every replicated spot across the whole set of samples, we demanded that at least 75% of the replicated probes in at least one experimental condition had a quantification flag denoting that the signal is within the dynamic range. To keep features of good quality for the analysis, for each replicated spot across the whole set of samples we filtered out those probes  that had more than 25% of the replicates in at least one experimental condition with a flag indicating presence of outliers. The Bioconductor annotation package hgug4112a.db was employed to assign to each Agilent probe ID the corresponding gene accession number code."	"ID_REF = <br>VALUE = normalized signal"
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	""	""	""	""	""	""	""	""	""	""	""	""	""	""
Study Protocol Components Type	""	""	""	""	""	""	""	""	""	""	""	""	""	""
Study Protocol Components Type Term Accession Number	""	""	""	""	""	""	""	""	""	""	""	""	""	""
Study Protocol Components Type Term Source REF	""	""	""	""	""	""	""	""	""	""	""	""	""	""
STUDY CONTACTS
Study Person Last Name	"Dopazo"	"González"	"González"	"Tomé"	"López-Romero"	"Fernández-Gutiérrez"	"Bernad"
Study Person First Name	"Ana"	"Manuel"	"Manuel"	"María"	"Pedro"	"Benjamín"	"Antonio"
Study Person Mid Initials	""	""	"A"	""	""	""	""
Study Person Email	"adopazo@cnic.es"	"magonzalez@cnic.es"	""	""	""	""	""
Study Person Phone	"34914531217"	""	""	""	""	""	""
Study Person Fax	""	""	""	""	""	""	""
Study Person Address	"Genomics Unit, CNIC, Melchor Fernandez Almagro, Madrid, Spain"	"CNIC, Melchor Fernandez Almagro, 3, Madrid, Spain"	""	""	""	""	""
Study Person Affiliation	"CNIC"	"CNIC"	""	""	""	""	""
Study Person Roles	"submitter"	"submitter"	""	""	""	""	""
Study Person Roles Term Accession Number	""	""	""	""	""	""	""
Study Person Roles Term Source REF	""	""	""	""	""	""	""
Comment[Study Person REF]	""	""	""	""	""	""	""