ONTOLOGY SOURCE REFERENCE
Term Source Name	"CHEBI"	"BTO"	"NCBITAXON"	"UO"	
Term Source File	"http://data.bioontology.org/ontologies/CHEBI"	"http://data.bioontology.org/ontologies/BTO"	"http://data.bioontology.org/ontologies/NCBITAXON"	"http://data.bioontology.org/ontologies/UO"	
Term Source Version	"78"	"20"	"2"	"42"	
Term Source Description	"Chemical Entities of Biological Interest Ontology"	"BRENDA Tissue and Enzyme Source Ontology"	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Units of Measurement Ontology"	
INVESTIGATION
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-37836"
Study Title	"Time course of gene expression during adipogenesis. Adipogenic induction medium contained indomethacin. [original title: Differentially expressed zinc finger proteins during human adipogenesis]"
Study Description	"To investigate the collective role of zinc finger proteins in adipogenesis, we induced adipogenesis using human mesenchymal stem cells (MSC) and compared the gene expression profiles using human Illumina beads arrays. We performed three independent experiments of time-series analysis (0h, 1h, 12h, 24h, 2d, 4d, 6d, 9d, 12d, 15d after induction of adipogenesis) in order to comprehensively capture the dynamic profiles of transcriptome during differentiation. Statistical filtering based on Analysis of Variance (ANOVA; p-value < 0.001, FDR 5%) and Gene Ontology classification using the Human Gene Nomenclature Database (HGNC) identified 618 out of 678 zinc finger proteins (ZFPs) that were significantly expressed during adipogenesis. Moreover, 34 out of 618 genes were differentially expressed more than 2-fold up or down regulated. The K-means clustering analysis further revealed four dynamic expression patterns: one gene in early-response, seven genes in transient, twenty genes in progressively-induced and four genes in the down-regulated, demonstrating the dynamic involvement of ZFPs in the process of adipocyte differentiation and maturation. Total RNA obtained from 10 different time points (0h, 1h, 12h, 24h, 2d, 4d, 6d, 9d, 12d, 15d) during adipogenesis from human Mesenchymal stem cell (MSC) to Adipocyte (ADP). Adipogenesis was induced by the different cocktail of chemical compounds containing human-insulin, dexamethasone, indomethacin and IBMX."
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Study Public Release Date	"2012-12-01"
Study File Name	"s_E-GEOD-37836_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"transcription profiling by array"
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STUDY PUBLICATIONS
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STUDY FACTORS
Study Factor Name	"time after induction"	"time after induction - hours"
Study Factor Type	"time after induction"	"time (hours)"
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STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-37836_GeneChip_assay.txt"
Study Assay Measurement Type	"transcription profiling"
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Study Assay Technology Type	"DNA microarray"
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STUDY PROTOCOLS
Study Protocol Name	"P-GSE37836-3"	"P-GSE37836-2"	"P-GSE37836-4"	"P-GSE37836-5"	"P-GSE37836-6"	"P-GSE37836-7"	"P-GSE37836-8"	"P-GSE37836-1"
Study Protocol Type	"grow"	"specified_biomaterial_action"	"nucleic_acid_extraction"	"labeling"	"hybridization"	"image_acquisition"	"feature_extraction"	"bioassay_data_transformation"
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Study Protocol Description	"Human bone marrow derived mesenchymal stem cells (MSC) were maintained in Mesenchymal stem cell basal medium (MSCBM) supplemented with 10% fetal bovine serum (FBS), 10ml of L-Glutamine and 0.5 ul of antibiotics (Takara Inc). They were cultured at 37°C, 5% CO2. Medium was changed every 2 or 3 days."	"Adipocyte differentiation was induced by incubating 100% confluent MSCs in Adipogenic induction medium (Takara Inc) containing 2ml of human insulin, 1ml of dexamethasone, and 0.4ml of indomethacin and 0.2ml of IBMX. Three days post induction cells were maintained with the maintenance medium (Takara Inc) containing 2ml of human insulin for 1 day. Both induction and maintenance medium were supplemented with 10% fetal bovine serum (FBS) 4ml of L-Glutamine and 0.2 ul of antibiotics (Takara Inc). Total four cycles of induction medium (3d) and maintenance medium (1d) was performed to differentiate into adipocyte."	"RNA was extracted with QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser."	"Biotinylated cRNA were prepared with TotalPrep™ RNA Amplification Kit for Illumina arrays"	"Standard Illumina hybridization protocol"	"Standard Illumina scanning protocol"	"The data were normalized using quantile normalization with lumi in R"	"ID_REF =  VALUE = quantile normalized signal Detection Pval = "
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STUDY CONTACTS
Study Person Last Name	"Hasegawa"	"Ryota"	"Ogawa"	"Yoshihide"	"Suzuki"	"Shin"
Study Person First Name	"Ryota"	"H"	"A"	"H"	"H"	"Jay"
Study Person Mid Initials	""	""	""	""	""	"W"
Study Person Email	"r-hase@gsc.riken.jp"	""	""	""	""	""
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Study Person Address	"Omics science center, RIKEN Yokohama, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama , Kanagawa, Japan"	""	""	""	""	""
Study Person Affiliation	"RIKEN Yokohama"	""	""	""	""	""
Study Person Roles	"submitter"	""	""	""	""	""
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