ONTOLOGY SOURCE REFERENCE
Term Source Name	"CHEBI"	"CL"	"EFO"	"BTO"	"NCBITAXON"	"UBERON"	
Term Source File	"http://data.bioontology.org/ontologies/CHEBI"	"http://data.bioontology.org/ontologies/CL"	"http://data.bioontology.org/ontologies/EFO"	"http://data.bioontology.org/ontologies/BTO"	"http://data.bioontology.org/ontologies/NCBITAXON"	"http://data.bioontology.org/ontologies/UBERON"	
Term Source Version	"78"	"43"	"111"	"20"	"2"	"191"	
Term Source Description	"Chemical Entities of Biological Interest Ontology"	"Cell Ontology"	"Experimental Factor Ontology"	"BRENDA Tissue and Enzyme Source Ontology"	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Uber Anatomy Ontology"	
INVESTIGATION
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INVESTIGATION PUBLICATIONS
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-28628"
Study Title	"Human adipocytes induced to differentiate with indomethacin. [original title: Identification of new genes involved in human adipogenesis and fat storage]"
Study Description	"Three donors, three time points each (0d, 3,d, 7d). [original description: Since the worldwide increase in obesity represents a growing challenge for the health care systems, new approaches are needed to treat obesity and associated disease effectively. The food intake is primarily stored in the adipose tissue and therefore this organ is in focus to develop new anti-obesity treatments. To provide a systematic analysis of genes that regulate adipose tissue biology and to establish a target-oriented compound screening, we performed a high throughput siRNA screen with primary (pre)adipocytes, using a druggable siRNA library targeting 7,784 human genes. Beside well known regulators of adipogenesis and neutral lipid storage (like PPAR?, RXR, Perilipin A) the screening revealed a large number of genes which were not previously described in the context of fatty tissue biology. An enrichment of genes was observed for axonemal dyneins. Five out of ten axonemal dyneins were identified in our primary screen and retested positive with independent siRNAs and cell-donors. Quantitative RT-PCR- and immunoblot analysis revealed that axonemal dyneins are expressed in preadipocytes and maturing adipocytes. Using microarray analysis, we further characterize the remaining genes identified in our primary screen to determine their expression pattern during adipogenesis. In the course of fat cell differentiation, 149 among the 459 positive genes were regulated on the gene expression level. Assuming that an adipogenesis-specific expression pattern is another independent hind [hint? -ed.], that these genes are involved in neutral lipid storage and/or adipocyte differentiation, we retested this gene-pool with independent siRNAs and cell donors. Finally, to show that the genes identified are per se druggable we performed a proof of principle experiment using an antagonist for one randomly chosen gene. The results showed a very similar phenotype compared to knock-down experiments proofing the druggability. Thus, we identified new adipogenesis-associated genes and those involved in neutral lipid storage. Moreover, by using a druggable siRNA library the screen data provides a very attractive starting point, to identify anti-obesity compounds targeting the adipose tissue. For microarray analysis, RNA was isolated at 3 different points in time during adipogenesis (day 0, day 3 and day 7 after induction of differentiation). This experiment was carried out with cells obtained from three different donors. No replicates are included for each point in time.]"
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Study Public Release Date	"2012-03-06"
Study File Name	"s_E-GEOD-28628_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"transcription profiling by array"
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STUDY PUBLICATIONS
Study PubMed ID	"22384002"
Study Publication DOI	"10.1371/journal.pone.0031193"
Study Publication Author List	"Sšhle J, Machuy N, Smailbegovic E, Holtzmann U, Gršnniger E, Wenck H, StŠb F, Winnefeld M"
Study Publication Title	"Identification of new genes involved in human adipogenesis and fat storage."
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STUDY FACTORS
Study Factor Name	"time"	"individual"
Study Factor Type	"time"	"individual"
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STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-28628_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-GSE28628-1"	"P-GSE28628-6"	"P-GSE28628-3"	"P-GSE28628-8"	"P-GSE28628-7"	"P-GSE28628-2"	"P-GSE28628-4"	"P-GSE28628-5"
Study Protocol Type	"bioassay_data_transformation"	"hybridization"	"grow"	"feature_extraction"	"image_aquisition"	"specified_biomaterial_action"	"nucleic_acid_extraction"	"labeling"
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Study Protocol Description	"ID_REF = <br>VALUE = median normalized signal intensities"	"Cy3 labeled cRNAs were hybridized overnight (17 hours, 65¡C) to an Agilent Whole Mouse Genome Oligo Microarray (44K) using Agilent's recommended hybridization chamber and oven.  Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37¡C and a final wash step with acetonitrile for 30 sec at RT."	"Subcutaneous human preadipocytes were incubated in basal growth medium (Cambrex) containing 10% fetal calf serum, 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin (= culture medium)."	"The Agilent Feature Extraction Software (FES 10.5.1.1 ) was used to read out and process the microarray image files."	"Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA)."	"Differentiation into adipocytes was initiated by addition of 10 µg/ml insulin, 1 µM dexamethasone, 200 µM indomethacin and 500 µM isobutylmethylxanthine (Cambrex) to the culture medium."	"RNA was extracted using Trizol (Invitrogen) following manufacturer's instructions."	"1 µg of each RNA was used as template to produce Cy3-labeled cRNA. The RNA samples were amplified and labeled using the Agilent Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's protocol."
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STUDY CONTACTS
Study Person Last Name	"Rueberg"	"Winnefeld"	"Sšhle"
Study Person First Name	"Silvia "	"Marc"	"Jšrn"
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Study Person Email	""	"marc.winnefeld@beiersdorf.com"	""
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Study Person Address	"Genomic Services Department, Miltenyi Biotec GmbH, Friedrich-Ebert-Str. 68, Bergisch Gladbach, Germany"	""	""
Study Person Affiliation	"Miltenyi Biotec GmbH"	""	""
Study Person Roles	"submitter"	""	""
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