ONTOLOGY SOURCE REFERENCE
Term Source Name	"OBI"	
Term Source File	"http://data.bioontology.org/ontologies/OBI"	
Term Source Version	"21"	
Term Source Description	"Ontology for Biomedical Investigations"	
INVESTIGATION
Investigation Identifier	"1408375035696"
Investigation Title	""
Investigation Description	""
Investigation Submission Date	""
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Comment [Created with configuration]	""
Comment [Last Opened With Configuration]	""
Comment[Created With Configuration]	""
Comment[Last Opened With Configuration]	"isaconfig-default_v2011-02-18"
INVESTIGATION PUBLICATIONS
Investigation PubMed ID	""
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INVESTIGATION CONTACTS
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STUDY
Study Identifier	"E-GEOD-42686"
Study Title	"Chip-chip from undifferentiated and neuron-differentiated hMSCs cells with EZH2"
Study Description	"Half the samples were treated with indomethacin and several other chemicals. [original description: EZH2 plays an important role in stem cell renewal and maintenance by inducing gene silencing via its histone methyltransferase activity. Previously, we showed EZH2 downregulation markedly enhances neuron differentiation of human mesenchymal stem cells (hMSCs). To understand how EZH2 regulates neuron differentiation of hMSCs, we wanted to identify the target genes of EZH2. For this reasons we performed ChIP-on-chip experiments using specific EZH2 antibodies followed by a human promoter array for the whole human genome. The 3A6-hMSCs were differentiated into neuron for 5 days, and then 109 cells were harvested for the ChIP-on-chip assay. The procedure was based on the manufacturer's instructions (NimbleGen).]"
Study Submission Date	""
Study Public Release Date	"2012-12-05"
Study File Name	"s_E-GEOD-42686_study_samples.txt"
Comment[Study Grant Number]	""
Comment[Study Funding Agency]	""
STUDY DESIGN DESCRIPTORS
Study Design Type	"ChIP-chip design"
Study Design Type Term Accession Number	"http://purl.obolibrary.org/obo/OBI_0001403"
Study Design Type Term Source REF	"OBI"
STUDY PUBLICATIONS
Study PubMed ID	"23526793"
Study Publication DOI	"10.1002/emmm.201201783"
Study Publication Author List	"Yu YL, Chou RH, Shyu WC, Hsieh SC, Wu CS, Chiang SY, Chang WJ, Chen JN, Tseng YJ, Lin YH, Lee W, Yeh SP, Hsu JL, Yang CC, Hung SC, Hung MC."
Study Publication Title	"Smurf2-mediated degradation of EZH2 enhances neuron differentiation and improves functional recovery after ischaemic stroke."
Study Publication Status	"Published"
Study Publication Status Term Accession Number	""
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STUDY FACTORS
Study Factor Name	"cell type"
Study Factor Type	"cell type"
Study Factor Type Term Accession Number	""
Study Factor Type Term Source REF	""
STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-42686_ChIP-Chip_assay.txt"
Study Assay Measurement Type	"protein-DNA binding site identification"
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	"OBI"
Study Assay Technology Platform	""
STUDY PROTOCOLS
Study Protocol Name	"P-GSE42686-2"	"P-GSE42686-9"	"P-GSE42686-5"	"P-GSE42686-3"	"P-GSE42686-4"	"P-GSE42686-6"	"P-GSE42686-13"	"P-GSE42686-8"	"P-GSE42686-1"	"library construction"	"untreated"
Study Protocol Type	"grow"	"specified_biomaterial_action"	"specified_biomaterial_action"	"nucleic_acid_extraction"	"labeling"	"hybridization"	"image_acquisition"	"feature_extraction"	"bioassay_data_transformation"	"library construction"	"specified_biomaterial_action"
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Study Protocol Description	"The 3A6 cells were grown in Dulbecco's modified Eagle's medium-low glucose (DMEM-LG) with 10% fetal bovine serum (FBS)."	"The 3A6 cells were grown in Dulbecco�s modified Eagle�s medium-low glucose (DMEM-LG) with 10% fetal bovine serum (FBS). The 3A6 were treated with DMEM-HG neuronal induction medium (NIM) containing 10-7 M dexamethasone, 50 ?g/ml ascorbic acid-2-phosphate, 50 ?M indomethacin, 10 ?g/ml insulin, and 0.45 mM 3-isobutyl-1-methyl-xanthine for 5 days."	"no special treatment"	"cell lines were cross-linked with formaldehyde and the chromatin extracts were sonicated (Misonix Sonicater 3000). Following immunoprecipitation with anti-mouse EZH2 antibody (Cell Signaling, #3147, lot 4), DNAs were purified from ChIP samples and input control samples. Purified DNAs were blunt ended, ligated with linkers and amplified by PCR."	"standard Nimblegen ChIP labeling protocol (1 ug of Amplified ChIP DNA, direct incorporation of Cy labeled primers with Klenow extension)."	"standard Nimblegen hybridization kits and protocols were used."	"arrays were scanned with Axon scanner at 5 um resolution according to standard Nimblegen protocols"	"Signal intensity data is extracted from the scanned images of each array using NimbleScan (version 2.3.78), a NimbleGen's data extraction software. Arrays were scanned with Axon scanner at 5 um resolution according to standard NimbleGen protocols.Log2 ChIP/input ratios were created from the two raw pair files. Each feature on the array has a corresponding scaled log2-ratio. This is the ratio of the input signals for the experimental and test samples that were co-hybridized to the array. The log2-ratio is computed and scaled to center the ratio data around zero. Using NimbleScan, peak data files are generated from the scaled log2-ratio data. The ratio data is then randomized 20 times to evaluate the probability of false positives. Each peak is then assigned a false discovery rate (FDR) score based on the randomization. NimbleScan searches for peaks that appear in a specified promoter region around the transcription start site (TSS). Lists all peaks with an FDR 0.2 and maps them to promoter regions. Each row in the report lists a peak-transcript pair. For each transcript, if more than one peak lies within the promoter region, there will be multiple rows for that transcript."	"ID_REF = VALUE = scaled log2 ratios (Cy5/Cy3) by Nimblegen standard protocol"	"library mid"	"The 3A6 cells were grown in Dulbecco�s modified Eagle�s medium-low glucose (DMEM-LG) with 10% fetal bovine serum (FBS)."
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STUDY CONTACTS
Study Person Last Name	"Wu"	"Yu"	"Wu"
Study Person First Name	"chanshiou"	"Yung-Luen"	"Chen-Shiou"
Study Person Mid Initials	""	""	""
Study Person Email	"sddrwu7679@yahoo.com.tw"	""	""
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Study Person Address	"china medical university, No6,Hsueh-shih road, Taichung, Taiwan"	""	""
Study Person Affiliation	"china medical university"	""	""
Study Person Roles	"submitter"	""	""
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