{"text_format":"2","workbook":"xls","n_sheets":11,"sheets":["Metadata Template","Metadata Example","wksowlv0","wksowlv1","wksowlv2","wksowlv3","wksowlv4","wksowlv5","wksowlv6","wksowlv7","wksowlv8"],"not_rendered":{"charts":0,"images":0,"macros":0,"external_links":1,"defined_names":9,"comments":72,"pivot_tables":0},"unopened":[],"bounds":{"document_bytes":16777216,"sheet_cells":100000,"run_cost":"one","rows_first":2000,"rows_last":500,"rows_between":2000,"halvings":0,"cell_chars":16384,"cell_head_chars":4096},"cells_cut":0,"cells_raw":0,"read":"whole","date_system":"1900","formulas":"cached_only"}

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["# This template/example is based on an Affymetrix ChIP-chip study where the results of the primary analysis are reported in BAR and BED files."]
["# This template is suitable for other genomic comparison studies (e.g. aCGH, DNA metylation) in which test and control groups are analyzed together (using Tiling Array Software (TAS), for instance)."]
["# A complete submission will consist of: (1) a completed metadata worksheet, (2) the primary analysis results files (usually BAR/BED but can also be other file types), and (3) the original CEL files."]
["# Click the Metadata Example tab below to view a completed worksheet"]
["# Field names (in blue on this page) should not be edited. Hover over cells containing field names to view field content guidelines or, "]
["# CLICK HERE for Field Content Guidelines Web page."]
[]
["SERIES"]
["# This section describes the overall experiment."]
[]
["title"]
["summary"]
["summary"]
["overall design"]
["contributor"]
["contributor (SEEKID)"]
["SEEK Project","Project"]
["Experiment Class (assay Type)","transcripomics"]
["Experiment Design type","ExperimentDesignType"]
["Technology type","microarray"]
["quality control type","QualityControlDescriptionType"]
[]
["SAMPLES"]
["# The Sample names in the first column are arbitrary"]
["# CLICK HERE to find the Affymetrix platform accession number (GPLxxxx)."]
[]
["Sample name","title","results file","test: source name","test: CEL file","test: organism","characteristics:NCBI_ID","characteristics:Strain","characteristics:Genotype","characteristics:Phenotype","test: characteristics: tag","test: molecule","test: label","ctrl: source name","ctrl: CEL file","ctrl: organism","ctrl: characteristics: tag","ctrl: molecule","ctrl: label","description","platform"]
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[]
[]
["PROTOCOLS"]
["# This section includes protocols and fields which are common to all Samples."]
["# Protocols which are applicable to specific Samples (i.e. test or control) should be included in additional columns of the SAMPLES section instead."]
[]
["growth protocol"]
["treatment protocol"]
["extract protocol"]
["label protocol"]
["hyb protocol"]
["scan protocol"]
["data processing"]
["additional results files"]
["results file descriptions"]

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["SERIES"]
["title","Genome-Wide Gli3 Binding Sites in the E11.5 Mouse Limb Bud"]
["summary","Sonic hedgehog (Shh) signals via Gli transcription factors to direct digit number and identity in the vertebrate limb. We have characterized the Gli-dependent cis-regulatory network through a combination of whole genome ChIP-on-chip and transcriptional profiling of the developing mouse limb. These analyses identified approximately 5,000 high quality Gli3 binding sites, including all known Gli-dependent enhancers. Discrete binding regions exhibit a higher-order clustering, highlighting the complexity of cis-regulatory interactions. Further, Gli3 binds inertly to previously identified neural-specific Gli enhancers, demonstrating the accessibility of their cis-regulatory elements. Intersection of DNA binding data with gene expression profiles predicted 205 putative limb target genes."]
["summary","The supplementary bed file contains all 5,274 high quality binding Gli3 binding sites reported in the paper."]
["overall design","RosaGli3T-FLAG limb buds ChIPed with FLAG (Gli3-repressor binding sites) vs. Input in E11.5 mouse limb buds."]
["contributor","Hongkai,,Ji"]
["contributor","Steven,A,Vokes"]
[]
["SAMPLES"]
["# The corresponding example matrix table is included in the next worksheet."]
["Sample name","title","results file","results file","test: source name","test: CEL file","test: CEL file","test: CEL file","test: organism","test: characteristics: age","test: characteristics: tissue","test: characteristics: tissue","test: characteristics: antibody","test: molecule","test: label","ctrl: source name","ctrl: CEL file","ctrl: CEL file","ctrl: CEL file","ctrl: organism","ctrl: characteristics: age","ctrl: characteristics: tissue","ctrl: characteristics: tissue","ctrl: characteristics: antibody","ctrl: molecule","ctrl: label","description","platform"]
["Gli3Genome_mm8_1","Gli3Genome_mm8_1","Gli3Genome_mm8_1.fc.bar","Gli3Genome_mm8_1.ma.bar","FLAG ChIP DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds","060706_ChIP(A)_Gli3T_1_31.CEL","060723_ChIP(A)_Gli3T_2_02.CEL","060725_ChIP(A)_Gli3T_2_03.CEL","Mus musculus","E11.5","embryo","limb buds","FLAG M2 mouse monoclonal","genomic DNA","biotin","Input DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds","060706_Input(A)_Gli3T_1_31.CEL","060723_Input(A)_Gli3T_2_02.CEL","060725_Input(A)_Gli3T_2_03.CEL","Mus musculus","E11.5","embryo","limb buds","none","genomic DNA","biotin","GLI3 ChIP Biological Rep 1-3, chip A","GPL6444"]
["Gli3Genome_mm8_2","Gli3Genome_mm8_2","Gli3Genome_mm8_2.fc.bar","Gli3Genome_mm8_2.ma.bar","FLAG ChIP DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds","060706_ChIP(B)_Gli3T_1_31.CEL","060723_ChIP(B)_Gli3T_2_02.CEL","060725_ChIP(B)_Gli3T_2_03.CEL","Mus musculus","E11.5","embryo","limb buds","FLAG M2 mouse monoclonal","genomic DNA","biotin","Input DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds","060706_Input(B)_Gli3T_1_31_Rescan.CEL","060723_Input(B)_Gli3T_2_02.CEL","060725_Input(B)_Gli3T_2_03.CEL","Mus musculus","E11.5","embryo","limb buds","none","genomic DNA","biotin","GLI3 ChIP Biological Rep 1-3, chip B","GPL6445"]
["Gli3Genome_mm8_3","Gli3Genome_mm8_3","Gli3Genome_mm8_3.fc.bar","Gli3Genome_mm8_3.ma.bar","FLAG ChIP DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds","060706_ChIP(C)_Gli3T_1_31.CEL","060723_ChIP(C)_Gli3T_2_02.CEL","060725_ChIP(C)_Gli3T_2_03.CEL","Mus musculus","E11.5","embryo","limb buds","FLAG M2 mouse monoclonal","genomic DNA","biotin","Input DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds","060706_Input(C)_Gli3T_1_31.CEL","060723_Input(C)_Gli3T_2_02.CEL","060815_Input(C)_Gli3T_2_03.CEL","Mus musculus","E11.5","embryo","limb buds","none","genomic DNA","biotin","GLI3 ChIP Biological Rep 1-3, chip C","GPL6446"]
["Gli3Genome_mm8_4","Gli3Genome_mm8_4","Gli3Genome_mm8_4.fc.bar","Gli3Genome_mm8_4.ma.bar","FLAG ChIP DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds","060706_ChIP(D)_Gli3T_1_31.CEL","060723_ChIP(D)_Gli3T_2_02.CEL","060725_ChIP(D)_Gli3T_2_03.CEL","Mus musculus","E11.5","embryo","limb buds","FLAG M2 mouse monoclonal","genomic DNA","biotin","Input DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds","060706_Input(D)_Gli3T_1_31.CEL","060723_Input(D)_Gli3T_2_02.CEL","060725_Input(D)_Gli3T_2_03.CEL","Mus musculus","E11.5","embryo","limb buds","none","genomic DNA","biotin","GLI3 ChIP Biological Rep 1-3, chip D","GPL6447"]
["Gli3Genome_mm8_5","Gli3Genome_mm8_5","Gli3Genome_mm8_5.fc.bar","Gli3Genome_mm8_5.ma.bar","FLAG ChIP DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds","060706_ChIP(E)_Gli3T_1_31.CEL","060724_ChIP(E)_Gli3T_2_02.CEL","060726_ChIP(E)_Gli3T_2_03.CEL","Mus musculus","E11.5","embryo","limb buds","FLAG M2 mouse monoclonal","genomic DNA","biotin","Input DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds","060706_Input(E)_Gli3T_1_31.CEL","060724_Input(E)_Gli3T_2_02.CEL","060726_Input(E)_Gli3T_2_03.CEL","Mus musculus","E11.5","embryo","limb buds","none","genomic DNA","biotin","GLI3 ChIP Biological Rep 1-3, chip E","GPL6448"]
["Gli3Genome_mm8_6","Gli3Genome_mm8_6","Gli3Genome_mm8_6.fc.bar","Gli3Genome_mm8_6.ma.bar","FLAG ChIP DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds","060706_ChIP(F)_Gli3T_1_31.CEL","060724_ChIP(F)_Gli3T_2_02.CEL","060726_ChIP(F)_Gli3T_2_03.CEL","Mus musculus","E11.5","embryo","limb buds","FLAG M2 mouse monoclonal","genomic DNA","biotin","Input DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds","060706_Input(F)_Gli3T_1_31.CEL","060724_Input(F)_Gli3T_2_02.CEL","060726_Input(F)_Gli3T_2_03.CEL","Mus musculus","E11.5","embryo","limb buds","none","genomic DNA","biotin","GLI3 ChIP Biological Rep 1-3, chip F","GPL6449"]
["Gli3Genome_mm8_7","Gli3Genome_mm8_7","Gli3Genome_mm8_7.fc.bar","Gli3Genome_mm8_7.ma.bar","FLAG ChIP DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds","060706_ChIP(G)_Gli3T_1_31.CEL","060724_ChIP(G)_Gli3T_2_02.CEL","060726_ChIP(G)_Gli3T_2_03.CEL","Mus musculus","E11.5","embryo","limb buds","FLAG M2 mouse monoclonal","genomic DNA","biotin","Input DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds","060706_Input(G)_Gli3T_1_31.CEL","060724_Input(G)_Gli3T_2_02.CEL","060815_Input(G)_Gli3T_2_03.CEL","Mus musculus","E11.5","embryo","limb buds","none","genomic DNA","biotin","GLI3 ChIP Biological Rep 1-3, chip G","GPL6450"]
["Gli1Promoter_mm8","Gli1Promoter_mm8","Gli1Limb_peak_1.fc.bar","Gli1Limb_peak_1.ma.bar","FLAG ChIP DNA from E11.5 Prrx1Cre;Gli1-Flag limb buds","060605_ChIP_Gli1_4_10.CEL","060605_ChIP_Gli1_4_11.CEL","060605_ChIP_Gli1_5_22.CEL","Mus musculus","E11.5","embryo","limb buds","FLAG M2 mouse monoclonal","genomic DNA","biotin","Input DNA from E11.5 Prrx1Cre;Gli1-Flag limb buds","060605_Input_Gli1_4_10.CEL","060605_Input_Gli1_4_11.CEL","060605_Input_Gli1_5_22.CEL","Mus musculus","E11.5","embryo","limb buds","none","genomic DNA","biotin","GLI1 ChIP Biological Rep 1-3, promoter","GPL5811"]
["Gli3Promoter_mm8","Gli3Promoter_mm8","Gli3Limb_peak_1.fc.bar","Gli3Limb_peak_1.ma.bar","FLAG ChIP DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds","060504_ChIP_GliAct_EB.CEL","516_ChIP_Gli3T_5_10.CEL","060516_ChIP_Gli3T_5_8.CEL","Mus musculus","E11.5","embryo","limb buds","FLAG M2 mouse monoclonal","genomic DNA","biotin","Input DNA from E11.5 Prrx1Cre;Gli3T-Flag limb buds","060504_Input_EB.CEL","060516_Input_Gli3T_5_11.CEL","060516_Input_Gli3T_5_8.CEL","Mus musculus","E11.5","embryo","limb buds","none","genomic DNA","biotin","GLI3 ChIP Biological Rep 1-3, promoter","GPL5811"]
["Ant_K4","Ant_K4","Ant_K4_1.fc.bar","Ant_K4_1.ma.bar","H3K4me3 ChIP DNA from E11.5 anterior limb buds","060926_ChIP_Ant_K4.CEL","061006_ChIP_Ant_K4.CEL",null,"Mus musculus","E11.5","embryo","limb buds (anterior 1/3d)","H3K4Me3","genomic DNA","biotin","Input DNA from E11.5 anterior limb buds","060926_ChIP_Ant_Input.CEL","061006_ChIP_Ant_Input.CEL",null,"Mus musculus","E11.5","embryo","limb buds (anterior 1/3d)","none","genomic DNA","biotin","H3K4 ChIP Anterior Limb Bud, Biological Rep 1-3, promoter","GPL5811"]
["Ant_K27","Ant_K27","Ant_K27_1.fc.bar","Ant_K27_1.ma.bar","H3K27me3 ChIP DNA from E11.5 anterior limb buds","060926_ChIP_Ant_K27.CEL","061006_ChIP_Ant_K27.CEL",null,"Mus musculus","E11.5","embryo","limb buds (anterior 1/3d)","H3K27Me3","genomic DNA","biotin","Input DNA from E11.5 anterior limb buds","060926_ChIP_Ant_Input.CEL","061006_ChIP_Ant_Input.CEL",null,"Mus musculus","E11.5","embryo","limb buds (anterior 1/3d)","none","genomic DNA","biotin","H3K27 ChIP Anterior Limb Bud, Biological Rep 1-3, promoter","GPL5811"]
["Ant_PanH3","Ant_PanH3","Ant_PanH3_1.fc.bar","Ant_PanH3_1.ma.bar","Pan Histone H3 ChIP DNA from E11.5 anterior limb buds","060926_ChIP_Ant_PanH3.CEL","061006_ChIP_Ant_PanH3.CEL",null,"Mus musculus","E11.5","embryo","limb buds (anterior 1/3d)","Histone H3","genomic DNA","biotin","Input DNA from E11.5 anterior limb buds","060926_ChIP_Ant_Input.CEL","061006_ChIP_Ant_Input.CEL",null,"Mus musculus","E11.5","embryo","limb buds (anterior 1/3d)","none","genomic DNA","biotin","PanH3 ChIP Anterior Limb Bud, Biological Rep 1-3, promoter","GPL5811"]
["Post_K4","Post_K4","Post_K4_1.fc.bar","Post_K4_1.ma.bar","H3K4me3 ChIP DNA from E11.5 posterior limb buds","060926_ChIP_Post_K4.CEL","061006_ChIP_Post_K4.CEL",null,"Mus musculus","E11.5","embryo","limb buds (posterior 2/3d)","H3K4Me3","genomic DNA","biotin","Input DNA from E11.5 posterior limb buds","060926_ChIP_Post_Input.CEL","061006_ChIP_Post_Input.CEL",null,"Mus musculus","E11.5","embryo","limb buds (posterior 2/3d)","none","genomic DNA","biotin","H3K4 ChIP Posterior Limb Bud, Biological Rep 1-3, promoter","GPL5811"]
["Post_K27","Post_K27","Post_K27_1.fc.bar","Post_K27_1.ma.bar","H3K27me3 ChIP DNA from E11.5 posterior limb buds","060926_ChIP_Post_K27.CEL","061006_ChIP_Post_K27.CEL",null,"Mus musculus","E11.5","embryo","limb buds (posterior 2/3d)","H3K27Me3","genomic DNA","biotin","Input DNA from E11.5 posterior limb buds","060926_ChIP_Post_Input.CEL","061006_ChIP_Post_Input.CEL",null,"Mus musculus","E11.5","embryo","limb buds (posterior 2/3d)","none","genomic DNA","biotin","H3K27 ChIP Posterior Limb Bud, Biological Rep 1-3, promoter","GPL5811"]
["Post_PanH3","Post_PanH3","Post_PanH3_1.fc.bar","Post_PanH3_1.ma.bar","Pan Histone H3 ChIP DNA from E11.5 posterior limb buds","060926_ChIP_Post_PanH3.CEL","061006_ChIP_Post_PanH3.CEL",null,"Mus musculus","E11.5","embryo","limb buds (posterior 2/3d)","Histone H3","genomic DNA","biotin","Input DNA from E11.5 posterior limb buds","060926_ChIP_Post_Input.CEL","061006_ChIP_Post_Input.CEL",null,"Mus musculus","E11.5","embryo","limb buds (posterior 2/3d)","none","genomic DNA","biotin","PanH3 ChIP Posterior Limb Bud, Biological Rep 1-3, promoter","GPL5811"]
[]
[]
["PROTOCOLS"]
["growth protocol"]
["treatment protocol"]
["extract protocol","Rosa Gli3TFLAG c/c females mice were crossed with Prrx1Cre homozygous male drivers and litters were taken at E11.5. Embryos (generally 9) were dissected and forelimbs and hindlimbs were dissected into PBS, trypsinized in 300μl trypsin-EDTA for 5 minutes at 37º, inactivated by adding 700μl of DMEM with 10% calf serum, and cross-linked with 1% formaldehyde for 30 minutes. ChIP and LMPCR was performed according to our previous protocol (Vokes et al., 2007) with the following modifications. Chromatin was sonicated in 2ml of buffer 3 using 10x30 second pulses on a Branson 450 Sonifier (3 pulses on setting 4, then 7 on setting 5). For whole genome arrays, three ChIP reactions were set up in parallel with 500μl each (with 15μl of each biological sample reserved for an input control) – single promoter arrays used a single ChIP sample. At the final step, the samples were pooled and enrichment was validated using qPCR. For LMPCR, the pooled samples were divided into three and processed in parallel using 0.25mM dATP, dCTP, dGTP, 0.2mM dTTP and 0.05mM dUTP with 27 total cycles and then re-pooled after PCR cleanup. Each pooled set of reaction yielded >38μg of amplified sample. The linearity of amplification was confirmed by comparing qPCR values with the values from the unamplified samples."]
["label protocol","Samples (37.5-44μg of DNA) were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments"]
["hyb protocol","Approximately 8.25μg of DNA was hybridzed per array using the Affymetrix hybridization kit. For these 7 array sets, 4 arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven. The probe was removed from these arrays and reused to hybridize the remaining three arrays."]
["scan protocol","Arrays were scanned on an Affymetrix Scanner 3000 7G"]
["data processing","Data was quantile normalized and analyzed with TileMap. Log2(IP/Input) fold changes (fc) and TileMap moving average (ma) statistics were reported in BAR files."]
["additional results files","GLI3SD6.bed"]
["results file descriptions","fc.bar and ma.bar are generated by CisGenome software (previously TileMap). fc.bar contains log2(IP/Input) fold changes for each probe. ma.bar contains a moving average statistic (i.e. the MA statistic in TileMap) for each probe. File GLI3SD6.bed contains all 5,274 high quality binding Gli3 binding sites reported in the paper."]

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["<http://www.mygrid.org.uk/ontology/JERMOntology#BaCell>","BaCell"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#COSMIC>","COSMIC"]
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["<http://www.mygrid.org.uk/ontology/JERMOntology#MOSES>","MOSES"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Noisy-Strep>","Noisy-Strep"]
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["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#total_RNA>","total RNA"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#virus>","virus"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#whole_organism>","whole organism"]

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["ontology","<http://mged.sourceforge.net/ontologies/MGEDOntology.owl>","<http://rest.bioontology.org/bioportal/virtual/download/1131>"]
["ontology","<http://protege.stanford.edu/plugins/owl/protege>","<http://protege.stanford.edu/plugins/owl/protege>"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Bacillus_subtilis>","Bacillus subtilis"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Clostridium_acetobutylicum>","Clostridium acetobutylicum"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Enterococcus_faecalis>","Enterococcus faecalis"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Escherichia_coli>","Escherichia coli"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Lactococcus_lactis>","Lactococcus lactis"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Pseudomonas_fluorescens>","Pseudomonas fluorescens"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Pseudomonas_putida>","Pseudomonas putida"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Saccharomyces_cerevisiae>","Saccharomyces cerevisiae"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Streptococcus_pneumoniae>","Streptococcus pneumoniae"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Streptococcus_pyogenes>","Streptococcus pyogenes"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Streptomyces_coelicolor>","Streptomyces coelicolor"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Sulfolobus_solfataricus>","Sulfolobus solfataricus"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Trypanosoma_brucei>","Trypanosoma brucei"]

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["INDIVIDUALS","<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#LabelCompound>"]
["ontology","<http://www.mygrid.org.uk/ontology/JERMOntology>","<http://rest.bioontology.org/bioportal/virtual/download/1488>"]
["ontology","<http://mged.sourceforge.net/ontologies/MGEDOntology.owl>","<http://rest.bioontology.org/bioportal/virtual/download/1131>"]
["ontology","<http://protege.stanford.edu/plugins/owl/protege>","<http://protege.stanford.edu/plugins/owl/protege>"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#_32P>"," 32P"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#_33P>"," 33P"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_350>","alexa 350"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_430>","alexa 430"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_488>","alexa 488"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_532>","alexa 532"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_546>","alexa 546"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_568>","alexa 568"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_594>","alexa 594"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_633>","alexa 633"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_660>","alexa 660"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#alexa_680>","alexa 680"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#biotin>","biotin"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Cy3>","Cy3"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Cy5>","Cy5"]

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["SUBCLASSES","<http://www.mygrid.org.uk/ontology/JERMOntology#transcripomics>"]
["ontology","<http://www.mygrid.org.uk/ontology/JERMOntology>","<http://rest.bioontology.org/bioportal/virtual/download/1488>"]
["ontology","<http://mged.sourceforge.net/ontologies/MGEDOntology.owl>","<http://rest.bioontology.org/bioportal/virtual/download/1131>"]
["ontology","<http://protege.stanford.edu/plugins/owl/protege>","<http://protege.stanford.edu/plugins/owl/protege>"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Comparative_genomic_hybridization>","Comparative genomic hybridization"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#gene_expression_profiling>","gene expression profiling"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#methylation_profiling>","methylation profiling"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#microRNA_profiling>","microRNA profiling"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#RNAi>","RNAi"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#tiling_path>","tiling path"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#transcriptional_profiling>","transcriptional profiling"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#translational_profiling>","translational profiling"]

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["INDIVIDUALS","<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ExperimentDesignType>"]
["ontology","<http://mged.sourceforge.net/ontologies/MGEDOntology.owl>","<http://mged.sourceforge.net/ontologies/MGEDOntology.owl>"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#all_pairs>","all pairs"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#array_platform_variation_design>","array platform variation design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#binding_site_identification_design>","binding site identification design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cell_component_comparison_design>","cell component comparison design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cell_cycle_design>","cell cycle design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cell_type_comparison_design>","cell type comparison design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cellular_modification_design>","cellular modification design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cellular_process_design>","cellular process design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#clinical_history_design>","clinical history design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#co-expression_design>","co-expression design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#comparative_genome_hybridization_design>","comparative genome hybridization design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#compound_treatment_design>","compound treatment design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#development_or_differentiation_design>","development or differentiation design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#disease_state_design>","disease state design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#dose_response_design>","dose response design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#dye_swap_design>","dye swap design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#ex_vivo_design>","ex vivo design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#family_history_design>","family history design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#genetic_modification_design>","genetic modification design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#genotyping_design>","genotyping design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#growth_condition_design>","growth condition design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#hardware_variation_design>","hardware variation design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#imprinting_design>","imprinting design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#in_vitro_design>","in vitro design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#in_vivo_design>","in vivo design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#individual_genetic_characteristics_design>","individual genetic characteristics design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#injury_design>","injury design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#innate_behavior_design>","innate behavior design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#is_expressed_design>","is expressed design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#loop_design>","loop design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#non-targeted_transgenic_variation_design>","non-targeted transgenic variation design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#normalization_testing_design>","normalization testing design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#operator_variation_design>","operator variation design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#operon_identification_design>","operon identification design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#optimization_design>","optimization design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#organism_part_comparison_design>","organism part comparison design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#organism_status_design>","organism status design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#pathogenicity_design>","pathogenicity design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#physiological_process_design>","physiological process design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#quality_control_testing_design>","quality control testing design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#reference_design>","reference design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#replicate_design>","replicate design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#RNA_stability_design>","RNA stability design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#secreted_protein_identification_design>","secreted protein identification design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#self_vs_self_design>","self vs self design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#sex_design>","sex design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#software_variation_design>","software variation design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#species_design>","species design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#stimulated_design_type>","stimulated design type"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#stimulus_or_stress_design>","stimulus or stress design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#strain_or_line_design>","strain or line design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#tiling_path_design>","tiling path design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#time_series_design>","time series design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#transcript_identification_design>","transcript identification design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#translational_bias_design>","translational bias design"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_experiment_design_type>","unknown experiment design type"]

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["SUBCLASSES","<http://www.mygrid.org.uk/ontology/JERMOntology#microarray>"]
["ontology","<http://www.mygrid.org.uk/ontology/JERMOntology>","<http://rest.bioontology.org/bioportal/virtual/download/1488>"]
["ontology","<http://mged.sourceforge.net/ontologies/MGEDOntology.owl>","<http://rest.bioontology.org/bioportal/virtual/download/1131>"]
["ontology","<http://protege.stanford.edu/plugins/owl/protege>","<http://protege.stanford.edu/plugins/owl/protege>"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#ChIP-on-chip>","ChIP-on-chip"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#custom_Array>","custom Array"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#DNA_Methylation>","DNA Methylation"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Exon_array>","Exon array"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#miRNA_microarray>","miRNA microarray"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#small_molecule_microarray>","small molecule microarray"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#SNP_array>","SNP array"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#tiling_array>","tiling array"]

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["INDIVIDUALS","<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#QualityControlDescriptionType>"]
["ontology","<http://www.mygrid.org.uk/ontology/JERMOntology>","<http://rest.bioontology.org/bioportal/virtual/download/1488>"]
["ontology","<http://mged.sourceforge.net/ontologies/MGEDOntology.owl>","<http://rest.bioontology.org/bioportal/virtual/download/1131>"]
["ontology","<http://protege.stanford.edu/plugins/owl/protege>","<http://protege.stanford.edu/plugins/owl/protege>"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#biological_replicate>","biological replicate"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#dye_swap_quality_control>","dye swap quality control"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#peer_review_quality_control>","peer review quality control"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#real_time_PCR_quality_control>","real time PCR quality control"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#reverse_transcription_PCR_quality_control>","reverse transcription PCR quality control"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#spike_quality_control>","spike quality control"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#technical_replicate>","technical replicate"]

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["INDIVIDUALS","<http://www.mygrid.org.uk/ontology/JERMOntology#organism>"]
["ontology","<http://www.mygrid.org.uk/ontology/JERMOntology>","<http://rest.bioontology.org/bioportal/virtual/download/1488>"]
["ontology","<http://mged.sourceforge.net/ontologies/MGEDOntology.owl>","<http://rest.bioontology.org/bioportal/virtual/download/1131>"]
["ontology","<http://protege.stanford.edu/plugins/owl/protege>","<http://protege.stanford.edu/plugins/owl/protege>"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Bacillus_subtilis>","Bacillus subtilis"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Clostridium_acetobutylicum>","Clostridium acetobutylicum"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Enterococcus_faecalis>","Enterococcus faecalis"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Escherichia_coli>","Escherichia coli"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Lactococcus_lactis>","Lactococcus lactis"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Pseudomonas_fluorescens>","Pseudomonas fluorescens"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Pseudomonas_putida>","Pseudomonas putida"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Saccharomyces_cerevisiae>","Saccharomyces cerevisiae"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Streptococcus_pneumoniae>","Streptococcus pneumoniae"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Streptococcus_pyogenes>","Streptococcus pyogenes"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Streptomyces_coelicolor>","Streptomyces coelicolor"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Sulfolobus_solfataricus>","Sulfolobus solfataricus"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Trypanosoma_brucei>","Trypanosoma brucei"]