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["# Use this template for 3' or whole Gene expression studies when summarization probe set data will be provided in Matrix table format"]
[]
[]
["Series"]
["# This section describes the overall experiment"]
["title"]
["Summary"]
["Overall Design description"]
["Experiment Class (assay Type)","methylation_profiling"]
["Experiment Design type","ExperimentDesignType"]
["Technology type","microarray"]
["quality control type","QualityControlDescriptionType"]
["contributer (person or SEEK ID)"]
["project","Project"]
[]
["Samples"]
["# The Sample names in the first column are arbitrary but they must match the column headers of the Matrix table (see next worksheet)."]
["#To find the Affymetrix platform accession numbers (GPLxxxx), go to http://www.ncbi.nlm.nih.gov/projects/geo/query/browse.cgi?mode=findplatform"]
["Sample name","title","CEL file","source name","organism","characteristics: Strain or line","characteristic:tag","moelcule","label","description","platform"]
["SAMPLE 1",null,null,null,"organism",null,null,"MaterialType","LabelCompound"]
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["SAMPLE 3",null,null,null,"organism",null,null,"MaterialType","LabelCompound"]
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["SAMPLE 7",null,null,null,"organism",null,null,"MaterialType","LabelCompound"]
["SAMPLE 8 ",null,null,null,"organism",null,null,"MaterialType","LabelCompound"]
["SAMPLE 9",null,null,null,"organism",null,null,"MaterialType","LabelCompound"]
["SAMPLE X",null,null,null,"organism",null,null,"MaterialType","LabelCompound"]
[]
[]
["Protocols"]
["# This section includes protocols and fields which are common to all Samples."]
["# Protocols which are applicable to specific Samples or specific channels 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"]
["value definition"]

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["# Template for an Affymetrix matrix table submission."]
["# The ID_REF column should include the full list of probeset ids of the Affymetrix array (see Matrix Example tabs at bottom)"]
["# The sample names in the Matrix table (e.g. 'SAMPLE 1') must match the Sample name in the SAMPLES section of the Metadata file."]
["# The Matrix table should include summarized/scaled/normalized probeset data generated by GC-RMA, dCHIP, MAS 5.0, or whatever algorithm/software was used for primary analysis."]
[]
["# P-values or other measurements can be added as additional columns for each sample "]
[]
["ID_REF","SAMPLE 1","SAMPLE 2","SAMPLE 3","SAMPLE 4","SAMPLE 5","SAMPLE 6","SAMPLE 7","SAMPLE 8","SAMPLE 9","SAMPLE X"]

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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>"]
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["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#miRNA_microarray>","miRNA_microarray"]
["<http://www.w3.org/2002/07/owl#Nothing>","Nothing"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#small_molecule_microarray>","small_molecule_microarray"]

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["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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["ontology","<http://protege.stanford.edu/plugins/owl/protege>","<http://protege.stanford.edu/plugins/owl/protege>"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#BaCell>","BaCell"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#COSMIC>","COSMIC"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#KOSMOBAC>","KOSMOBAC"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#MOSES>","MOSES"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Noisy-Strep>","Noisy-Strep"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#PSYSMO>","PSYSMO"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#ScaRAB>","ScaRAB"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#SilicoTryp>","SilicoTryp"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#STREAM>","STREAM"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#SulfoSys>","SulfoSys"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#SUMO>","SUMO"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#SysmoLab>","SysmoLab"]
["<http://www.mygrid.org.uk/ontology/JERMOntology#Translucent>","Translucent"]

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["SUBCLASSES","<http://www.mygrid.org.uk/ontology/JERMOntology#transcripomics>"]
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["<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.w3.org/2002/07/owl#Nothing>","Nothing"]
["<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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["<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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["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cell>","cell"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cell_lysate>","cell_lysate"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cytoplasmic_RNA>","cytoplasmic_RNA"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#DNA>","DNA"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#genomic_DNA>","genomic_DNA"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#molecular_mixture>","molecular_mixture"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#nuclear_RNA>","nuclear_RNA"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#organellar_DNA>","organellar_DNA"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#organellar_RNA>","organellar_RNA"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#organism_part>","organism_part"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#polyA_RNA>","polyA_RNA"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#protein>","protein"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#synthetic_DNA>","synthetic_DNA"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#synthetic_RNA>","synthetic_RNA"]
["<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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["<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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["<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"]

{"sheet":"wksowlv8","index":10,"n_rows":23,"n_cols":3,"rows_kept":23,"cut":false,"hidden":true,"merged":[],"flags":["formulas_cached_only"]}
["INDIVIDUALS","<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioMaterialCharacteristicCategory>"]
["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#age>","age"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#biomaterial_provider>","biomaterial_provider"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cell_line>","cell_line"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#cell_type>","cell_type"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#clinical_information>","clinical_information"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#clinical_treatment>","clinical_treatment"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#developmental_stage>","developmental_stage"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#disease_staging>","disease_staging"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#disease_state>","disease_state"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#individual>","individual"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#individual_genetic_characteristic>","individual_genetic_characteristic"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#organism>","organism"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#organism_part>","organism_part"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#organism_status>","organism_status"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#physical_characteristics>","physical_characteristics"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#sampling_time_point>","sampling_time_point"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#sex>","sex"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#strain_or_line>","strain_or_line"]
["<http://mged.sourceforge.net/ontologies/MGEDOntology.owl#tumor_grading>","tumor_grading"]