« any species » Acanthamoeba polyphaga mimivirus Acidithiobacillus ferrooxidans Acinetobacter baumannii Actinobacillus pleuropneumoniae Acyrthosiphon pisum Aedes aegypti Aegilops tauschii Aegilops tauschii x Triticum turgidum Agrotis ipsilon Agrotis segetum Amphimedon queenslandica Anaplasma phagocytophilum Anas platyrhynchos Anguilla anguilla Anopheles gambiae Anopheles gambiae s.s. Apis cerana Apis dorsata Apis florea Apis mellifera Apis mellifera ligustica Apis mellifera natural colony Arabidopsis arenosa Arabidopsis halleri Arabidopsis lyrata Arabidopsis lyrata subsp. petraea Arabidopsis petraea Arabidopsis suecica Arabidopsis thaliana Ashbya gossypii Aspergillus clavatus Aspergillus fumigatus Aspergillus niger Aspergillus oryzae Austrofundulus limnaeus Bacillus anthracis Bacillus cereus Bacillus cereus ATCC 14579 Bacillus subtilis Bacillus subtilis strain 168 Bacillus thuringiensis Bt407 Bartonella grahamii Bartonella henselae Bartonella koehlerae Bartonella quintana Betula pendula Biomphalaria glabrata Bombyx mori Bordetella bronchiseptica Bordetella holmesii Bordetella parapertussis Bordetella pertussis Bordetella sp. Borrelia burgdorferi Bos indicus Bos taurus Brachypodium distachyon Branchiostoma belcheri Brassica juncea Brassica napus Brassica oleracea Brassica rapa Brassica rapa subsp. pekinensis Brucella abortus Brugia malayi Bubalus bubalis Buchnera aphidicola Buchnera sp. Burkholderia cepacia Burkholderia mallei Burkholderia pseudomallei Caenorhabditis briggsae Caenorhabditis elegans Caenorhabditis remanei Callipepla californica Callithrix jacchus Campylobacter jejuni Candida albicans Candida dubliniensis Candida glabrata Canis familiaris Cannabis sativa Capra hircus Capsella bursa pastoris Capsicum annuum Cardamine sp. SIM 2007 Carpus carpio Ceratopteris thalictroides Cervus elaphus Chlamydomonas reinhardtii Chlamydotis undulata Chlorocebus aethiops Chlorocebus sabaeus Chrysolophus amherstiae Chrysolophus pictus Ciona intestinalis Citrus aurantifolia Citrus clementina Clostridium acetobutylicum Clostridium botulinum Clostridium difficile Clostridium difficle Clostridium sporogenes Cocksfoot streak virus Colinus virginianus Coregonus clupeaformis Corynebacterium glutamicum Coturnix japonica Coxiella burnetii Cricetulus griseus Crocosphaera watsonii WH 8501 Cryptococcus gattii Cryptopygus antarcticus Cucumber mosaic virus Cucumber mosaic virus (strain FNY) Cucumis melo Cuscuta pentagona Cyanothece sp. Cyanothece sp. ATCC 51142 Cyclamen persicum Cymbidium ringspot virus Cyprinus carpio Danio rerio Daphnia magna Dickeya dadantii Dictyostelium discoideum Drosophila Drosophila erecta Drosophila mauritiana Drosophila melanogaster Drosophila melanogaster x Drosophila sechellia Drosophila pseudoobscura Drosophila santomea Drosophila sechellia Drosophila simulans Drosophila teissieri Drosophila yakuba Ectocarpus fasciulatus Ectocarpus siliculosus Ectomycorrhizal tissue: Paxillus involutus/Betula pendula Emiliania huxleyi Emiliania huxleyi CCMP1516 Entamoeba histolytica Enterococcus faecalis Equus caballus Erwinia chrysanthemi Escherichia coli Escherichia coli K 12 Escherichia coli K12 Escherichia coli O157:H7 Escherichia coli O157:H7 EDL933 Escherichia coli UTI89 Escherichia coli str. K 12 substr. MG1655 Escherichia coli str. K 12 substr. MG1656 Escherichia coli str. K 12 substr. MG1657 Escherichia coli str. K 12 substr. MG1658 Escherichia coli str. K 12 substr. MG1659 Escherichia coli str. K 12 substr. MG1660 Escherichia coli str. K 12 substr. MG1661 Escherichia coli str. K 12 substr. MG1662 Escherichia coli str. K 12 substr. W3110 Escherichia coli str. K12 substr. MG1655 Euphausia superba Falco chicquera Falco chiquera Falco rusticolus Felis catus Festuca arundinacea Festuca brevipila Festuca rubra subsp. fallax Festuca rubra subsp. littoralis Fragaria x ananassa Francisella tularensis Gadus morhua Gallus gallus Gasterosteus aculeatus Geobacter sulfurreducens Geospiza conirostris Geospiza difficilis Geospiza fortis Geospiza magnirostris Geospiza scandens Gephyrocapsa oceanica Gerbera hybrid cultivar Glycine max Gorilla gorilla Granulibacter bethesdensis Gyps africanus Gyps fulvus Gyps rueppelli Haemophilus influenzae Halobacterium salinarum Haloferax volcanii Harpagifer antarcticus Helicobacter pylori Herminiimonas arsenicoxydans Heterodera glycines Homo sapiens Hordeum vulgare Hordeum vulgare subsp. spontaneum Human adenovirus 5 Isochrysis galbana Lactobacillus sakei Lactobacillus salivarius Laternula elliptica Legionella longbeachae Legionella pneumophila Leishmania braziliensis Leishmania donovani Leishmania infantum Leishmania major Leishmania mexicana Lepeophteirus salmonis Lepeophtheirus salmonis Lepidium sativum Leymus cinereus Leymus triticoides Linum usitatissimum Liriodendron tulipifera Listeria monocytogenes Locusta migratoria Lolium perenne Lophura nycthemera Lotus burttii Lotus corniculatus Lotus filicaulis Lotus glaber Lotus japonicus Lotus uliginosus Lumbrius rubellus Lycopersicon esculentum Macaca fascicularis Macaca mulatta Macropus eugenii Magnaporthe oryzae Marmota monax Mastomys natalensis Medicago sativa Medicago truncatula Megaphorura arctica Melon necrotic spot virus Methanobacteria Methanobacterium thermoautotrophicum Methanococcoides burtonii Methanococcus jannaschii Methanosarcina mazei Miscanthus x giganteus Monacrosporium haptotylum Monodelphis domestica Monosiga brevicollis Mus Musculus Mus caroli Mus musculus Mus musculus castaneus Mus musculus domesticus Mus musculus musculus Mus musculus musculus x Mus musculus castaneus Mus musculus musculus x Mus musculus domesticus Mus musculus x Mus spretus Mus spretus Musa sp. Mycobacterium avium subspecies hominissuis Mycobacterium avium subspecies paratuberculosis Mycobacterium bovis Mycobacterium smegmatis Mycobacterium tuberculosis Mycobacterium tuberculosis H37Rv Mycosphaerella graminicola Mytilus californianus Neisseria cinerea Neisseria gonorrhoeae Neisseria lactamica Neisseria meningitidis Neisseria sp. Nematostella vectensis Neosartorya fennelliae Neosartorya fischeri Nicotiana benthamiana Nicotiana tabacum Oncorhynchus mykiss Oryza sativa Oryza sativa (indica cultivar group) Oryza sativa (japonica cultivar group) Oryza sativa Indica Group Oryza sativa Japonica Group Ovis aries Pan paniscus Pan troglodytes Papio anubis Papio hamadryas Paracoccidioides brasiliensis Pavo cristatus Paxillus filamentosus Paxillus involutus Pectobacterium atrosepticum Pectobacterium carotovorum Pepper mild mottle virus Peromyscus polionotus Petunia x hybrida Phaseolus coccineus Phaseolus vulgaris Phodopus sungorus Photobacterium profundum Physcomitrella patens Phytophthora sojae Picea glauca Pichia pastoris Pinus resinosa Pisum sativum Plasmodium berghei Plasmodium falciparum Plasmodium knowlesi Plasmodium yoelii Platichthys flesus Pleuronichthys verticalis Polistes metricus Polytrichum juniperinum Pongo pygmaeus Populus Populus balsamifera Populus euphratica Populus fremontii x Populus angustifolia Populus tremula Populus tremula x Populus alba Populus tremuloides Populus trichocarpa Populus trichocarpa x Populus deltoides Porphyromonas gingivalis Potato virus X Pristionchus pacificus Prochlorococcus marinus Pseudomonas aeruginosa Pseudomonas aeruginosa PAO1 Pseudomonas aeruginosa UCBPP PA14 Pseudomonas putida Ralstonia eutropha H16 Ralstonia pickettii Ralstonia solanacearum Ralstonia syzygii Rattus norvegicus Rattus rattus Rhizobium leguminosarum Ribes nigrum Rorippa amphibia Rorippa amphibia x Rorippa sylvestris Rorippa sylvestris Rubus idaeus SARS coronavirus Saccharomyces bayanus Saccharomyces bayanus x Saccharomyces cerevisiae Saccharomyces boulardii Saccharomyces cerevisiae Saccharomyces cerevisiae x Saccharomyces paradoxus Saccharomyces paradoxus Saccharomyces pastorianus Salmo salar Salmo trutta Salmon salar Salmonella bongori Salmonella enterica Salmonella enterica serotype Typhimurium Salmonella enterica serovar Typhimurium Salmonella enterica subspecies I Salmonella enteritidis Salmonella typhi Salmonella typhimurium Schistosoma japonicum Schistosoma mansoni Schizosaccharomyces pombe Schmidtea mediterranea Selaginella Senecio aethnensis Senecio cambrensis Senecio chrysanthemifolius Senecio squalidus subsp. squalidus Senecio vulgaris subsp. vulgaris Sinorhizobium meliloti Solanum lycopersicum Solanum tuberosum Sordaria macrospora Sparus auratus Staphylococcus aureus Strelkovimermis Streptococcus agalactiae Streptococcus gordonii Streptococcus mitis Streptococcus mutans UA159 Streptococcus pneumoniae Streptococcus pyogenes Streptococcus suis Streptomyces coelicolor Streptomyces coelicolor A3(2) Strongyloides ratti Sulfolobus acidocaldarius Sulfolobus solfataricus Sus scrofa Sylvia communis Synechococcus elongatus Synechococcus phage S PM2 Synechocystis sp. PCC 6803 Taeniopygia guttata Thermoproteus tenax Thiomonas sp. 3As Thlaspi caerulescens Tobacco rattle virus Tomato yellow leaf curl virus Toxoplasma gondii Treponema pallidum Tribolium castaneum Trichoderma reesei QM6a Trichomonas vaginalis Trichoplax adhaerens Trifolium repens Triticum aestivum Triticum turgidum subsp. dicoccoides Triticum turgidum subsp. durum Trypanosoma brucei Trypanosoma cruzi Turnip mosaic virus Veionella parvula Vibrio cholerae Vicia narbonensis Vigna unguiculata Vitis aestivalis Vitis hybrid cultivar Vitis riparia Vitis riparia x Vitis berlandieri Vitis rotundifolia Vitis vinifera Vulpes vulpes Watermelon mosaic virus Xenopus (Silurana) tropicalis Xenopus laevis Xenopus laevis x Xenopus muelleri Xenopus tropicalis Xylella fastidiosa Yersinia enterocolitica Yersinia pestis Yersinia pseudotuberculosis Youcai mosaic virus Zea mays Zymomonas mobilis null synthetic construct unknown

« any type » age all pairs all pairs antisense array comparison array platform variation behavior behavioral design type binding site identification binding site identification biological process biological replicate cell component comparison cell cycle cell process cell type comparison cell type comparison design, array platform comparison design, replicate design, co expression cell type comparisson cellular modification desig cellular modification cellular process chromatin immunoprecipitation classifier clinical history clinical treatment co expression co expression design disease state co expression design, disease state co expression design, individual genetic characteristics comarative genomic hybridization comparative genome hybridization comparative genome hybridization compound based compound treatment compound treatment design;co expression compound treatment desing compound treatment dsign data integration development or differentiation development or differentiation design,co expression development or differentiation design;transcription profiling developmenta stage disease stage disease state disease state design, in vivo design, co expression design, compound treatment disease state design, replicate design, co expression DNA methylation profiling dose response Dye swap dye swap environmental history environmental history envrionmental history ex vivo ex vivo ExperimentDesignType expression analysis family history gene mutation genetic modification genetic modification genetic modification design, in vivo design, comparative genome hybridization genetic variation genotype comparison genotyping grow condition growth condition Growth phase comparison growth condition hardware variation high throughput sequencing high throughput sequencing immunoprecipitation imprinting in vitro in vivo individual strain or line individual comparison individual comparison design,disease state individual genetic characteristics individual genetic characteristics design unknown design type individual genetic characteristics design, co expression individual genetic charactersitics individual genetics characteristics infection immunotherapy infection or injury injury innate behavior is expressed Logical Set loop metabolomics methylation profiling Mutant / Wild type comparison non targeted transgenic variation normalization testing operator variation operon identification optimization organism organism part comparison organism status pathogenicity perturbational phenotype physiological process quality control testing reference reference design, comparative genome hybridization design, disease state design, co expression replicate retrospective study RNA stability self vs self sequencing sex software variation species stimulated design type stimulus or stress stimulus or stress design,co expression strain or line strain abundance strain line strain line strain or line strain or line strain or line design;compound treatment tiling path time series time series transcript identification Transcription profiling of skeletal muscle after gene transfer by electroporation translational bias treatment unknown experiment design type

« any factor » # cells 15 metagroups 369 groups 4 metagroups 6 metagroups a rna yield action Age age age (years) age at diagnosis age(d) age(months) age(years) age at diagnosis agent albumin level alive at endpoint amount to core amount labeled extract amp labeling input mass amplification amplification batch antibody antibody catalog number antibody manufacturer ara c sensitivity assay type atmosphere batch behavior behaviour bio source bio material purity bio source bio source provider bio source type bioanalyzer results bioassay data transformation biopsy biopsy number biopsy site biosource type BioSourceProvider blood nonblood metagroups bmngrd buffer c rna yield ug cancer site carbon source castrated cell ine cell line cell surface antigens cell surface markers cell treatment cell type cell)line cell line cell property cell type CellLine cellular component change light chemotherapeutic response chemotherapy chemotherapy response chemotherapy treatment chip antibody chip antibody / mbd affinity column ChiP antibody chip antibody chip antibody chip column chip lot chip row chromosomal aberration chromosomal aberration classification chromosomal deletion chromosomal translocation circadian time (hrs after lights on) classifier clinial information clinical history clinical history age clinical history extra intestinal clinical history fibrostenotic clinical history fistula Clinical Information clinical information clinical treatment ClinicalHistory clinincal treatment cohort complex action compound compound1 compound2 compound based treatment compound treatment compund concentration condition control spike calibration coriell catalog id cover slip type cultivar culture culture density culture synchrony cultured cell type current milliamperes cycle phase/ gestational age damage intensity damage response data analysis algorithm data transformation protocol type dead of disease delay of relapse delivery method development of metastasis development stage developmental stage developmental time developmental stage developmental stage(units) dha diagnosis diet differentiation factor differentiation state differentiation state disease disease stage disease state disease status disease free survival disease location disease stage disease staging disease state DiseaseState distal recurrence distal recurrence time distance distant metastasis free survival donor Dose dose dose or concentration dose(ng/ml) dose(u m) dose(ug per l) dose(units) dose1 dose (n m) duration ebv status ecotype enviromental factor environment environmental stress environmental history environmental stress EnvironmentalHistory epigenetic status er er status erb b2 positive (ihc) estrogen receptor status ethnicity event death event distant metastases event free survival time exercise experiment experimental ExperimentalFactorCategory exposure external control ratio extraction protocol family history family relationship feature extraction final rna type fluidics machine fluidics station follow up followup time fraction fragment (size selected) Gender gender gene knock out generation genetic modification genetic modifiation genetic modification genetic trait GeneticModification genome/variation genomic region amplification genotype genotype/variation gentype geographic location gravity greowth condition group group assignment grow growth medium growth plate zone growth protocol growth stage growth temperature (°c) growth time growth conditiion growth condition growth condtion growth phase GROWTHCONDITION growthcondition GrowthCondition gsh localization harvest hcg treatment time hemoglobin level her2 fish her2 ihc her2 status histological subtype histology histology::type hormonal therapy host hours post fertilization hours post infection human chorionic gonadotropin (hcg) treatment hyb operator hybridization hybridization date hybridization volume hydrostatic pressure Immunoprecipitate immunoprecipitate in vivo treatment Individual individual individual id individual chromosomal abnormality individual genetic characteristic Infect infect infection condition infection duration (days) infection status initial time point injury integer international prognostic score (ips) irradiate irradiation Karyotype knock in expression label labeling laboratory Light light line lps lymph node stage lymph node status lymphocyte percentage material type media melanoma type metastasis molecular diagnosis mouse type mutant description mutation nbefore node positive nucleic acid nucleic acid extraction number of mice per chip number of injections nutrient composition nutrients Observation observation od260 od280 operator variation Organism organism organism part organism part organism status OrganismPart other other: fti treatment other: rin overall survival oxygen growth conditions p53 positive (ihc) passage passages pathogen pathogen test pathology diagnosis patient patient number pcr vs rd percent oxygen performer phase Phenotype phenotype physical characteristics plasmid plate location platform ploidy pmt gain pool pooled population pr status pretreatment progesterone receptor status prognostic subgroup Protocol protocol protocol type ptip status: race radiation sensitivity class radiation treatment radiotherapy (number of fractions; dose) ratio recurrence recurrence time region relapse type replicate replicate description type risk status rna integrity number rna integrity rna rin number RNAi rnai route of exposure Sample sample sample preservation sample type sample preparation kit sample preparation user sample time sample type sampling site sampling time sampling time point scanner scanner model serotype sex shear stress si rna siRNA sirna site site1 site2 slide number small rna capture method smoking status software software version Source: Organ species stage starvation stimulus stimulus or stress Strain strain/genotype strain or line StrainOrLine stress study sub array subject subtype surgery survey by magnetic resonance imaging survival time targeted cell type tbefore temperature temperature(degree c test test result Time time time (post inoculation) time point time(h) time(m) time(min) time(units) time9h) time before disease progression time of follow up time to development of distant metastases time unit tissue tissue origin tissue origin of cancer cell tissue type transfect transplant state Treatment treatment treatment code treatment group treatment protocol treatment repeat treatment time treatment variable treatment time treatments comments treatments comments: 00 005 treatments comments: 98 240 treatments comments: 99 146 tumor tumor biopsy origin tumor type tumor grading tumor location tumor percentage tumor reduction tumor size tumor size (mm) TumorStaging units of amount units of amount of vehicle units of dose or concentration units of duration units of treatment repeat units of treatment time vehicle vehicle for chemical wash white blood count zinc dose

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Ann Neurol Anticancer Res Antimicrob Agents Chemother Antimicrobial Agents Chemother Antimicrobial Agents Chemother (Bethesda) Antivir Ther (Lond) Appl Environ Microbiol Appl Microbiol Biotechnol April CS and Barsh GS (2007) PLoS Genet 3(1):e9 Aquat Toxicol Aquat. Toxicol Arch Biochem Biophys Arch Gen Psychiatry Arch Oral Biol Arch Physiol Biochem Arterioscler Thromb Vasc Biol Arteriosclerosis, Thrombosis, and Vascular Biology Arthitis Research Therapy Arthritis Res Ther Arthritis Rheum Assaad FF, et al. (2004) Mol Biol Cell 15(11):5118 29 Atherosclerosis BMC Bioinformatics BMC Biol BMC Biotechnol BMC Cancer BMC Cardiovasc Disord BMC Cell Biol BMC Dev Biol BMC Developmental Biology BMC Evol Biol BMC Genomics BMC Genomics. BMC Immunol BMC Med Genet BMC Med Genomics BMC Microbiol BMC Microbiol. 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« any type » #grow #hybridization #labeling #scanning #treatment acclimatization acquisition across bioassay data set function adjustment alignment and animal care array manufacturing array manufacturing protocol behavioral stimulus bioassay data transformation biological fluid collection biopsy cell culture cell growth and RNA isolation cell culture cell growth cell purification Cell subpopulation isolation compound Cultivation of S. meliloti strain 2011 cy3 labeling data collection data generation data transformation differential expression dissect dissection dye swap merge Extraction extraction Feature extraction feature extraction feature extraction flag filter fractionate genetic modification Grow grow Growth growth growth protocol harvest high throughput sequencing HigherLevelAnalysisProtocolType histological slide preparation Hybridisation hybridization image acquisition image acqusition image aquisition immunoprecipitate immunoprecipitation incubate infect inoculate irradiate Labeling labeling Labelling linear amplification loess group normalization loess scaled group normalization lowess group normalization lowess normalization mean log normalization median log normalization Mouse primary Megakaryocytes stage MK3: none. mouse CD1 day 14.5 fetal liver cultured megakaryocytes collected at day 3 Mouse primary Megakaryocytes stage MK4: none. mouse CD1 day 14.5 fetal liver cultured megakaryocytes collected at day 4 Mouse primary Megakaryocytes stage MK6: none. mouse CD1 day 14.5 fetal liver cultured megakaryocytes collected at day 6 Mouse primary Megakaryocytes stage MKP : none. mouse CD1 day 14.5 fetal liver cultured megakaryocytes collected at day 4 normalisation normalization normalization data transformation nucelic acid extraction nucleic acid extraction nucleic acid hybridization nucleic acid extraction PCR amplification pool pooling ProtocolType purify quality control quantification quantile normalization protocol type ratio statistics normalization replicate analysis reverse transcription RNA RNA Extraction RNA extraction sacrifice sample Sample Growth Conditions sample hybridization sample labeling Sample Treatment sample treatment protocol Sampling Scanning scanning protocol sequencing Skeletal muscle biopsy was obtained after a two hours of hyperinsulinaemic (40 mU/m2/min) euglycemic clamp. Muscle biopsy was obtained from the vastus lateralis muscle SkeSkeletal muscle biopsy was obtained before a two hours of hyperinsulinaemic (40 mU/m2/min) euglycemic clamp. Muscle biopsy was obtained from the vastus lateralis muscle specified biomaterial action spike preparation split starvation store Stress induction test Total RNA transcript profiling transfect Transformation transformation transformation protocol series unknown protocol type wash