2010
Multi-targeted priming for genome-wide gene expression assays
Adomas AB, Lopez-Giraldez F, Clark TA, Wang Z, Townsend JP. Multi-targeted priming for genome-wide gene expression assays. BMC Genomics 2010, 11: 477. PMID: 20716356, PMCID: PMC3091673, DOI: 10.1186/1471-2164-11-477.Peer-Reviewed Original ResearchMeSH KeywordsDNA PrimersGene Expression ProfilingGene Expression Regulation, FungalGenes, FungalMetabolic Networks and PathwaysMyceliumNeurospora crassaNitrogenOligonucleotide Array Sequence AnalysisReproducibility of ResultsReverse Transcriptase Polymerase Chain ReactionReverse TranscriptionRNA, FungalRNA, MessengerSaccharomyces cerevisiaeSequence Analysis, RNAConceptsGene expressionGene expression assaysNeurospora crassaRibosomal RNAExpression assaysMost protein-coding genesEarly sexual developmentGenome-wide gene expressionTransfer RNA genesProtein-coding genesNitrogen starvation responseGenome of SaccharomycesPreponderance of genesGlobal gene expressionResponse of SaccharomycesCommon sequence motifsSexual developmentDetailed expression profilesReverse transcriptionRNA genesStarvation responseTag sequencingSequence motifsTransfer RNATranscriptomic assays
2005
Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination
Kasuga T, Townsend JP, Tian C, Gilbert LB, Mannhaupt G, Taylor JW, Glass NL. Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination. Nucleic Acids Research 2005, 33: 6469-6485. PMID: 16287898, PMCID: PMC1283539, DOI: 10.1093/nar/gki953.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBayes TheoremBlotting, NorthernCluster AnalysisDatabases, Nucleic AcidDictyosteliumExpressed Sequence TagsGene Expression ProfilingGenes, FungalNeurospora crassaOligonucleotide Array Sequence AnalysisOligonucleotide ProbesPromoter Regions, GeneticReproducibility of ResultsRNA, MessengerSpores, FungalTranscription, GeneticUstilagoConceptsConidial germinationGene expression levelsNeurospora crassaGene expressionPhytopathogenic fungus Ustilago maydisSocial amoeba Dictyostelium discoideumFilamentous ascomycete speciesPutative regulatory componentFungus Ustilago maydisAmoeba Dictyostelium discoideumExpression levelsAscomycete speciesRibosomal biogenesisRelative gene expression levelsNovel genesTranscriptional programsUstilago maydisTranscriptional profilingDictyostelium discoideumFunctional predictionTranscriptional mechanismsRegulatory componentsFilamentous fungiExpression profilesMicroarray profiling
2003
Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays
Townsend JP. Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays. BMC Genomics 2003, 4: 41. PMID: 14525623, PMCID: PMC239860, DOI: 10.1186/1471-2164-4-41.Peer-Reviewed Original Research