2011
High Throughput Determination of TGFβ1/SMAD3 Targets in A549 Lung Epithelial Cells
Zhang Y, Handley D, Kaplan T, Yu H, Bais AS, Richards T, Pandit KV, Zeng Q, Benos PV, Friedman N, Eickelberg O, Kaminski N. High Throughput Determination of TGFβ1/SMAD3 Targets in A549 Lung Epithelial Cells. PLOS ONE 2011, 6: e20319. PMID: 21625455, PMCID: PMC3098871, DOI: 10.1371/journal.pone.0020319.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceCell LineChromatin ImmunoprecipitationDNA PrimersElectrophoretic Mobility Shift AssayEpithelial CellsHumansLungOligonucleotide Array Sequence AnalysisPromoter Regions, GeneticProtein BindingReverse Transcriptase Polymerase Chain ReactionSmad3 ProteinTransforming Growth Factor beta1ConceptsGene expression microarraysLung epithelial cellsMolecular pathwaysTranscriptional regulationExpression microarraysGlobal transcriptional regulationTGFβ1/Smad3Epithelial cellsHuman promoter regionsSignal transduction cascadeTarget gene expressionEpithelial cell phenotypeGene expression analysisTranscription factor Smad3Primary lung epithelial cellsSmad3 targetsQuantitative real-time RT-PCRFOXA2 promoterHuman A549 alveolar epithelial cellsChromatin immunoprecipitationTransduction cascadeTarget genesA549 lung epithelial cellsExpression analysisGene expression
2009
Features of Mammalian microRNA Promoters Emerge from Polymerase II Chromatin Immunoprecipitation Data
Corcoran DL, Pandit KV, Gordon B, Bhattacharjee A, Kaminski N, Benos PV. Features of Mammalian microRNA Promoters Emerge from Polymerase II Chromatin Immunoprecipitation Data. PLOS ONE 2009, 4: e5279. PMID: 19390574, PMCID: PMC2668758, DOI: 10.1371/journal.pone.0005279.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChromatin ImmunoprecipitationComputational BiologyCpG IslandsHumansMicroRNAsPromoter Regions, GeneticRNA Polymerase IIRNA, UntranslatedConceptsProtein coding genesMiRNA genesCoding genesIntragenic miRNAsPol II chromatin immunoprecipitationNon-coding RNA regulatorsRNA polymerase II promoterChromatin immunoprecipitation dataDiverse biological processesOwn unique promoterPolymerase II promoterTranscription start siteIntergenic miRNAsTranscription regulationMiRNA promotersRNA regulatorsChromatin immunoprecipitationPromoter organizationHost genesPrimary transcriptTranscript organizationStart siteImmunoprecipitation dataUnique promoterBiological processes