Kang, DanielSherwood, RichardBarkal, AmiraHashimoto, TatsunoriEngstrom, LoganGifford, David2018-02-262017Kang, Daniel, Richard Sherwood, Amira Barkal, Tatsunori Hashimoto, Logan Engstrom, and David Gifford. 2017. “DNase-capture reveals differential transcription factor binding modalities.” PLoS ONE 12 (12): e0187046. doi:10.1371/journal.pone.0187046. http://dx.doi.org/10.1371/journal.pone.0187046.http://nrs.harvard.edu/urn-3:HUL.InstRepos:34868902We describe DNase-capture, an assay that increases the analytical resolution of DNase-seq by focusing its sequencing phase on selected genomic regions. We introduce a new method to compensate for capture bias called BaseNormal that allows for accurate recovery of transcription factor protection profiles from DNase-capture data. We show that these normalized data allow for nuanced detection of transcription factor binding heterogeneity with as few as dozens of sites.en-USBiology and Life SciencesComputational BiologyGenome AnalysisGenomic LibrariesGeneticsGenomicsBiology and life sciencesBiochemistryProteinsDNA-binding proteinsNucleasesDeoxyribonucleasesEnzymologyEnzymesHydrolasesDatabase and Informatics MethodsBioinformaticsSequence AnalysisSequence Motif AnalysisTranscription FactorsGene ExpressionGene RegulationRegulatory ProteinsAnimal GenomicsMammalian GenomicsDNADNA librariesNucleic acidsMolecular biologyMolecular biology techniquesMolecular probe techniquesProbe hybridizationDNA hybridizationGenetic LociJournal Article2018-02-2610.1371/journal.pone.0187046