Publication: DNase-capture reveals differential transcription factor binding modalities
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Date
2017
Published Version
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Public Library of Science
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Citation
Kang, 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.
Research Data
Abstract
We 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.
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Keywords
Biology and Life Sciences, Computational Biology, Genome Analysis, Genomic Libraries, Genetics, Genomics, Biology and life sciences, Biochemistry, Proteins, DNA-binding proteins, Nucleases, Deoxyribonucleases, Enzymology, Enzymes, Hydrolases, Database and Informatics Methods, Bioinformatics, Sequence Analysis, Sequence Motif Analysis, Transcription Factors, Gene Expression, Gene Regulation, Regulatory Proteins, Animal Genomics, Mammalian Genomics, DNA, DNA libraries, Nucleic acids, Molecular biology, Molecular biology techniques, Molecular probe techniques, Probe hybridization, DNA hybridization, Genetic Loci
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