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Keywords {🔍}

chipseq, atacseq, encode, human, accessed, accession, jul, cleavage, bias, reads, protocol, snyder, data, dnaseseq, myers, hintatac, binding, footprints, cells, tfs, additional, methods, file, signals, sites, fig, fragments, dna, regions, correction, number, position, hhesc, based, figure, peaks, cell, article, protocols, distinct, genome, footprinting, size, libraries, higher, type, nfr, nucleosome, footprint, transcription,

Topics {✒️}

included double-hit dnase-seq single-cell atac-seq data updated open-access database perform omni-atac-seq experiments human h1-hesc produced dup auto –call-summits paired-end atac-seq libraries chip-seq encode accession atac-seq-based studies deposited strand-specific cleavage patterns helix-loop-helix families average atac-seq profile omni-atac protocol enrich protein-binding microarray data improve downstream analysis divide chip-seq peaks omin-atac-seq analysis strand-specific cleavage profiles average atac-seq profiles atac-seq protocol artifacts full size image omni-atac-seq protocol chip-seq peak summit explores strand-specific bias hint-atac significantly improves transposase-accessible chromatin sequencing related subjects //wwwncbinlmnihgov/geo/query/acccgi analyze atac-seq experiments sequence alignment/map format atac-seq protocols disfavor atac-seq protocols arises atac-seq data k562 atac-seq cleavage sites savitzky–golay smoothing filter providing atac-seq signals modeling dna-protein interactions sequence-specific cleavage bias tf chip-seq peaks double-hit dnase-seq tf chip-seq data atac-seq protocol determined batf3 chip-seq peaks naked dna atac-seq tf chip-seq experiments omni atac-seq data batf3 chip-seq data ctcf chip-seq peaks atac/dnase-seq data experiments including atac-seq

Questions {❓}

• Https://wwwncbinlmnihgov/geo/query/acccgi?

Schema {🗺️}

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         headline:Identification of transcription factor binding sites using ATAC-seq
         description:Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly understood for ATAC-seq. We propose the first footprinting method considering ATAC-seq protocol artifacts. HINT-ATAC uses a position dependency model to learn the cleavage preferences of the transposase. We observe strand-specific cleavage patterns around transcription factor binding sites, which are determined by local nucleosome architecture. By incorporating all these biases, HINT-ATAC is able to significantly outperform competing methods in the prediction of transcription factor binding sites with footprints.
         datePublished:2019-02-26T00:00:00Z
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            Open chromatin
            ATAC-seq
            Cleavage bias
            Animal Genetics and Genomics
            Human Genetics
            Plant Genetics and Genomics
            Microbial Genetics and Genomics
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      headline:Identification of transcription factor binding sites using ATAC-seq
      description:Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly understood for ATAC-seq. We propose the first footprinting method considering ATAC-seq protocol artifacts. HINT-ATAC uses a position dependency model to learn the cleavage preferences of the transposase. We observe strand-specific cleavage patterns around transcription factor binding sites, which are determined by local nucleosome architecture. By incorporating all these biases, HINT-ATAC is able to significantly outperform competing methods in the prediction of transcription factor binding sites with footprints.
      datePublished:2019-02-26T00:00:00Z
      dateModified:2019-02-26T00:00:00Z
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         Computational footprinting
         Open chromatin
         ATAC-seq
         Cleavage bias
         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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      name:Cluster of Excellence for Multimodal Computing and Interaction, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
      name:Computational Biology & Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
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      name:Department of Cell Biology, Institute of Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany
      name:Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
      name:Institute of Human Genetics, RWTH Aachen University Medical School, Aachen, Germany
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      name:Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Aachen, Germany
      name:Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany

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