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Systematic evaluation of DNase-seq experimental parameters

ABSTRACT: We systematicaly evaluated two major factors, enzyme digestion level and fragment size, that would affect DNase-seq experiment. We found that while under- or over-digestion sigificantly decreases the DNase-seq signal, there is a broad range of suitable digestion level. In addition, we found fragment smaller than nucleosome size is optimal to identify transcription factor binding events.

ORGANISM(S): Homo sapiens

PROVIDER: GSE51915 | GEO | 2013/11/25

SECONDARY ACCESSION(S): PRJNA225824

REPOSITORIES: GEO

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Systematic evaluation of DNase-seq experimental parameters

Project description:We systematicaly evaluated two major factors, enzyme digestion level and fragment size, that would affect DNase-seq experiment. We found that while under- or over-digestion sigificantly decreases the DNase-seq signal, there is a broad range of suitable digestion level. In addition, we found fragment smaller than nucleosome size is optimal to identify transcription factor binding events. We tested digestion level of 5U, 25U, 50U, 75U, 100U and fragment size of 50-100bp, 100-200bp, 200-300bp

2013-11-25 | E-GEOD-51915 | biostudies-arrayexpress

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Systematic Evaluation of Parameters in RNA Cytosine Methylation Analysis

Project description:Systematic Evaluation of Parameters in RNA Cytosine Methylation Analysis

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