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Open Access Highly Accessed Methodology article

Standardized collection of MNase-seq experiments enables unbiased dataset comparisons

Jason M Rizzo12, Jonathan E Bard2 and Michael J Buck123*

Author Affiliations

1 Department of Biochemistry, State University of New York, Buffalo, NY, USA

2 Center of Excellence in Bioinformatics and Life Sciences, State University of New York, Buffalo, NY, USA

3 Genetics, Roswell Park Cancer Institute, Buffalo, NY, USA

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BMC Molecular Biology 2012, 13:15  doi:10.1186/1471-2199-13-15

Published: 6 May 2012

Additional files

Additional file 1:

Supplementary Protocol. Matched Micrococcal Nuclease Digestions.

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Additional file 2:

Supplemental Figure 1. Unmatched preparations show poor consistency in identifying changes in MNase protection signals. Supplemental Figure 2. Matched MNase digests identify biologically relevant differences in chromatin structure. Supplemental Figure 3. Comparison between wild-type and tup1? MNase-seq experiments at a single region of Tup1-dependent chromatin. Supplemental Figure 4. The ability of matched MNase digests to specifically detect biologically-relevant differences in chromatin structure is NOT dependent on dissimilarity cutoff values used in analysis. Supplemental Figure 5. MNase cut probability function for nucleosomal DNA templates. Supplemental Table 1: MNase-seq datasets used in this study.

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Additional file 3:

Supplemental Methods: Standardized MNase-seq Analysis.

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