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  • 99
    Thermo Fisher dnasei
    Dnasei, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dnasei/product/Thermo Fisher
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    dnasei - by Bioz Stars, 2021-04
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    99
    New England Biolabs dnasei
    Dnasei, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dnasei/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    dnasei - by Bioz Stars, 2021-04
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    86
    Roche dnasei
    CTCF footprint (a) Nucleotide resolution DNase cleavage frequencies across CTCF recognition sequences at CTCF ChIP-seq peaks in LNCaP. DNase-seq signals were normalized to 1M reads in a non-strand specific manner. Short 50-100bp fragments produce clearer cleavage signals than 100-200bp or 200-300bp fragments. (b) <t>DNaseI</t> enzyme strength is most effective for detecting CTCF cleavage patterns in the <t>25U-75U</t> range. (c) The positional distribution of oriented tags relative to the CTCF motif at CTCF ChIP-seq peaks in LNCaP reveals a strong directionality in the DNaseI cleavage pattern. Heatmaps show cleavage patterns at each locus for plus (red) and minus (blue) strands independently. The heatmap rows are ranked by the total DNase-seq tag count in each 100bp region. (d) The pattern of cleavage across the CTCF recognition sequence in naked DNA derived from the IMR90 cell line is very different from that observed in LNCaP chromatin at CTCF binding sites.
    Dnasei, supplied by Roche, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dnasei/product/Roche
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    dnasei - by Bioz Stars, 2021-04
    86/100 stars
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    99
    Millipore dnasei
    CTCF footprint (a) Nucleotide resolution DNase cleavage frequencies across CTCF recognition sequences at CTCF ChIP-seq peaks in LNCaP. DNase-seq signals were normalized to 1M reads in a non-strand specific manner. Short 50-100bp fragments produce clearer cleavage signals than 100-200bp or 200-300bp fragments. (b) <t>DNaseI</t> enzyme strength is most effective for detecting CTCF cleavage patterns in the <t>25U-75U</t> range. (c) The positional distribution of oriented tags relative to the CTCF motif at CTCF ChIP-seq peaks in LNCaP reveals a strong directionality in the DNaseI cleavage pattern. Heatmaps show cleavage patterns at each locus for plus (red) and minus (blue) strands independently. The heatmap rows are ranked by the total DNase-seq tag count in each 100bp region. (d) The pattern of cleavage across the CTCF recognition sequence in naked DNA derived from the IMR90 cell line is very different from that observed in LNCaP chromatin at CTCF binding sites.
    Dnasei, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dnasei/product/Millipore
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    dnasei - by Bioz Stars, 2021-04
    99/100 stars
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    Image Search Results


    CTCF footprint (a) Nucleotide resolution DNase cleavage frequencies across CTCF recognition sequences at CTCF ChIP-seq peaks in LNCaP. DNase-seq signals were normalized to 1M reads in a non-strand specific manner. Short 50-100bp fragments produce clearer cleavage signals than 100-200bp or 200-300bp fragments. (b) DNaseI enzyme strength is most effective for detecting CTCF cleavage patterns in the 25U-75U range. (c) The positional distribution of oriented tags relative to the CTCF motif at CTCF ChIP-seq peaks in LNCaP reveals a strong directionality in the DNaseI cleavage pattern. Heatmaps show cleavage patterns at each locus for plus (red) and minus (blue) strands independently. The heatmap rows are ranked by the total DNase-seq tag count in each 100bp region. (d) The pattern of cleavage across the CTCF recognition sequence in naked DNA derived from the IMR90 cell line is very different from that observed in LNCaP chromatin at CTCF binding sites.

    Journal: Nature methods

    Article Title: Analysis of optimized DNase-seq reveals intrinsic bias in transcription factor footprint identification

    doi: 10.1038/nmeth.2762

    Figure Lengend Snippet: CTCF footprint (a) Nucleotide resolution DNase cleavage frequencies across CTCF recognition sequences at CTCF ChIP-seq peaks in LNCaP. DNase-seq signals were normalized to 1M reads in a non-strand specific manner. Short 50-100bp fragments produce clearer cleavage signals than 100-200bp or 200-300bp fragments. (b) DNaseI enzyme strength is most effective for detecting CTCF cleavage patterns in the 25U-75U range. (c) The positional distribution of oriented tags relative to the CTCF motif at CTCF ChIP-seq peaks in LNCaP reveals a strong directionality in the DNaseI cleavage pattern. Heatmaps show cleavage patterns at each locus for plus (red) and minus (blue) strands independently. The heatmap rows are ranked by the total DNase-seq tag count in each 100bp region. (d) The pattern of cleavage across the CTCF recognition sequence in naked DNA derived from the IMR90 cell line is very different from that observed in LNCaP chromatin at CTCF binding sites.

    Article Snippet: Add 0U, 25U, 50U and 75U of DNaseI (Roche) respectively.

    Techniques: Chromatin Immunoprecipitation, Sequencing, Derivative Assay, Binding Assay

    Effect of digestion level and fragment size on recovering known transcription factor binding sites. (a) Proportion of ChIP-seq enriched regions discovered as DNaseI hypersensitive (DHS) sites for CTCF (left), androgen receptor (AR, center) and FOXA1 (right) in LNCaP cells. As the DNase-seq read depth strongly influences performance, for this comparison 15M reads were sampled from each experimental condition. In each heatmap, rows correspond to the DNaseI enzyme strength and columns represent fragment sizes. The colors represent the proportion of binding sites detected by DNase-seq. (b) Influence of read depth and fragment size on the overlap between TF binding sites and DHS sites. At the 50U strength the performance of the three size fractions are compared across a range of read depths. The results are consistent between different read depths, showing how shallow sampling is informative about the results obtained with deeper sequencing. Diminishing returns in performance with read depth, especially in the case of CTCF, shows that a vast increase in sequencing depth would be required before the 100-200bp and 200-300bp fragments could recover the proportion of CTCF binding sites that can be recovered by the 50-100bp fragments at a read depth of 30M.

    Journal: Nature methods

    Article Title: Analysis of optimized DNase-seq reveals intrinsic bias in transcription factor footprint identification

    doi: 10.1038/nmeth.2762

    Figure Lengend Snippet: Effect of digestion level and fragment size on recovering known transcription factor binding sites. (a) Proportion of ChIP-seq enriched regions discovered as DNaseI hypersensitive (DHS) sites for CTCF (left), androgen receptor (AR, center) and FOXA1 (right) in LNCaP cells. As the DNase-seq read depth strongly influences performance, for this comparison 15M reads were sampled from each experimental condition. In each heatmap, rows correspond to the DNaseI enzyme strength and columns represent fragment sizes. The colors represent the proportion of binding sites detected by DNase-seq. (b) Influence of read depth and fragment size on the overlap between TF binding sites and DHS sites. At the 50U strength the performance of the three size fractions are compared across a range of read depths. The results are consistent between different read depths, showing how shallow sampling is informative about the results obtained with deeper sequencing. Diminishing returns in performance with read depth, especially in the case of CTCF, shows that a vast increase in sequencing depth would be required before the 100-200bp and 200-300bp fragments could recover the proportion of CTCF binding sites that can be recovered by the 50-100bp fragments at a read depth of 30M.

    Article Snippet: Add 0U, 25U, 50U and 75U of DNaseI (Roche) respectively.

    Techniques: Binding Assay, Chromatin Immunoprecipitation, Sampling, Sequencing