fragmentation buffer Thermo Fisher Search Results


  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    Thermo Fisher 10x fragmentation buffer
    10x Fragmentation Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/10x fragmentation buffer/product/Thermo Fisher
    Average 99 stars, based on 19 article reviews
    Price from $9.99 to $1999.99
    10x fragmentation buffer - by Bioz Stars, 2020-08
    99/100 stars
      Buy from Supplier

    90
    Thermo Fisher fragment buffer
    Fragment Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 69 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/fragment buffer/product/Thermo Fisher
    Average 90 stars, based on 69 article reviews
    Price from $9.99 to $1999.99
    fragment buffer - by Bioz Stars, 2020-08
    90/100 stars
      Buy from Supplier

    94
    Thermo Fisher fragmentation buffer
    Fragmentation Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 2264 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/fragmentation buffer/product/Thermo Fisher
    Average 94 stars, based on 2264 article reviews
    Price from $9.99 to $1999.99
    fragmentation buffer - by Bioz Stars, 2020-08
    94/100 stars
      Buy from Supplier

    88
    Thermo Fisher ambion s fragmentation buffer
    Ambion S Fragmentation Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ambion s fragmentation buffer/product/Thermo Fisher
    Average 88 stars, based on 8 article reviews
    Price from $9.99 to $1999.99
    ambion s fragmentation buffer - by Bioz Stars, 2020-08
    88/100 stars
      Buy from Supplier

    88
    Thermo Fisher fastap buffer
    Fastap Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 144 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/fastap buffer/product/Thermo Fisher
    Average 88 stars, based on 144 article reviews
    Price from $9.99 to $1999.99
    fastap buffer - by Bioz Stars, 2020-08
    88/100 stars
      Buy from Supplier

    99
    Thermo Fisher 5x fragmentation buffer
    5x Fragmentation Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 248 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/5x fragmentation buffer/product/Thermo Fisher
    Average 99 stars, based on 248 article reviews
    Price from $9.99 to $1999.99
    5x fragmentation buffer - by Bioz Stars, 2020-08
    99/100 stars
      Buy from Supplier

    94
    Thermo Fisher first strand buffer
    First Strand Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 9945 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/first strand buffer/product/Thermo Fisher
    Average 94 stars, based on 9945 article reviews
    Price from $9.99 to $1999.99
    first strand buffer - by Bioz Stars, 2020-08
    94/100 stars
      Buy from Supplier

    88
    Thermo Fisher zinc solution
    Zinc Solution, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 67 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/zinc solution/product/Thermo Fisher
    Average 88 stars, based on 67 article reviews
    Price from $9.99 to $1999.99
    zinc solution - by Bioz Stars, 2020-08
    88/100 stars
      Buy from Supplier

    88
    Thermo Fisher magnesium acetate buffer
    Magnesium Acetate Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 32 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/magnesium acetate buffer/product/Thermo Fisher
    Average 88 stars, based on 32 article reviews
    Price from $9.99 to $1999.99
    magnesium acetate buffer - by Bioz Stars, 2020-08
    88/100 stars
      Buy from Supplier

    92
    Thermo Fisher array fragmentation buffer
    Array Fragmentation Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/array fragmentation buffer/product/Thermo Fisher
    Average 92 stars, based on 11 article reviews
    Price from $9.99 to $1999.99
    array fragmentation buffer - by Bioz Stars, 2020-08
    92/100 stars
      Buy from Supplier

    99
    Thermo Fisher 3 ivt express kit
    3 Ivt Express Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 730 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/3 ivt express kit/product/Thermo Fisher
    Average 99 stars, based on 730 article reviews
    Price from $9.99 to $1999.99
    3 ivt express kit - by Bioz Stars, 2020-08
    99/100 stars
      Buy from Supplier

    93
    Thermo Fisher rnaseiii buffer
    Rnaseiii Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rnaseiii buffer/product/Thermo Fisher
    Average 93 stars, based on 15 article reviews
    Price from $9.99 to $1999.99
    rnaseiii buffer - by Bioz Stars, 2020-08
    93/100 stars
      Buy from Supplier

    91
    Thermo Fisher ambion fragmentation solution
    Ambion Fragmentation Solution, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 37 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ambion fragmentation solution/product/Thermo Fisher
    Average 91 stars, based on 37 article reviews
    Price from $9.99 to $1999.99
    ambion fragmentation solution - by Bioz Stars, 2020-08
    91/100 stars
      Buy from Supplier

    89
    Thermo Fisher alkaline hydrolysis buffer
    Alkaline Hydrolysis Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 89/100, based on 216 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/alkaline hydrolysis buffer/product/Thermo Fisher
    Average 89 stars, based on 216 article reviews
    Price from $9.99 to $1999.99
    alkaline hydrolysis buffer - by Bioz Stars, 2020-08
    89/100 stars
      Buy from Supplier

    99
    Thermo Fisher rna fragmentation buffer
    DMS-seq effectively probes <t>RNA</t> structures in E. coli . ( A ) Schematic for obtaining mRNA structure and translation efficiency using DMS-seq, mRNA-seq, and ribosome profiling from the same sample. ( B ) Plot showing the effect of DMS-seq read coverage on the reproducibility of structure determination. X-axis: DMS-seq read depth cutoff (reads/nucleotide); Y-axis: median of Pearson’s R values calculated by comparing two replicates of in vivo DMS-seq signals of the first 200nt of ORFs passing the DMS-seq depth cutoff indicated in X-axis. A read coverage of ~15 reads/nucleotide is sufficient for reproducible structure determination. ( C ) Receiver operating characteristic (ROC) curve on the in vivo DMS-seq signals for A and C bases in the 16S rRNA using the E.coli ribosome crystal structure ( Zhang et al., 2009 ) as a model. True positives are defined as bases that are both unpaired and solvent-accessible, and true negatives are bases that are paired. The total number of evaluated A/C bases is 438. Signal threshold of 0.2 has 90% agreement with the crystal structure. ( D ) Structural prediction for rimM . The predicted rimM structure is based on a minimum free-energy prediction constrained by our DMS-seq measurements, using the same 0.2 threshold used for the 16S rRNA in ( B ), which agrees with the rimM structure proposed and mutationally verified in Wikström et al. (1992 ). The DMS-seq signal across rimM is shown below the structure. The color bar indicates the intensity of the DMS-seq signal at each position. ( E ) Calculation of the Gini index from the DMS-seq signal is indicated schematically by comparing highly structured regions to less structured regions. For a region of mRNA, the cumulative fraction of the total DMS-seq signal is plotted against the cumulative fraction of the total number of positions as a Lorenz Curve. The extent to which the curve sags below the diagonal indicates the degree of inequality of distribution, which is quantified by the Gini index defined as the ratio of the area between the diagonal line and the Lorenz Curve (a) to the area below the diagonal line (a + b). A high Gini index indicates high level of mRNA structure, and vice versa. ( F ) Histogram of Gini indices of E. coli ORFs calculated from in vivo DMS-seq data at 37°C. All ORFs selected have ≥15 DMS-seq reads/nt (N = 1116). The Gini index of 16S rRNA and rimM , and the mean of Gini indices of in vitro heat-denatured mRNAs at <t>95°C</t> are indicated. DOI: http://dx.doi.org/10.7554/eLife.22037.003
    Rna Fragmentation Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 209 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna fragmentation buffer/product/Thermo Fisher
    Average 99 stars, based on 209 article reviews
    Price from $9.99 to $1999.99
    rna fragmentation buffer - by Bioz Stars, 2020-08
    99/100 stars
      Buy from Supplier

    93
    Thermo Fisher cold d hank s buffer
    DMS-seq effectively probes <t>RNA</t> structures in E. coli . ( A ) Schematic for obtaining mRNA structure and translation efficiency using DMS-seq, mRNA-seq, and ribosome profiling from the same sample. ( B ) Plot showing the effect of DMS-seq read coverage on the reproducibility of structure determination. X-axis: DMS-seq read depth cutoff (reads/nucleotide); Y-axis: median of Pearson’s R values calculated by comparing two replicates of in vivo DMS-seq signals of the first 200nt of ORFs passing the DMS-seq depth cutoff indicated in X-axis. A read coverage of ~15 reads/nucleotide is sufficient for reproducible structure determination. ( C ) Receiver operating characteristic (ROC) curve on the in vivo DMS-seq signals for A and C bases in the 16S rRNA using the E.coli ribosome crystal structure ( Zhang et al., 2009 ) as a model. True positives are defined as bases that are both unpaired and solvent-accessible, and true negatives are bases that are paired. The total number of evaluated A/C bases is 438. Signal threshold of 0.2 has 90% agreement with the crystal structure. ( D ) Structural prediction for rimM . The predicted rimM structure is based on a minimum free-energy prediction constrained by our DMS-seq measurements, using the same 0.2 threshold used for the 16S rRNA in ( B ), which agrees with the rimM structure proposed and mutationally verified in Wikström et al. (1992 ). The DMS-seq signal across rimM is shown below the structure. The color bar indicates the intensity of the DMS-seq signal at each position. ( E ) Calculation of the Gini index from the DMS-seq signal is indicated schematically by comparing highly structured regions to less structured regions. For a region of mRNA, the cumulative fraction of the total DMS-seq signal is plotted against the cumulative fraction of the total number of positions as a Lorenz Curve. The extent to which the curve sags below the diagonal indicates the degree of inequality of distribution, which is quantified by the Gini index defined as the ratio of the area between the diagonal line and the Lorenz Curve (a) to the area below the diagonal line (a + b). A high Gini index indicates high level of mRNA structure, and vice versa. ( F ) Histogram of Gini indices of E. coli ORFs calculated from in vivo DMS-seq data at 37°C. All ORFs selected have ≥15 DMS-seq reads/nt (N = 1116). The Gini index of 16S rRNA and rimM , and the mean of Gini indices of in vitro heat-denatured mRNAs at <t>95°C</t> are indicated. DOI: http://dx.doi.org/10.7554/eLife.22037.003
    Cold D Hank S Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 93/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/cold d hank s buffer/product/Thermo Fisher
    Average 93 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    cold d hank s buffer - by Bioz Stars, 2020-08
    93/100 stars
      Buy from Supplier

    85
    Thermo Fisher reaction employing 1x buffer
    DMS-seq effectively probes <t>RNA</t> structures in E. coli . ( A ) Schematic for obtaining mRNA structure and translation efficiency using DMS-seq, mRNA-seq, and ribosome profiling from the same sample. ( B ) Plot showing the effect of DMS-seq read coverage on the reproducibility of structure determination. X-axis: DMS-seq read depth cutoff (reads/nucleotide); Y-axis: median of Pearson’s R values calculated by comparing two replicates of in vivo DMS-seq signals of the first 200nt of ORFs passing the DMS-seq depth cutoff indicated in X-axis. A read coverage of ~15 reads/nucleotide is sufficient for reproducible structure determination. ( C ) Receiver operating characteristic (ROC) curve on the in vivo DMS-seq signals for A and C bases in the 16S rRNA using the E.coli ribosome crystal structure ( Zhang et al., 2009 ) as a model. True positives are defined as bases that are both unpaired and solvent-accessible, and true negatives are bases that are paired. The total number of evaluated A/C bases is 438. Signal threshold of 0.2 has 90% agreement with the crystal structure. ( D ) Structural prediction for rimM . The predicted rimM structure is based on a minimum free-energy prediction constrained by our DMS-seq measurements, using the same 0.2 threshold used for the 16S rRNA in ( B ), which agrees with the rimM structure proposed and mutationally verified in Wikström et al. (1992 ). The DMS-seq signal across rimM is shown below the structure. The color bar indicates the intensity of the DMS-seq signal at each position. ( E ) Calculation of the Gini index from the DMS-seq signal is indicated schematically by comparing highly structured regions to less structured regions. For a region of mRNA, the cumulative fraction of the total DMS-seq signal is plotted against the cumulative fraction of the total number of positions as a Lorenz Curve. The extent to which the curve sags below the diagonal indicates the degree of inequality of distribution, which is quantified by the Gini index defined as the ratio of the area between the diagonal line and the Lorenz Curve (a) to the area below the diagonal line (a + b). A high Gini index indicates high level of mRNA structure, and vice versa. ( F ) Histogram of Gini indices of E. coli ORFs calculated from in vivo DMS-seq data at 37°C. All ORFs selected have ≥15 DMS-seq reads/nt (N = 1116). The Gini index of 16S rRNA and rimM , and the mean of Gini indices of in vitro heat-denatured mRNAs at <t>95°C</t> are indicated. DOI: http://dx.doi.org/10.7554/eLife.22037.003
    Reaction Employing 1x Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/reaction employing 1x buffer/product/Thermo Fisher
    Average 85 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    reaction employing 1x buffer - by Bioz Stars, 2020-08
    85/100 stars
      Buy from Supplier

    88
    Thermo Fisher slidehyb glass array hybridization buffer
    DMS-seq effectively probes <t>RNA</t> structures in E. coli . ( A ) Schematic for obtaining mRNA structure and translation efficiency using DMS-seq, mRNA-seq, and ribosome profiling from the same sample. ( B ) Plot showing the effect of DMS-seq read coverage on the reproducibility of structure determination. X-axis: DMS-seq read depth cutoff (reads/nucleotide); Y-axis: median of Pearson’s R values calculated by comparing two replicates of in vivo DMS-seq signals of the first 200nt of ORFs passing the DMS-seq depth cutoff indicated in X-axis. A read coverage of ~15 reads/nucleotide is sufficient for reproducible structure determination. ( C ) Receiver operating characteristic (ROC) curve on the in vivo DMS-seq signals for A and C bases in the 16S rRNA using the E.coli ribosome crystal structure ( Zhang et al., 2009 ) as a model. True positives are defined as bases that are both unpaired and solvent-accessible, and true negatives are bases that are paired. The total number of evaluated A/C bases is 438. Signal threshold of 0.2 has 90% agreement with the crystal structure. ( D ) Structural prediction for rimM . The predicted rimM structure is based on a minimum free-energy prediction constrained by our DMS-seq measurements, using the same 0.2 threshold used for the 16S rRNA in ( B ), which agrees with the rimM structure proposed and mutationally verified in Wikström et al. (1992 ). The DMS-seq signal across rimM is shown below the structure. The color bar indicates the intensity of the DMS-seq signal at each position. ( E ) Calculation of the Gini index from the DMS-seq signal is indicated schematically by comparing highly structured regions to less structured regions. For a region of mRNA, the cumulative fraction of the total DMS-seq signal is plotted against the cumulative fraction of the total number of positions as a Lorenz Curve. The extent to which the curve sags below the diagonal indicates the degree of inequality of distribution, which is quantified by the Gini index defined as the ratio of the area between the diagonal line and the Lorenz Curve (a) to the area below the diagonal line (a + b). A high Gini index indicates high level of mRNA structure, and vice versa. ( F ) Histogram of Gini indices of E. coli ORFs calculated from in vivo DMS-seq data at 37°C. All ORFs selected have ≥15 DMS-seq reads/nt (N = 1116). The Gini index of 16S rRNA and rimM , and the mean of Gini indices of in vitro heat-denatured mRNAs at <t>95°C</t> are indicated. DOI: http://dx.doi.org/10.7554/eLife.22037.003
    Slidehyb Glass Array Hybridization Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 88/100, based on 63 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/slidehyb glass array hybridization buffer/product/Thermo Fisher
    Average 88 stars, based on 63 article reviews
    Price from $9.99 to $1999.99
    slidehyb glass array hybridization buffer - by Bioz Stars, 2020-08
    88/100 stars
      Buy from Supplier

    86
    Thermo Fisher divalent cation hydrolysis
    DMS-seq effectively probes <t>RNA</t> structures in E. coli . ( A ) Schematic for obtaining mRNA structure and translation efficiency using DMS-seq, mRNA-seq, and ribosome profiling from the same sample. ( B ) Plot showing the effect of DMS-seq read coverage on the reproducibility of structure determination. X-axis: DMS-seq read depth cutoff (reads/nucleotide); Y-axis: median of Pearson’s R values calculated by comparing two replicates of in vivo DMS-seq signals of the first 200nt of ORFs passing the DMS-seq depth cutoff indicated in X-axis. A read coverage of ~15 reads/nucleotide is sufficient for reproducible structure determination. ( C ) Receiver operating characteristic (ROC) curve on the in vivo DMS-seq signals for A and C bases in the 16S rRNA using the E.coli ribosome crystal structure ( Zhang et al., 2009 ) as a model. True positives are defined as bases that are both unpaired and solvent-accessible, and true negatives are bases that are paired. The total number of evaluated A/C bases is 438. Signal threshold of 0.2 has 90% agreement with the crystal structure. ( D ) Structural prediction for rimM . The predicted rimM structure is based on a minimum free-energy prediction constrained by our DMS-seq measurements, using the same 0.2 threshold used for the 16S rRNA in ( B ), which agrees with the rimM structure proposed and mutationally verified in Wikström et al. (1992 ). The DMS-seq signal across rimM is shown below the structure. The color bar indicates the intensity of the DMS-seq signal at each position. ( E ) Calculation of the Gini index from the DMS-seq signal is indicated schematically by comparing highly structured regions to less structured regions. For a region of mRNA, the cumulative fraction of the total DMS-seq signal is plotted against the cumulative fraction of the total number of positions as a Lorenz Curve. The extent to which the curve sags below the diagonal indicates the degree of inequality of distribution, which is quantified by the Gini index defined as the ratio of the area between the diagonal line and the Lorenz Curve (a) to the area below the diagonal line (a + b). A high Gini index indicates high level of mRNA structure, and vice versa. ( F ) Histogram of Gini indices of E. coli ORFs calculated from in vivo DMS-seq data at 37°C. All ORFs selected have ≥15 DMS-seq reads/nt (N = 1116). The Gini index of 16S rRNA and rimM , and the mean of Gini indices of in vitro heat-denatured mRNAs at <t>95°C</t> are indicated. DOI: http://dx.doi.org/10.7554/eLife.22037.003
    Divalent Cation Hydrolysis, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/divalent cation hydrolysis/product/Thermo Fisher
    Average 86 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    divalent cation hydrolysis - by Bioz Stars, 2020-08
    86/100 stars
      Buy from Supplier

    99
    Thermo Fisher ripa buffer
    DMS-seq effectively probes <t>RNA</t> structures in E. coli . ( A ) Schematic for obtaining mRNA structure and translation efficiency using DMS-seq, mRNA-seq, and ribosome profiling from the same sample. ( B ) Plot showing the effect of DMS-seq read coverage on the reproducibility of structure determination. X-axis: DMS-seq read depth cutoff (reads/nucleotide); Y-axis: median of Pearson’s R values calculated by comparing two replicates of in vivo DMS-seq signals of the first 200nt of ORFs passing the DMS-seq depth cutoff indicated in X-axis. A read coverage of ~15 reads/nucleotide is sufficient for reproducible structure determination. ( C ) Receiver operating characteristic (ROC) curve on the in vivo DMS-seq signals for A and C bases in the 16S rRNA using the E.coli ribosome crystal structure ( Zhang et al., 2009 ) as a model. True positives are defined as bases that are both unpaired and solvent-accessible, and true negatives are bases that are paired. The total number of evaluated A/C bases is 438. Signal threshold of 0.2 has 90% agreement with the crystal structure. ( D ) Structural prediction for rimM . The predicted rimM structure is based on a minimum free-energy prediction constrained by our DMS-seq measurements, using the same 0.2 threshold used for the 16S rRNA in ( B ), which agrees with the rimM structure proposed and mutationally verified in Wikström et al. (1992 ). The DMS-seq signal across rimM is shown below the structure. The color bar indicates the intensity of the DMS-seq signal at each position. ( E ) Calculation of the Gini index from the DMS-seq signal is indicated schematically by comparing highly structured regions to less structured regions. For a region of mRNA, the cumulative fraction of the total DMS-seq signal is plotted against the cumulative fraction of the total number of positions as a Lorenz Curve. The extent to which the curve sags below the diagonal indicates the degree of inequality of distribution, which is quantified by the Gini index defined as the ratio of the area between the diagonal line and the Lorenz Curve (a) to the area below the diagonal line (a + b). A high Gini index indicates high level of mRNA structure, and vice versa. ( F ) Histogram of Gini indices of E. coli ORFs calculated from in vivo DMS-seq data at 37°C. All ORFs selected have ≥15 DMS-seq reads/nt (N = 1116). The Gini index of 16S rRNA and rimM , and the mean of Gini indices of in vitro heat-denatured mRNAs at <t>95°C</t> are indicated. DOI: http://dx.doi.org/10.7554/eLife.22037.003
    Ripa Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 33949 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ripa buffer/product/Thermo Fisher
    Average 99 stars, based on 33949 article reviews
    Price from $9.99 to $1999.99
    ripa buffer - by Bioz Stars, 2020-08
    99/100 stars
      Buy from Supplier

    Image Search Results


    DMS-seq effectively probes RNA structures in E. coli . ( A ) Schematic for obtaining mRNA structure and translation efficiency using DMS-seq, mRNA-seq, and ribosome profiling from the same sample. ( B ) Plot showing the effect of DMS-seq read coverage on the reproducibility of structure determination. X-axis: DMS-seq read depth cutoff (reads/nucleotide); Y-axis: median of Pearson’s R values calculated by comparing two replicates of in vivo DMS-seq signals of the first 200nt of ORFs passing the DMS-seq depth cutoff indicated in X-axis. A read coverage of ~15 reads/nucleotide is sufficient for reproducible structure determination. ( C ) Receiver operating characteristic (ROC) curve on the in vivo DMS-seq signals for A and C bases in the 16S rRNA using the E.coli ribosome crystal structure ( Zhang et al., 2009 ) as a model. True positives are defined as bases that are both unpaired and solvent-accessible, and true negatives are bases that are paired. The total number of evaluated A/C bases is 438. Signal threshold of 0.2 has 90% agreement with the crystal structure. ( D ) Structural prediction for rimM . The predicted rimM structure is based on a minimum free-energy prediction constrained by our DMS-seq measurements, using the same 0.2 threshold used for the 16S rRNA in ( B ), which agrees with the rimM structure proposed and mutationally verified in Wikström et al. (1992 ). The DMS-seq signal across rimM is shown below the structure. The color bar indicates the intensity of the DMS-seq signal at each position. ( E ) Calculation of the Gini index from the DMS-seq signal is indicated schematically by comparing highly structured regions to less structured regions. For a region of mRNA, the cumulative fraction of the total DMS-seq signal is plotted against the cumulative fraction of the total number of positions as a Lorenz Curve. The extent to which the curve sags below the diagonal indicates the degree of inequality of distribution, which is quantified by the Gini index defined as the ratio of the area between the diagonal line and the Lorenz Curve (a) to the area below the diagonal line (a + b). A high Gini index indicates high level of mRNA structure, and vice versa. ( F ) Histogram of Gini indices of E. coli ORFs calculated from in vivo DMS-seq data at 37°C. All ORFs selected have ≥15 DMS-seq reads/nt (N = 1116). The Gini index of 16S rRNA and rimM , and the mean of Gini indices of in vitro heat-denatured mRNAs at 95°C are indicated. DOI: http://dx.doi.org/10.7554/eLife.22037.003

    Journal: eLife

    Article Title: Operon mRNAs are organized into ORF-centric structures that predict translation efficiency

    doi: 10.7554/eLife.22037

    Figure Lengend Snippet: DMS-seq effectively probes RNA structures in E. coli . ( A ) Schematic for obtaining mRNA structure and translation efficiency using DMS-seq, mRNA-seq, and ribosome profiling from the same sample. ( B ) Plot showing the effect of DMS-seq read coverage on the reproducibility of structure determination. X-axis: DMS-seq read depth cutoff (reads/nucleotide); Y-axis: median of Pearson’s R values calculated by comparing two replicates of in vivo DMS-seq signals of the first 200nt of ORFs passing the DMS-seq depth cutoff indicated in X-axis. A read coverage of ~15 reads/nucleotide is sufficient for reproducible structure determination. ( C ) Receiver operating characteristic (ROC) curve on the in vivo DMS-seq signals for A and C bases in the 16S rRNA using the E.coli ribosome crystal structure ( Zhang et al., 2009 ) as a model. True positives are defined as bases that are both unpaired and solvent-accessible, and true negatives are bases that are paired. The total number of evaluated A/C bases is 438. Signal threshold of 0.2 has 90% agreement with the crystal structure. ( D ) Structural prediction for rimM . The predicted rimM structure is based on a minimum free-energy prediction constrained by our DMS-seq measurements, using the same 0.2 threshold used for the 16S rRNA in ( B ), which agrees with the rimM structure proposed and mutationally verified in Wikström et al. (1992 ). The DMS-seq signal across rimM is shown below the structure. The color bar indicates the intensity of the DMS-seq signal at each position. ( E ) Calculation of the Gini index from the DMS-seq signal is indicated schematically by comparing highly structured regions to less structured regions. For a region of mRNA, the cumulative fraction of the total DMS-seq signal is plotted against the cumulative fraction of the total number of positions as a Lorenz Curve. The extent to which the curve sags below the diagonal indicates the degree of inequality of distribution, which is quantified by the Gini index defined as the ratio of the area between the diagonal line and the Lorenz Curve (a) to the area below the diagonal line (a + b). A high Gini index indicates high level of mRNA structure, and vice versa. ( F ) Histogram of Gini indices of E. coli ORFs calculated from in vivo DMS-seq data at 37°C. All ORFs selected have ≥15 DMS-seq reads/nt (N = 1116). The Gini index of 16S rRNA and rimM , and the mean of Gini indices of in vitro heat-denatured mRNAs at 95°C are indicated. DOI: http://dx.doi.org/10.7554/eLife.22037.003

    Article Snippet: Specifically, DMS treated mRNA samples were denatured for 2 min at 95°C and fragmented at 95°C for 2 min in 1x RNA fragmentation buffer (Zn2+ based, Ambion).

    Techniques: In Vivo, In Vitro