lambda gdna  (New England Biolabs)


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    New England Biolabs lambda gdna
    Assessing the impact of SYBR Green I quantity on real-time amplification profiles . Replicate amplification reactions were prepared using three commercial enzyme formulations supplemented with increasing amounts of SYBR Green I. Each amplification reaction contained 100 femtograms of <t>lambda</t> <t>gDNA</t> (1,876 genomes) and 500 μM of the primers K7B and K12. The gain setting for each run was adjusted to ensure that reaction fluorescence remained below the saturation level of the photomultiplier tube (about 40,000 FU). (A) , (C) and (E) Screen shots of amplification profiles generated by the Stratagene MxPro qPCR software. This reveals that fluorescence intensity is dependent on SYBR Green I quantity, reflected by the large increase in the height of the amplification profiles as SYBR Green I quantity is increased. (B) , (D) and (F) LRE plot of each respective amplification profile. This reveals a linear domain corresponding to the central region of each amplification profile, confirming the mathematical prediction that amplification efficiency is linearly coupled to amplicon quantity. A consecutive group of points was selected (designated by red circles) for linear regression analysis (referred to as
    Lambda Gdna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "A kinetic-based sigmoidal model for the polymerase chain reaction and its application to high-capacity absolute quantitative real-time PCR"

    Article Title: A kinetic-based sigmoidal model for the polymerase chain reaction and its application to high-capacity absolute quantitative real-time PCR

    Journal: BMC Biotechnology

    doi: 10.1186/1472-6750-8-47

    Assessing the impact of SYBR Green I quantity on real-time amplification profiles . Replicate amplification reactions were prepared using three commercial enzyme formulations supplemented with increasing amounts of SYBR Green I. Each amplification reaction contained 100 femtograms of lambda gDNA (1,876 genomes) and 500 μM of the primers K7B and K12. The gain setting for each run was adjusted to ensure that reaction fluorescence remained below the saturation level of the photomultiplier tube (about 40,000 FU). (A) , (C) and (E) Screen shots of amplification profiles generated by the Stratagene MxPro qPCR software. This reveals that fluorescence intensity is dependent on SYBR Green I quantity, reflected by the large increase in the height of the amplification profiles as SYBR Green I quantity is increased. (B) , (D) and (F) LRE plot of each respective amplification profile. This reveals a linear domain corresponding to the central region of each amplification profile, confirming the mathematical prediction that amplification efficiency is linearly coupled to amplicon quantity. A consecutive group of points was selected (designated by red circles) for linear regression analysis (referred to as
    Figure Legend Snippet: Assessing the impact of SYBR Green I quantity on real-time amplification profiles . Replicate amplification reactions were prepared using three commercial enzyme formulations supplemented with increasing amounts of SYBR Green I. Each amplification reaction contained 100 femtograms of lambda gDNA (1,876 genomes) and 500 μM of the primers K7B and K12. The gain setting for each run was adjusted to ensure that reaction fluorescence remained below the saturation level of the photomultiplier tube (about 40,000 FU). (A) , (C) and (E) Screen shots of amplification profiles generated by the Stratagene MxPro qPCR software. This reveals that fluorescence intensity is dependent on SYBR Green I quantity, reflected by the large increase in the height of the amplification profiles as SYBR Green I quantity is increased. (B) , (D) and (F) LRE plot of each respective amplification profile. This reveals a linear domain corresponding to the central region of each amplification profile, confirming the mathematical prediction that amplification efficiency is linearly coupled to amplicon quantity. A consecutive group of points was selected (designated by red circles) for linear regression analysis (referred to as "LRE analysis"), generating estimates for E max (intercept) and ΔE (slope), from which F max was calculated using equation 4 (see Figure 1 for additional details). Details as to how the boundaries of the linear region were determined are described later in the study. [SG] : quantity of supplementary SYBR Green I, r2 : linear regression correlation coefficient.

    Techniques Used: SYBR Green Assay, Amplification, Fluorescence, Generated, Software

    Optical calibrations of five reaction formulations supplemented with various quantities of SYBR Green I . Spreadsheet summary of the lambda gDNA (primer pair K7B-K12) optical calibrations conducted for the five reaction formulations used for LRE quantification in this study. Based on data presented in Figure 2, these formulations were designed to assess the impact of SYBR Green I quantity, the highest supplemented quantity (2.0X) estimated to be > 10X than that present in these three commercial formulations. Each row of values was derived from an individual amplification run (see additional file for more details). (A) QuantiTect 0X SYBR Green I. (B) QuantiTect 0.2X SYBR Green I. (C) DyNAmo 0.5X SYBR Green I. (D) DyNAmo 1.5X SYBR Green I. (E) FullVelocity 2.0X SYBR Green I. Lam : lambda gDNA quantity in femtograms, QT : QuantiTect, DyNa : DyNAmo; FV : FullVelocity, SG : SYBR Green I, SD : standard deviation, CV : coefficient of variation (SD/Average × 100%).
    Figure Legend Snippet: Optical calibrations of five reaction formulations supplemented with various quantities of SYBR Green I . Spreadsheet summary of the lambda gDNA (primer pair K7B-K12) optical calibrations conducted for the five reaction formulations used for LRE quantification in this study. Based on data presented in Figure 2, these formulations were designed to assess the impact of SYBR Green I quantity, the highest supplemented quantity (2.0X) estimated to be > 10X than that present in these three commercial formulations. Each row of values was derived from an individual amplification run (see additional file for more details). (A) QuantiTect 0X SYBR Green I. (B) QuantiTect 0.2X SYBR Green I. (C) DyNAmo 0.5X SYBR Green I. (D) DyNAmo 1.5X SYBR Green I. (E) FullVelocity 2.0X SYBR Green I. Lam : lambda gDNA quantity in femtograms, QT : QuantiTect, DyNa : DyNAmo; FV : FullVelocity, SG : SYBR Green I, SD : standard deviation, CV : coefficient of variation (SD/Average × 100%).

    Techniques Used: SYBR Green Assay, Derivative Assay, Amplification, Standard Deviation

    An example of primer-specific baseline drift . An extreme example of baseline drift produced by lambda primer K30. (A) Amplification profiles of 100 femtograms of lambda gDNA with K23 and K30 primers (blue profile), K30 alone with no lambda gDNA (green profile) and K23 alone with no lambda gDNA (red profile) with no baseline subtraction. (B) The same profiles following baseline subtraction (F b = average F C of cycles 7–18). This illustraties the distortions that can be produced by the MxPro software used in this study, which attempts to correct for the baseline drift by modifying the F C dataset. This can compromise, sometimes severely, the efficacy of LRE quantification, even in the absence of any apparent baseline drifting (data not shown)
    Figure Legend Snippet: An example of primer-specific baseline drift . An extreme example of baseline drift produced by lambda primer K30. (A) Amplification profiles of 100 femtograms of lambda gDNA with K23 and K30 primers (blue profile), K30 alone with no lambda gDNA (green profile) and K23 alone with no lambda gDNA (red profile) with no baseline subtraction. (B) The same profiles following baseline subtraction (F b = average F C of cycles 7–18). This illustraties the distortions that can be produced by the MxPro software used in this study, which attempts to correct for the baseline drift by modifying the F C dataset. This can compromise, sometimes severely, the efficacy of LRE quantification, even in the absence of any apparent baseline drifting (data not shown)

    Techniques Used: Produced, Amplification, Software

    lambda gdna  (New England Biolabs)


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    New England Biolabs lambda gdna
    Assessing the impact of SYBR Green I quantity on real-time amplification profiles . Replicate amplification reactions were prepared using three commercial enzyme formulations supplemented with increasing amounts of SYBR Green I. Each amplification reaction contained 100 femtograms of <t>lambda</t> <t>gDNA</t> (1,876 genomes) and 500 μM of the primers K7B and K12. The gain setting for each run was adjusted to ensure that reaction fluorescence remained below the saturation level of the photomultiplier tube (about 40,000 FU). (A) , (C) and (E) Screen shots of amplification profiles generated by the Stratagene MxPro qPCR software. This reveals that fluorescence intensity is dependent on SYBR Green I quantity, reflected by the large increase in the height of the amplification profiles as SYBR Green I quantity is increased. (B) , (D) and (F) LRE plot of each respective amplification profile. This reveals a linear domain corresponding to the central region of each amplification profile, confirming the mathematical prediction that amplification efficiency is linearly coupled to amplicon quantity. A consecutive group of points was selected (designated by red circles) for linear regression analysis (referred to as
    Lambda Gdna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "A kinetic-based sigmoidal model for the polymerase chain reaction and its application to high-capacity absolute quantitative real-time PCR"

    Article Title: A kinetic-based sigmoidal model for the polymerase chain reaction and its application to high-capacity absolute quantitative real-time PCR

    Journal: BMC Biotechnology

    doi: 10.1186/1472-6750-8-47

    Assessing the impact of SYBR Green I quantity on real-time amplification profiles . Replicate amplification reactions were prepared using three commercial enzyme formulations supplemented with increasing amounts of SYBR Green I. Each amplification reaction contained 100 femtograms of lambda gDNA (1,876 genomes) and 500 μM of the primers K7B and K12. The gain setting for each run was adjusted to ensure that reaction fluorescence remained below the saturation level of the photomultiplier tube (about 40,000 FU). (A) , (C) and (E) Screen shots of amplification profiles generated by the Stratagene MxPro qPCR software. This reveals that fluorescence intensity is dependent on SYBR Green I quantity, reflected by the large increase in the height of the amplification profiles as SYBR Green I quantity is increased. (B) , (D) and (F) LRE plot of each respective amplification profile. This reveals a linear domain corresponding to the central region of each amplification profile, confirming the mathematical prediction that amplification efficiency is linearly coupled to amplicon quantity. A consecutive group of points was selected (designated by red circles) for linear regression analysis (referred to as
    Figure Legend Snippet: Assessing the impact of SYBR Green I quantity on real-time amplification profiles . Replicate amplification reactions were prepared using three commercial enzyme formulations supplemented with increasing amounts of SYBR Green I. Each amplification reaction contained 100 femtograms of lambda gDNA (1,876 genomes) and 500 μM of the primers K7B and K12. The gain setting for each run was adjusted to ensure that reaction fluorescence remained below the saturation level of the photomultiplier tube (about 40,000 FU). (A) , (C) and (E) Screen shots of amplification profiles generated by the Stratagene MxPro qPCR software. This reveals that fluorescence intensity is dependent on SYBR Green I quantity, reflected by the large increase in the height of the amplification profiles as SYBR Green I quantity is increased. (B) , (D) and (F) LRE plot of each respective amplification profile. This reveals a linear domain corresponding to the central region of each amplification profile, confirming the mathematical prediction that amplification efficiency is linearly coupled to amplicon quantity. A consecutive group of points was selected (designated by red circles) for linear regression analysis (referred to as "LRE analysis"), generating estimates for E max (intercept) and ΔE (slope), from which F max was calculated using equation 4 (see Figure 1 for additional details). Details as to how the boundaries of the linear region were determined are described later in the study. [SG] : quantity of supplementary SYBR Green I, r2 : linear regression correlation coefficient.

    Techniques Used: SYBR Green Assay, Amplification, Fluorescence, Generated, Software

    Optical calibrations of five reaction formulations supplemented with various quantities of SYBR Green I . Spreadsheet summary of the lambda gDNA (primer pair K7B-K12) optical calibrations conducted for the five reaction formulations used for LRE quantification in this study. Based on data presented in Figure 2, these formulations were designed to assess the impact of SYBR Green I quantity, the highest supplemented quantity (2.0X) estimated to be > 10X than that present in these three commercial formulations. Each row of values was derived from an individual amplification run (see additional file for more details). (A) QuantiTect 0X SYBR Green I. (B) QuantiTect 0.2X SYBR Green I. (C) DyNAmo 0.5X SYBR Green I. (D) DyNAmo 1.5X SYBR Green I. (E) FullVelocity 2.0X SYBR Green I. Lam : lambda gDNA quantity in femtograms, QT : QuantiTect, DyNa : DyNAmo; FV : FullVelocity, SG : SYBR Green I, SD : standard deviation, CV : coefficient of variation (SD/Average × 100%).
    Figure Legend Snippet: Optical calibrations of five reaction formulations supplemented with various quantities of SYBR Green I . Spreadsheet summary of the lambda gDNA (primer pair K7B-K12) optical calibrations conducted for the five reaction formulations used for LRE quantification in this study. Based on data presented in Figure 2, these formulations were designed to assess the impact of SYBR Green I quantity, the highest supplemented quantity (2.0X) estimated to be > 10X than that present in these three commercial formulations. Each row of values was derived from an individual amplification run (see additional file for more details). (A) QuantiTect 0X SYBR Green I. (B) QuantiTect 0.2X SYBR Green I. (C) DyNAmo 0.5X SYBR Green I. (D) DyNAmo 1.5X SYBR Green I. (E) FullVelocity 2.0X SYBR Green I. Lam : lambda gDNA quantity in femtograms, QT : QuantiTect, DyNa : DyNAmo; FV : FullVelocity, SG : SYBR Green I, SD : standard deviation, CV : coefficient of variation (SD/Average × 100%).

    Techniques Used: SYBR Green Assay, Derivative Assay, Amplification, Standard Deviation

    An example of primer-specific baseline drift . An extreme example of baseline drift produced by lambda primer K30. (A) Amplification profiles of 100 femtograms of lambda gDNA with K23 and K30 primers (blue profile), K30 alone with no lambda gDNA (green profile) and K23 alone with no lambda gDNA (red profile) with no baseline subtraction. (B) The same profiles following baseline subtraction (F b = average F C of cycles 7–18). This illustraties the distortions that can be produced by the MxPro software used in this study, which attempts to correct for the baseline drift by modifying the F C dataset. This can compromise, sometimes severely, the efficacy of LRE quantification, even in the absence of any apparent baseline drifting (data not shown)
    Figure Legend Snippet: An example of primer-specific baseline drift . An extreme example of baseline drift produced by lambda primer K30. (A) Amplification profiles of 100 femtograms of lambda gDNA with K23 and K30 primers (blue profile), K30 alone with no lambda gDNA (green profile) and K23 alone with no lambda gDNA (red profile) with no baseline subtraction. (B) The same profiles following baseline subtraction (F b = average F C of cycles 7–18). This illustraties the distortions that can be produced by the MxPro software used in this study, which attempts to correct for the baseline drift by modifying the F C dataset. This can compromise, sometimes severely, the efficacy of LRE quantification, even in the absence of any apparent baseline drifting (data not shown)

    Techniques Used: Produced, Amplification, Software

    lambda gdna  (New England Biolabs)


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    New England Biolabs lambda gdna
    Amplification efficiency determination via standard curve analysis . (A) Screenshot of the amplification profiles generated by five quantities of <t>lambda</t> <t>gDNA,</t> ranging from 188,000 to 19 genomes in 10-fold increments. The fluorescence threshold is represented by the red line spanning the lower region of the profiles. Note that each amplification profile was produced by averaging the fluorescence readings of three replicate amplification reactions. (B) Plotting Log target quantity vs. C t generates a line in which the amplification efficiency is derived from the slope (E slope ) and the number of amplicon molecules at threshold (N t ) is derived from the intercept via linear regression analysis . fg Lambda: femtograms of lambda gDNA, N 0 : the number of lambda genomes, C t : the threshold cycle, r : linear regression correlation coefficient, F t : the fluorescence threshold, FU: fluorescence units
    Lambda Gdna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Critical evaluation of methods used to determine amplification efficiency refutes the exponential character of real-time PCR"

    Article Title: Critical evaluation of methods used to determine amplification efficiency refutes the exponential character of real-time PCR

    Journal: BMC Molecular Biology

    doi: 10.1186/1471-2199-9-96

    Amplification efficiency determination via standard curve analysis . (A) Screenshot of the amplification profiles generated by five quantities of lambda gDNA, ranging from 188,000 to 19 genomes in 10-fold increments. The fluorescence threshold is represented by the red line spanning the lower region of the profiles. Note that each amplification profile was produced by averaging the fluorescence readings of three replicate amplification reactions. (B) Plotting Log target quantity vs. C t generates a line in which the amplification efficiency is derived from the slope (E slope ) and the number of amplicon molecules at threshold (N t ) is derived from the intercept via linear regression analysis . fg Lambda: femtograms of lambda gDNA, N 0 : the number of lambda genomes, C t : the threshold cycle, r : linear regression correlation coefficient, F t : the fluorescence threshold, FU: fluorescence units
    Figure Legend Snippet: Amplification efficiency determination via standard curve analysis . (A) Screenshot of the amplification profiles generated by five quantities of lambda gDNA, ranging from 188,000 to 19 genomes in 10-fold increments. The fluorescence threshold is represented by the red line spanning the lower region of the profiles. Note that each amplification profile was produced by averaging the fluorescence readings of three replicate amplification reactions. (B) Plotting Log target quantity vs. C t generates a line in which the amplification efficiency is derived from the slope (E slope ) and the number of amplicon molecules at threshold (N t ) is derived from the intercept via linear regression analysis . fg Lambda: femtograms of lambda gDNA, N 0 : the number of lambda genomes, C t : the threshold cycle, r : linear regression correlation coefficient, F t : the fluorescence threshold, FU: fluorescence units

    Techniques Used: Amplification, Generated, Fluorescence, Produced, Derivative Assay

    lambda gdna  (New England Biolabs)


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    New England Biolabs lambda gdna
    Triplicate replicate amplifications of six quantities of <t>lambda</t> <t>gDNA</t> produce tight profile clustering, except for the two-molecule sample. Profile scattering implies loss of quantitative efficacy, a presumption supported by LRE quantification that generates target quantities that range from 1–4 molecules. Nevertheless, these LRE-based quantities produce an average of 2.3 molecules, which is close to the predicted target quantity. The numerical inlay summarizes the LRE analysis from which an average optical calibration factor (OCF) was derived.
    Lambda Gdna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Assessing the Performance Capabilities of LRE-Based Assays for Absolute Quantitative Real-Time PCR"

    Article Title: Assessing the Performance Capabilities of LRE-Based Assays for Absolute Quantitative Real-Time PCR

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0009731

    Triplicate replicate amplifications of six quantities of lambda gDNA produce tight profile clustering, except for the two-molecule sample. Profile scattering implies loss of quantitative efficacy, a presumption supported by LRE quantification that generates target quantities that range from 1–4 molecules. Nevertheless, these LRE-based quantities produce an average of 2.3 molecules, which is close to the predicted target quantity. The numerical inlay summarizes the LRE analysis from which an average optical calibration factor (OCF) was derived.
    Figure Legend Snippet: Triplicate replicate amplifications of six quantities of lambda gDNA produce tight profile clustering, except for the two-molecule sample. Profile scattering implies loss of quantitative efficacy, a presumption supported by LRE quantification that generates target quantities that range from 1–4 molecules. Nevertheless, these LRE-based quantities produce an average of 2.3 molecules, which is close to the predicted target quantity. The numerical inlay summarizes the LRE analysis from which an average optical calibration factor (OCF) was derived.

    Techniques Used: Derivative Assay

    Equal quantities of lambda gDNA were amplified in PCR reactions containing progressively greater volumes. ( A ) F C plots demonstrating that profile height is not only dependent on reaction volume, but that the concentration of amplicon DNA in the plateau phase (FU/µl) is similar for all reaction volumes. Predicted reaction fluorescence (circles) closely correlate with the actual fluorescence readings (dots). ( B ) LRE plots of the corresponding profiles demonstrates that increasing reaction volume has no impact on E max (Y intercept), but does produce a proportional increase in F max (X intercept). The numerical inlay provides a summary of the LRE analysis, which generated very similar F 0 values. The cycles included within the LRE window are designated by red circles. Vol, reaction volume; FU/µl, fluorescence units per µl of reaction at F max .
    Figure Legend Snippet: Equal quantities of lambda gDNA were amplified in PCR reactions containing progressively greater volumes. ( A ) F C plots demonstrating that profile height is not only dependent on reaction volume, but that the concentration of amplicon DNA in the plateau phase (FU/µl) is similar for all reaction volumes. Predicted reaction fluorescence (circles) closely correlate with the actual fluorescence readings (dots). ( B ) LRE plots of the corresponding profiles demonstrates that increasing reaction volume has no impact on E max (Y intercept), but does produce a proportional increase in F max (X intercept). The numerical inlay provides a summary of the LRE analysis, which generated very similar F 0 values. The cycles included within the LRE window are designated by red circles. Vol, reaction volume; FU/µl, fluorescence units per µl of reaction at F max .

    Techniques Used: Amplification, Concentration Assay, Fluorescence, Generated

    Equal quantities of lambda gDNA were amplified in which the time of annealing and elongation (A&E) was progressively reduced over four consecutive runs. ( A ) F C plots reveal a progressive reduction in F max along with changes in profile position and shape as E max was reduced. The predicted reaction fluorescence (circles) correlate well with the actual fluorescence readings (dots), further corroborating the ability of LRE to model PCR amplification. Nevertheless, it should be noted that loss of conformity within the plateau phase (referred to as plateau drift) is apparent at the two shortest A&E times, a trend that has been observed under other suboptimal assay conditions (data not shown). ( B ) LRE plots reveal little difference in ΔE (slope), with a progressive loss in F max (X intercept) as E max (Y intercept) is reduced, a trend that is very similar to the mathematical predictions shown in . The cycles included within the LRE window are designated by red circles.
    Figure Legend Snippet: Equal quantities of lambda gDNA were amplified in which the time of annealing and elongation (A&E) was progressively reduced over four consecutive runs. ( A ) F C plots reveal a progressive reduction in F max along with changes in profile position and shape as E max was reduced. The predicted reaction fluorescence (circles) correlate well with the actual fluorescence readings (dots), further corroborating the ability of LRE to model PCR amplification. Nevertheless, it should be noted that loss of conformity within the plateau phase (referred to as plateau drift) is apparent at the two shortest A&E times, a trend that has been observed under other suboptimal assay conditions (data not shown). ( B ) LRE plots reveal little difference in ΔE (slope), with a progressive loss in F max (X intercept) as E max (Y intercept) is reduced, a trend that is very similar to the mathematical predictions shown in . The cycles included within the LRE window are designated by red circles.

    Techniques Used: Amplification, Fluorescence

    Three datasets are presented, demonstrating that the fluorescence intensity generated by SYBR Green I is independent of reaction volume, GC content and amplicon size. Note that the mathematics of optical calibration is described in more detail in a previous study . ( A ) A known quantity of lambda gDNA is first amplified, from which an average F 0 value is determined (LRE-Fo). An optical calibration factor (OCF) is then calculated by dividing the average F 0 by the mass of the amplicon region derived from the lambda gDNA added to the reaction (M 0 ). OCF is thus expressed as fluorescence units per nanogram of dsDNA (FU/ng). For lambda gDNA, M 0 is calculated by multiplying the nanograms of lambda gDNA that are amplified by the amplicon size (A S ), and dividing by the genome size of lambda (48,502 bp). Overall, the similarity of the respective OCF values indicates that any difference in fluorescence intensity generated by these eight lambda amplicons is small. ( B ) To determine the number of target molecules within a sample (N 0 ), the process is reversed. M 0 is first calculated by dividing F 0 by an average OCF. N 0 is then calculated by multiplying M 0 by the number of base pairs per nanogram of dsDNA (9.1×10 11 bp/ng) and dividing by the amplicon size (A s ). For single-stranded DNA targets, such as cDNA, N 0 must be doubled as the OCF is derived from a double-stranded standard. The level of accuracy that can be achieved using an average OCF is illustrated by taking the F 0 values from A and comparing their respective N 0 values to the predicted number of target molecules, expressed here as percent error. Note that the reaction volume dataset that were taken from was produced using the same reaction setup and instrument used for the GC content and amplicon size datasets.
    Figure Legend Snippet: Three datasets are presented, demonstrating that the fluorescence intensity generated by SYBR Green I is independent of reaction volume, GC content and amplicon size. Note that the mathematics of optical calibration is described in more detail in a previous study . ( A ) A known quantity of lambda gDNA is first amplified, from which an average F 0 value is determined (LRE-Fo). An optical calibration factor (OCF) is then calculated by dividing the average F 0 by the mass of the amplicon region derived from the lambda gDNA added to the reaction (M 0 ). OCF is thus expressed as fluorescence units per nanogram of dsDNA (FU/ng). For lambda gDNA, M 0 is calculated by multiplying the nanograms of lambda gDNA that are amplified by the amplicon size (A S ), and dividing by the genome size of lambda (48,502 bp). Overall, the similarity of the respective OCF values indicates that any difference in fluorescence intensity generated by these eight lambda amplicons is small. ( B ) To determine the number of target molecules within a sample (N 0 ), the process is reversed. M 0 is first calculated by dividing F 0 by an average OCF. N 0 is then calculated by multiplying M 0 by the number of base pairs per nanogram of dsDNA (9.1×10 11 bp/ng) and dividing by the amplicon size (A s ). For single-stranded DNA targets, such as cDNA, N 0 must be doubled as the OCF is derived from a double-stranded standard. The level of accuracy that can be achieved using an average OCF is illustrated by taking the F 0 values from A and comparing their respective N 0 values to the predicted number of target molecules, expressed here as percent error. Note that the reaction volume dataset that were taken from was produced using the same reaction setup and instrument used for the GC content and amplicon size datasets.

    Techniques Used: Fluorescence, Generated, SYBR Green Assay, Amplification, Derivative Assay, Produced

    Amplicon primer sequences.
    Figure Legend Snippet: Amplicon primer sequences.

    Techniques Used: Amplification

    phage lambda genomic dna  (New England Biolabs)


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    New England Biolabs phage lambda genomic dna
    Structural homologs of BrxA. (A) Scale comparison of the 17.5 ​kb phage defence island from Escherichia fergusonii ATCC 35469 plasmid pEFER and the 16.4 ​kb BREX system from the chromosome of M. magneticum AMB-1. Genbank accession numbers and sequence positions are indicated. (B) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with BrxA from M. magneticum (green, PDB: 3BHW ). (C) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with NusB from Aquifex aeolicus (gray, PDB: 3R2C ). RNA bound to NusB is shown in orange. (D) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with SspB from Streptomyces clavuligerus (salmon pink, PDB: 6LB9 ). (E) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with the recognition domain of BpuJI from Bacillus pumilis (yellow, PDB: 2VLA ). <t>DNA</t> bound to BpuJI is shown in orange. Inset shows a close-up of the HTH motifs. (F) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with FokI from Planomicrobium okeanokoites (deep red, PDB: 1FOK ). DNA bound to FokI is shown in orange. Inset shows a close-up of the HTH motifs. (G) Agarose gel Electrophoretic Mobility Shift Assay (EMSA) of BrxA titrated with phage <t>Lambda</t> <t>genomic</t> <t>DNA</t> (200 ​ng per lane). Gel was post-stained in ethidium bromide. Protein concentration is shown above each lane. Control lanes contain either BrxR or MenT 3 proteins, or BrxA incubated in the absence of DNA. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
    Phage Lambda Genomic Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Crystal structure of the BREX phage defence protein BrxA"

    Article Title: Crystal structure of the BREX phage defence protein BrxA

    Journal: Current Research in Structural Biology

    doi: 10.1016/j.crstbi.2022.06.001

    Structural homologs of BrxA. (A) Scale comparison of the 17.5 ​kb phage defence island from Escherichia fergusonii ATCC 35469 plasmid pEFER and the 16.4 ​kb BREX system from the chromosome of M. magneticum AMB-1. Genbank accession numbers and sequence positions are indicated. (B) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with BrxA from M. magneticum (green, PDB: 3BHW ). (C) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with NusB from Aquifex aeolicus (gray, PDB: 3R2C ). RNA bound to NusB is shown in orange. (D) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with SspB from Streptomyces clavuligerus (salmon pink, PDB: 6LB9 ). (E) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with the recognition domain of BpuJI from Bacillus pumilis (yellow, PDB: 2VLA ). DNA bound to BpuJI is shown in orange. Inset shows a close-up of the HTH motifs. (F) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with FokI from Planomicrobium okeanokoites (deep red, PDB: 1FOK ). DNA bound to FokI is shown in orange. Inset shows a close-up of the HTH motifs. (G) Agarose gel Electrophoretic Mobility Shift Assay (EMSA) of BrxA titrated with phage Lambda genomic DNA (200 ​ng per lane). Gel was post-stained in ethidium bromide. Protein concentration is shown above each lane. Control lanes contain either BrxR or MenT 3 proteins, or BrxA incubated in the absence of DNA. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
    Figure Legend Snippet: Structural homologs of BrxA. (A) Scale comparison of the 17.5 ​kb phage defence island from Escherichia fergusonii ATCC 35469 plasmid pEFER and the 16.4 ​kb BREX system from the chromosome of M. magneticum AMB-1. Genbank accession numbers and sequence positions are indicated. (B) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with BrxA from M. magneticum (green, PDB: 3BHW ). (C) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with NusB from Aquifex aeolicus (gray, PDB: 3R2C ). RNA bound to NusB is shown in orange. (D) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with SspB from Streptomyces clavuligerus (salmon pink, PDB: 6LB9 ). (E) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with the recognition domain of BpuJI from Bacillus pumilis (yellow, PDB: 2VLA ). DNA bound to BpuJI is shown in orange. Inset shows a close-up of the HTH motifs. (F) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with FokI from Planomicrobium okeanokoites (deep red, PDB: 1FOK ). DNA bound to FokI is shown in orange. Inset shows a close-up of the HTH motifs. (G) Agarose gel Electrophoretic Mobility Shift Assay (EMSA) of BrxA titrated with phage Lambda genomic DNA (200 ​ng per lane). Gel was post-stained in ethidium bromide. Protein concentration is shown above each lane. Control lanes contain either BrxR or MenT 3 proteins, or BrxA incubated in the absence of DNA. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

    Techniques Used: Plasmid Preparation, Sequencing, Agarose Gel Electrophoresis, Electrophoretic Mobility Shift Assay, Staining, Protein Concentration, Incubation

    lambda phage genomic dna  (New England Biolabs)


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    New England Biolabs lambda phage genomic dna
    GFP Knockout Screen. ( A ) <t>Genomic</t> <t>DNA</t> was isolated from HeLa cells stably expressing GFP-LC3. The four HpaII sites within the GFP ORF and the predicted sgRNAs are labeled. ( B ) FACS sorting of transfected and untransfected cells. GFP fluorescence is on the x-axis and counts are on the y-axis. ( C ) Mutation frequency at each of the HpaII sites based on high-throughput sequencing of the GFP locus. ( D ) The most common variants for each of the four HpaII sites.
    Lambda Phage Genomic Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "A simple and rapid method for enzymatic synthesis of CRISPR-Cas9 sgRNA libraries"

    Article Title: A simple and rapid method for enzymatic synthesis of CRISPR-Cas9 sgRNA libraries

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkab838

    GFP Knockout Screen. ( A ) Genomic DNA was isolated from HeLa cells stably expressing GFP-LC3. The four HpaII sites within the GFP ORF and the predicted sgRNAs are labeled. ( B ) FACS sorting of transfected and untransfected cells. GFP fluorescence is on the x-axis and counts are on the y-axis. ( C ) Mutation frequency at each of the HpaII sites based on high-throughput sequencing of the GFP locus. ( D ) The most common variants for each of the four HpaII sites.
    Figure Legend Snippet: GFP Knockout Screen. ( A ) Genomic DNA was isolated from HeLa cells stably expressing GFP-LC3. The four HpaII sites within the GFP ORF and the predicted sgRNAs are labeled. ( B ) FACS sorting of transfected and untransfected cells. GFP fluorescence is on the x-axis and counts are on the y-axis. ( C ) Mutation frequency at each of the HpaII sites based on high-throughput sequencing of the GFP locus. ( D ) The most common variants for each of the four HpaII sites.

    Techniques Used: Knock-Out, Isolation, Stable Transfection, Expressing, Labeling, Transfection, Fluorescence, Mutagenesis, Next-Generation Sequencing

    unmodified bacteriophage lambda genomic dna  (New England Biolabs)


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    New England Biolabs unmodified bacteriophage lambda genomic dna
    Unmodified Bacteriophage Lambda Genomic Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    lambda genomic dna  (New England Biolabs)


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    New England Biolabs lambda genomic dna
    (A) Diagram of <t>lambda</t> <t>genomic</t> <t>DNA</t> shows the relative positions of three Cas9/sgRNA complexes (Lambda F2, Lambda R6, and Lambda R4) and the 12 kb fragment protected by Lambda F2 and Lambda R6 or the 36 kb fragment protected by Lambda F2 and Lambda R4. Probe sets 1–4 are used in qPCR assays to determine relative enrichment of protected regions. (B) Gel electrophoresis shows lambda DNA without or with exonuclease III treatment (lanes 1 and 2); lambda DNA treated with a pair of Cas9/sgRNAs with no homology to lambda (sgRNAs CFTR F1 and CFTR R2 target human loci) with exonuclease VII (lanes 3) or with exonucleases III and VII (lane 4); lambda DNA complexed with Lambda F2 and Lambda R4 with exonuclease VII (lane 5) or with exonucleases III and VII (lanes 6); and lambda DNA complexed with Lambda F2 and Lambda R6 with exonuclease III (lane 7) or with exonucleases III and VII (lanes 8). (C) Concentrations, as determined by qPCR, of Probe set 2 (within the protected locus) were compared with the concentrations of Probe set 4 (outside of the protected locus) and presented as ratios.
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    1) Product Images from "A novel CRISPR/Cas9 associated technology for sequence-specific nucleic acid enrichment"

    Article Title: A novel CRISPR/Cas9 associated technology for sequence-specific nucleic acid enrichment

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0215441

    (A) Diagram of lambda genomic DNA shows the relative positions of three Cas9/sgRNA complexes (Lambda F2, Lambda R6, and Lambda R4) and the 12 kb fragment protected by Lambda F2 and Lambda R6 or the 36 kb fragment protected by Lambda F2 and Lambda R4. Probe sets 1–4 are used in qPCR assays to determine relative enrichment of protected regions. (B) Gel electrophoresis shows lambda DNA without or with exonuclease III treatment (lanes 1 and 2); lambda DNA treated with a pair of Cas9/sgRNAs with no homology to lambda (sgRNAs CFTR F1 and CFTR R2 target human loci) with exonuclease VII (lanes 3) or with exonucleases III and VII (lane 4); lambda DNA complexed with Lambda F2 and Lambda R4 with exonuclease VII (lane 5) or with exonucleases III and VII (lanes 6); and lambda DNA complexed with Lambda F2 and Lambda R6 with exonuclease III (lane 7) or with exonucleases III and VII (lanes 8). (C) Concentrations, as determined by qPCR, of Probe set 2 (within the protected locus) were compared with the concentrations of Probe set 4 (outside of the protected locus) and presented as ratios.
    Figure Legend Snippet: (A) Diagram of lambda genomic DNA shows the relative positions of three Cas9/sgRNA complexes (Lambda F2, Lambda R6, and Lambda R4) and the 12 kb fragment protected by Lambda F2 and Lambda R6 or the 36 kb fragment protected by Lambda F2 and Lambda R4. Probe sets 1–4 are used in qPCR assays to determine relative enrichment of protected regions. (B) Gel electrophoresis shows lambda DNA without or with exonuclease III treatment (lanes 1 and 2); lambda DNA treated with a pair of Cas9/sgRNAs with no homology to lambda (sgRNAs CFTR F1 and CFTR R2 target human loci) with exonuclease VII (lanes 3) or with exonucleases III and VII (lane 4); lambda DNA complexed with Lambda F2 and Lambda R4 with exonuclease VII (lane 5) or with exonucleases III and VII (lanes 6); and lambda DNA complexed with Lambda F2 and Lambda R6 with exonuclease III (lane 7) or with exonucleases III and VII (lanes 8). (C) Concentrations, as determined by qPCR, of Probe set 2 (within the protected locus) were compared with the concentrations of Probe set 4 (outside of the protected locus) and presented as ratios.

    Techniques Used: Nucleic Acid Electrophoresis, Lambda DNA Preparation

    Plots of aligned Illumina reads of the protection experiment mapped to the lambda target genome using BWA 0.7.12-r1039. Sample 1 had no Cas9/sgRNA and no exonuclease treatment with a 120,000:1 copy ratio of lambda to human DNA. Sample 2 had no Cas9/sgRNA and no exonuclease treatment with a 3,000:1 copy ratio of lambda to human DNA. Sample 3 had Cas9/sgRNA Lambda F2 and Lambda R6 treatment with exonucleases III and VII with a 120,000:1 lambda DNA to human genomic DNA copy ratio. Sample 4 had Cas9/sgRNA Lambda F2 and Lambda R6 treatment with exonucleases III and VII with a 3000:1 lambda DNA to human genomic DNA copy ratio.
    Figure Legend Snippet: Plots of aligned Illumina reads of the protection experiment mapped to the lambda target genome using BWA 0.7.12-r1039. Sample 1 had no Cas9/sgRNA and no exonuclease treatment with a 120,000:1 copy ratio of lambda to human DNA. Sample 2 had no Cas9/sgRNA and no exonuclease treatment with a 3,000:1 copy ratio of lambda to human DNA. Sample 3 had Cas9/sgRNA Lambda F2 and Lambda R6 treatment with exonucleases III and VII with a 120,000:1 lambda DNA to human genomic DNA copy ratio. Sample 4 had Cas9/sgRNA Lambda F2 and Lambda R6 treatment with exonucleases III and VII with a 3000:1 lambda DNA to human genomic DNA copy ratio.

    Techniques Used: Lambda DNA Preparation

    Plots of aligned Nanopore sequencing results for lambda Negative Enrichment. Sample 1 had lambda DNA without exonuclease. Sample 2 had lambda DNA treated with Lambda F2 and Lambda R6 Cas-RNA complexes and exonucleases III and VII.
    Figure Legend Snippet: Plots of aligned Nanopore sequencing results for lambda Negative Enrichment. Sample 1 had lambda DNA without exonuclease. Sample 2 had lambda DNA treated with Lambda F2 and Lambda R6 Cas-RNA complexes and exonucleases III and VII.

    Techniques Used: Nanopore Sequencing, Lambda DNA Preparation

    lambda phage genomic dna  (New England Biolabs)


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    New England Biolabs lambda phage genomic dna
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    lambda phage genomic dna  (New England Biolabs)


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    New England Biolabs lambda phage genomic dna
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    lambda phage genomic dna  (New England Biolabs)


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    New England Biolabs lambda phage genomic dna
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    New England Biolabs lambda gdna
    Assessing the impact of SYBR Green I quantity on real-time amplification profiles . Replicate amplification reactions were prepared using three commercial enzyme formulations supplemented with increasing amounts of SYBR Green I. Each amplification reaction contained 100 femtograms of <t>lambda</t> <t>gDNA</t> (1,876 genomes) and 500 μM of the primers K7B and K12. The gain setting for each run was adjusted to ensure that reaction fluorescence remained below the saturation level of the photomultiplier tube (about 40,000 FU). (A) , (C) and (E) Screen shots of amplification profiles generated by the Stratagene MxPro qPCR software. This reveals that fluorescence intensity is dependent on SYBR Green I quantity, reflected by the large increase in the height of the amplification profiles as SYBR Green I quantity is increased. (B) , (D) and (F) LRE plot of each respective amplification profile. This reveals a linear domain corresponding to the central region of each amplification profile, confirming the mathematical prediction that amplification efficiency is linearly coupled to amplicon quantity. A consecutive group of points was selected (designated by red circles) for linear regression analysis (referred to as
    Lambda Gdna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs phage lambda genomic dna
    Structural homologs of BrxA. (A) Scale comparison of the 17.5 ​kb phage defence island from Escherichia fergusonii ATCC 35469 plasmid pEFER and the 16.4 ​kb BREX system from the chromosome of M. magneticum AMB-1. Genbank accession numbers and sequence positions are indicated. (B) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with BrxA from M. magneticum (green, PDB: 3BHW ). (C) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with NusB from Aquifex aeolicus (gray, PDB: 3R2C ). RNA bound to NusB is shown in orange. (D) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with SspB from Streptomyces clavuligerus (salmon pink, PDB: 6LB9 ). (E) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with the recognition domain of BpuJI from Bacillus pumilis (yellow, PDB: 2VLA ). <t>DNA</t> bound to BpuJI is shown in orange. Inset shows a close-up of the HTH motifs. (F) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with FokI from Planomicrobium okeanokoites (deep red, PDB: 1FOK ). DNA bound to FokI is shown in orange. Inset shows a close-up of the HTH motifs. (G) Agarose gel Electrophoretic Mobility Shift Assay (EMSA) of BrxA titrated with phage <t>Lambda</t> <t>genomic</t> <t>DNA</t> (200 ​ng per lane). Gel was post-stained in ethidium bromide. Protein concentration is shown above each lane. Control lanes contain either BrxR or MenT 3 proteins, or BrxA incubated in the absence of DNA. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
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    New England Biolabs lambda phage genomic dna
    GFP Knockout Screen. ( A ) <t>Genomic</t> <t>DNA</t> was isolated from HeLa cells stably expressing GFP-LC3. The four HpaII sites within the GFP ORF and the predicted sgRNAs are labeled. ( B ) FACS sorting of transfected and untransfected cells. GFP fluorescence is on the x-axis and counts are on the y-axis. ( C ) Mutation frequency at each of the HpaII sites based on high-throughput sequencing of the GFP locus. ( D ) The most common variants for each of the four HpaII sites.
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    New England Biolabs unmodified bacteriophage lambda genomic dna
    GFP Knockout Screen. ( A ) <t>Genomic</t> <t>DNA</t> was isolated from HeLa cells stably expressing GFP-LC3. The four HpaII sites within the GFP ORF and the predicted sgRNAs are labeled. ( B ) FACS sorting of transfected and untransfected cells. GFP fluorescence is on the x-axis and counts are on the y-axis. ( C ) Mutation frequency at each of the HpaII sites based on high-throughput sequencing of the GFP locus. ( D ) The most common variants for each of the four HpaII sites.
    Unmodified Bacteriophage Lambda Genomic Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs lambda genomic dna
    (A) Diagram of <t>lambda</t> <t>genomic</t> <t>DNA</t> shows the relative positions of three Cas9/sgRNA complexes (Lambda F2, Lambda R6, and Lambda R4) and the 12 kb fragment protected by Lambda F2 and Lambda R6 or the 36 kb fragment protected by Lambda F2 and Lambda R4. Probe sets 1–4 are used in qPCR assays to determine relative enrichment of protected regions. (B) Gel electrophoresis shows lambda DNA without or with exonuclease III treatment (lanes 1 and 2); lambda DNA treated with a pair of Cas9/sgRNAs with no homology to lambda (sgRNAs CFTR F1 and CFTR R2 target human loci) with exonuclease VII (lanes 3) or with exonucleases III and VII (lane 4); lambda DNA complexed with Lambda F2 and Lambda R4 with exonuclease VII (lane 5) or with exonucleases III and VII (lanes 6); and lambda DNA complexed with Lambda F2 and Lambda R6 with exonuclease III (lane 7) or with exonucleases III and VII (lanes 8). (C) Concentrations, as determined by qPCR, of Probe set 2 (within the protected locus) were compared with the concentrations of Probe set 4 (outside of the protected locus) and presented as ratios.
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    Assessing the impact of SYBR Green I quantity on real-time amplification profiles . Replicate amplification reactions were prepared using three commercial enzyme formulations supplemented with increasing amounts of SYBR Green I. Each amplification reaction contained 100 femtograms of lambda gDNA (1,876 genomes) and 500 μM of the primers K7B and K12. The gain setting for each run was adjusted to ensure that reaction fluorescence remained below the saturation level of the photomultiplier tube (about 40,000 FU). (A) , (C) and (E) Screen shots of amplification profiles generated by the Stratagene MxPro qPCR software. This reveals that fluorescence intensity is dependent on SYBR Green I quantity, reflected by the large increase in the height of the amplification profiles as SYBR Green I quantity is increased. (B) , (D) and (F) LRE plot of each respective amplification profile. This reveals a linear domain corresponding to the central region of each amplification profile, confirming the mathematical prediction that amplification efficiency is linearly coupled to amplicon quantity. A consecutive group of points was selected (designated by red circles) for linear regression analysis (referred to as

    Journal: BMC Biotechnology

    Article Title: A kinetic-based sigmoidal model for the polymerase chain reaction and its application to high-capacity absolute quantitative real-time PCR

    doi: 10.1186/1472-6750-8-47

    Figure Lengend Snippet: Assessing the impact of SYBR Green I quantity on real-time amplification profiles . Replicate amplification reactions were prepared using three commercial enzyme formulations supplemented with increasing amounts of SYBR Green I. Each amplification reaction contained 100 femtograms of lambda gDNA (1,876 genomes) and 500 μM of the primers K7B and K12. The gain setting for each run was adjusted to ensure that reaction fluorescence remained below the saturation level of the photomultiplier tube (about 40,000 FU). (A) , (C) and (E) Screen shots of amplification profiles generated by the Stratagene MxPro qPCR software. This reveals that fluorescence intensity is dependent on SYBR Green I quantity, reflected by the large increase in the height of the amplification profiles as SYBR Green I quantity is increased. (B) , (D) and (F) LRE plot of each respective amplification profile. This reveals a linear domain corresponding to the central region of each amplification profile, confirming the mathematical prediction that amplification efficiency is linearly coupled to amplicon quantity. A consecutive group of points was selected (designated by red circles) for linear regression analysis (referred to as "LRE analysis"), generating estimates for E max (intercept) and ΔE (slope), from which F max was calculated using equation 4 (see Figure 1 for additional details). Details as to how the boundaries of the linear region were determined are described later in the study. [SG] : quantity of supplementary SYBR Green I, r2 : linear regression correlation coefficient.

    Article Snippet: For transcript quantifications, the target consisted of an aliquot of the diluted reverse transcriptase reaction containing the equivalent of 10 ng total RNA per amplification reaction, or for optical calibration, lambda gDNA (New England BioLabs) at a quantity specified in Figure , amplified with the lambda primers K7B-K12 (Table ).

    Techniques: SYBR Green Assay, Amplification, Fluorescence, Generated, Software

    Optical calibrations of five reaction formulations supplemented with various quantities of SYBR Green I . Spreadsheet summary of the lambda gDNA (primer pair K7B-K12) optical calibrations conducted for the five reaction formulations used for LRE quantification in this study. Based on data presented in Figure 2, these formulations were designed to assess the impact of SYBR Green I quantity, the highest supplemented quantity (2.0X) estimated to be > 10X than that present in these three commercial formulations. Each row of values was derived from an individual amplification run (see additional file for more details). (A) QuantiTect 0X SYBR Green I. (B) QuantiTect 0.2X SYBR Green I. (C) DyNAmo 0.5X SYBR Green I. (D) DyNAmo 1.5X SYBR Green I. (E) FullVelocity 2.0X SYBR Green I. Lam : lambda gDNA quantity in femtograms, QT : QuantiTect, DyNa : DyNAmo; FV : FullVelocity, SG : SYBR Green I, SD : standard deviation, CV : coefficient of variation (SD/Average × 100%).

    Journal: BMC Biotechnology

    Article Title: A kinetic-based sigmoidal model for the polymerase chain reaction and its application to high-capacity absolute quantitative real-time PCR

    doi: 10.1186/1472-6750-8-47

    Figure Lengend Snippet: Optical calibrations of five reaction formulations supplemented with various quantities of SYBR Green I . Spreadsheet summary of the lambda gDNA (primer pair K7B-K12) optical calibrations conducted for the five reaction formulations used for LRE quantification in this study. Based on data presented in Figure 2, these formulations were designed to assess the impact of SYBR Green I quantity, the highest supplemented quantity (2.0X) estimated to be > 10X than that present in these three commercial formulations. Each row of values was derived from an individual amplification run (see additional file for more details). (A) QuantiTect 0X SYBR Green I. (B) QuantiTect 0.2X SYBR Green I. (C) DyNAmo 0.5X SYBR Green I. (D) DyNAmo 1.5X SYBR Green I. (E) FullVelocity 2.0X SYBR Green I. Lam : lambda gDNA quantity in femtograms, QT : QuantiTect, DyNa : DyNAmo; FV : FullVelocity, SG : SYBR Green I, SD : standard deviation, CV : coefficient of variation (SD/Average × 100%).

    Article Snippet: For transcript quantifications, the target consisted of an aliquot of the diluted reverse transcriptase reaction containing the equivalent of 10 ng total RNA per amplification reaction, or for optical calibration, lambda gDNA (New England BioLabs) at a quantity specified in Figure , amplified with the lambda primers K7B-K12 (Table ).

    Techniques: SYBR Green Assay, Derivative Assay, Amplification, Standard Deviation

    An example of primer-specific baseline drift . An extreme example of baseline drift produced by lambda primer K30. (A) Amplification profiles of 100 femtograms of lambda gDNA with K23 and K30 primers (blue profile), K30 alone with no lambda gDNA (green profile) and K23 alone with no lambda gDNA (red profile) with no baseline subtraction. (B) The same profiles following baseline subtraction (F b = average F C of cycles 7–18). This illustraties the distortions that can be produced by the MxPro software used in this study, which attempts to correct for the baseline drift by modifying the F C dataset. This can compromise, sometimes severely, the efficacy of LRE quantification, even in the absence of any apparent baseline drifting (data not shown)

    Journal: BMC Biotechnology

    Article Title: A kinetic-based sigmoidal model for the polymerase chain reaction and its application to high-capacity absolute quantitative real-time PCR

    doi: 10.1186/1472-6750-8-47

    Figure Lengend Snippet: An example of primer-specific baseline drift . An extreme example of baseline drift produced by lambda primer K30. (A) Amplification profiles of 100 femtograms of lambda gDNA with K23 and K30 primers (blue profile), K30 alone with no lambda gDNA (green profile) and K23 alone with no lambda gDNA (red profile) with no baseline subtraction. (B) The same profiles following baseline subtraction (F b = average F C of cycles 7–18). This illustraties the distortions that can be produced by the MxPro software used in this study, which attempts to correct for the baseline drift by modifying the F C dataset. This can compromise, sometimes severely, the efficacy of LRE quantification, even in the absence of any apparent baseline drifting (data not shown)

    Article Snippet: For transcript quantifications, the target consisted of an aliquot of the diluted reverse transcriptase reaction containing the equivalent of 10 ng total RNA per amplification reaction, or for optical calibration, lambda gDNA (New England BioLabs) at a quantity specified in Figure , amplified with the lambda primers K7B-K12 (Table ).

    Techniques: Produced, Amplification, Software

    Structural homologs of BrxA. (A) Scale comparison of the 17.5 ​kb phage defence island from Escherichia fergusonii ATCC 35469 plasmid pEFER and the 16.4 ​kb BREX system from the chromosome of M. magneticum AMB-1. Genbank accession numbers and sequence positions are indicated. (B) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with BrxA from M. magneticum (green, PDB: 3BHW ). (C) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with NusB from Aquifex aeolicus (gray, PDB: 3R2C ). RNA bound to NusB is shown in orange. (D) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with SspB from Streptomyces clavuligerus (salmon pink, PDB: 6LB9 ). (E) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with the recognition domain of BpuJI from Bacillus pumilis (yellow, PDB: 2VLA ). DNA bound to BpuJI is shown in orange. Inset shows a close-up of the HTH motifs. (F) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with FokI from Planomicrobium okeanokoites (deep red, PDB: 1FOK ). DNA bound to FokI is shown in orange. Inset shows a close-up of the HTH motifs. (G) Agarose gel Electrophoretic Mobility Shift Assay (EMSA) of BrxA titrated with phage Lambda genomic DNA (200 ​ng per lane). Gel was post-stained in ethidium bromide. Protein concentration is shown above each lane. Control lanes contain either BrxR or MenT 3 proteins, or BrxA incubated in the absence of DNA. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

    Journal: Current Research in Structural Biology

    Article Title: Crystal structure of the BREX phage defence protein BrxA

    doi: 10.1016/j.crstbi.2022.06.001

    Figure Lengend Snippet: Structural homologs of BrxA. (A) Scale comparison of the 17.5 ​kb phage defence island from Escherichia fergusonii ATCC 35469 plasmid pEFER and the 16.4 ​kb BREX system from the chromosome of M. magneticum AMB-1. Genbank accession numbers and sequence positions are indicated. (B) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with BrxA from M. magneticum (green, PDB: 3BHW ). (C) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with NusB from Aquifex aeolicus (gray, PDB: 3R2C ). RNA bound to NusB is shown in orange. (D) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with SspB from Streptomyces clavuligerus (salmon pink, PDB: 6LB9 ). (E) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with the recognition domain of BpuJI from Bacillus pumilis (yellow, PDB: 2VLA ). DNA bound to BpuJI is shown in orange. Inset shows a close-up of the HTH motifs. (F) Sequence-independent superposition of BrxA monomer (cyan, PDB: 7ZGE , this study) with FokI from Planomicrobium okeanokoites (deep red, PDB: 1FOK ). DNA bound to FokI is shown in orange. Inset shows a close-up of the HTH motifs. (G) Agarose gel Electrophoretic Mobility Shift Assay (EMSA) of BrxA titrated with phage Lambda genomic DNA (200 ​ng per lane). Gel was post-stained in ethidium bromide. Protein concentration is shown above each lane. Control lanes contain either BrxR or MenT 3 proteins, or BrxA incubated in the absence of DNA. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

    Article Snippet: Each binding reaction contained 4 ​μl of 5 ​× ​EMSA binding buffer [750 ​mM KCl, 50 ​mM Tris-HCl (pH 8.0), 2.5 ​mM EDTA (pH 8.0), 0.5% Triton X-100, 1 ​mM DTT, 55% glycerol], and 200 ​ng of phage Lambda genomic DNA (NEB).

    Techniques: Plasmid Preparation, Sequencing, Agarose Gel Electrophoresis, Electrophoretic Mobility Shift Assay, Staining, Protein Concentration, Incubation

    GFP Knockout Screen. ( A ) Genomic DNA was isolated from HeLa cells stably expressing GFP-LC3. The four HpaII sites within the GFP ORF and the predicted sgRNAs are labeled. ( B ) FACS sorting of transfected and untransfected cells. GFP fluorescence is on the x-axis and counts are on the y-axis. ( C ) Mutation frequency at each of the HpaII sites based on high-throughput sequencing of the GFP locus. ( D ) The most common variants for each of the four HpaII sites.

    Journal: Nucleic Acids Research

    Article Title: A simple and rapid method for enzymatic synthesis of CRISPR-Cas9 sgRNA libraries

    doi: 10.1093/nar/gkab838

    Figure Lengend Snippet: GFP Knockout Screen. ( A ) Genomic DNA was isolated from HeLa cells stably expressing GFP-LC3. The four HpaII sites within the GFP ORF and the predicted sgRNAs are labeled. ( B ) FACS sorting of transfected and untransfected cells. GFP fluorescence is on the x-axis and counts are on the y-axis. ( C ) Mutation frequency at each of the HpaII sites based on high-throughput sequencing of the GFP locus. ( D ) The most common variants for each of the four HpaII sites.

    Article Snippet: Lambda-phage genomic DNA was obtained from New England Biolabs (Ipswich, MA).

    Techniques: Knock-Out, Isolation, Stable Transfection, Expressing, Labeling, Transfection, Fluorescence, Mutagenesis, Next-Generation Sequencing

    (A) Diagram of lambda genomic DNA shows the relative positions of three Cas9/sgRNA complexes (Lambda F2, Lambda R6, and Lambda R4) and the 12 kb fragment protected by Lambda F2 and Lambda R6 or the 36 kb fragment protected by Lambda F2 and Lambda R4. Probe sets 1–4 are used in qPCR assays to determine relative enrichment of protected regions. (B) Gel electrophoresis shows lambda DNA without or with exonuclease III treatment (lanes 1 and 2); lambda DNA treated with a pair of Cas9/sgRNAs with no homology to lambda (sgRNAs CFTR F1 and CFTR R2 target human loci) with exonuclease VII (lanes 3) or with exonucleases III and VII (lane 4); lambda DNA complexed with Lambda F2 and Lambda R4 with exonuclease VII (lane 5) or with exonucleases III and VII (lanes 6); and lambda DNA complexed with Lambda F2 and Lambda R6 with exonuclease III (lane 7) or with exonucleases III and VII (lanes 8). (C) Concentrations, as determined by qPCR, of Probe set 2 (within the protected locus) were compared with the concentrations of Probe set 4 (outside of the protected locus) and presented as ratios.

    Journal: PLoS ONE

    Article Title: A novel CRISPR/Cas9 associated technology for sequence-specific nucleic acid enrichment

    doi: 10.1371/journal.pone.0215441

    Figure Lengend Snippet: (A) Diagram of lambda genomic DNA shows the relative positions of three Cas9/sgRNA complexes (Lambda F2, Lambda R6, and Lambda R4) and the 12 kb fragment protected by Lambda F2 and Lambda R6 or the 36 kb fragment protected by Lambda F2 and Lambda R4. Probe sets 1–4 are used in qPCR assays to determine relative enrichment of protected regions. (B) Gel electrophoresis shows lambda DNA without or with exonuclease III treatment (lanes 1 and 2); lambda DNA treated with a pair of Cas9/sgRNAs with no homology to lambda (sgRNAs CFTR F1 and CFTR R2 target human loci) with exonuclease VII (lanes 3) or with exonucleases III and VII (lane 4); lambda DNA complexed with Lambda F2 and Lambda R4 with exonuclease VII (lane 5) or with exonucleases III and VII (lanes 6); and lambda DNA complexed with Lambda F2 and Lambda R6 with exonuclease III (lane 7) or with exonucleases III and VII (lanes 8). (C) Concentrations, as determined by qPCR, of Probe set 2 (within the protected locus) were compared with the concentrations of Probe set 4 (outside of the protected locus) and presented as ratios.

    Article Snippet: Experiments used 330 ng starting lambda genomic DNA (NEB, cat. #N3011L) or 500 ng starting human genomic DNA (Promega, cat. #G3041).

    Techniques: Nucleic Acid Electrophoresis, Lambda DNA Preparation

    Plots of aligned Illumina reads of the protection experiment mapped to the lambda target genome using BWA 0.7.12-r1039. Sample 1 had no Cas9/sgRNA and no exonuclease treatment with a 120,000:1 copy ratio of lambda to human DNA. Sample 2 had no Cas9/sgRNA and no exonuclease treatment with a 3,000:1 copy ratio of lambda to human DNA. Sample 3 had Cas9/sgRNA Lambda F2 and Lambda R6 treatment with exonucleases III and VII with a 120,000:1 lambda DNA to human genomic DNA copy ratio. Sample 4 had Cas9/sgRNA Lambda F2 and Lambda R6 treatment with exonucleases III and VII with a 3000:1 lambda DNA to human genomic DNA copy ratio.

    Journal: PLoS ONE

    Article Title: A novel CRISPR/Cas9 associated technology for sequence-specific nucleic acid enrichment

    doi: 10.1371/journal.pone.0215441

    Figure Lengend Snippet: Plots of aligned Illumina reads of the protection experiment mapped to the lambda target genome using BWA 0.7.12-r1039. Sample 1 had no Cas9/sgRNA and no exonuclease treatment with a 120,000:1 copy ratio of lambda to human DNA. Sample 2 had no Cas9/sgRNA and no exonuclease treatment with a 3,000:1 copy ratio of lambda to human DNA. Sample 3 had Cas9/sgRNA Lambda F2 and Lambda R6 treatment with exonucleases III and VII with a 120,000:1 lambda DNA to human genomic DNA copy ratio. Sample 4 had Cas9/sgRNA Lambda F2 and Lambda R6 treatment with exonucleases III and VII with a 3000:1 lambda DNA to human genomic DNA copy ratio.

    Article Snippet: Experiments used 330 ng starting lambda genomic DNA (NEB, cat. #N3011L) or 500 ng starting human genomic DNA (Promega, cat. #G3041).

    Techniques: Lambda DNA Preparation

    Plots of aligned Nanopore sequencing results for lambda Negative Enrichment. Sample 1 had lambda DNA without exonuclease. Sample 2 had lambda DNA treated with Lambda F2 and Lambda R6 Cas-RNA complexes and exonucleases III and VII.

    Journal: PLoS ONE

    Article Title: A novel CRISPR/Cas9 associated technology for sequence-specific nucleic acid enrichment

    doi: 10.1371/journal.pone.0215441

    Figure Lengend Snippet: Plots of aligned Nanopore sequencing results for lambda Negative Enrichment. Sample 1 had lambda DNA without exonuclease. Sample 2 had lambda DNA treated with Lambda F2 and Lambda R6 Cas-RNA complexes and exonucleases III and VII.

    Article Snippet: Experiments used 330 ng starting lambda genomic DNA (NEB, cat. #N3011L) or 500 ng starting human genomic DNA (Promega, cat. #G3041).

    Techniques: Nanopore Sequencing, Lambda DNA Preparation