qubit  (Thermo Fisher)


Bioz Verified Symbol Thermo Fisher is a verified supplier  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    Name:
    Qubit Assay Tubes
    Description:
    Qubit assay tubes are 500 µL thin-walled polypropylene tubes for use with the Qubit Fluorometer. 500 tubes per package.
    Catalog Number:
    Q32856
    Price:
    None
    Applications:
    DNA & RNA Purification & Analysis|DNA Quantitation|Protein Assays and Analysis|Protein Biology|Protein Quantitation|RNA Quantitation|Nucleic Acid Quantitation
    Size:
    500 tubes
    Category:
    Instruments and Equipment, Spectroscopy & Elemental Analysis Instruments & Equipment, Fluorometer Accessories
    Score:
    85
    Buy from Supplier


    Structured Review

    Thermo Fisher qubit
    Quantification and qualification of FFPE-DNA. (A) Each FFPE-DNA was serially diluted with distilled water, and the concentration of each diluent was measured by <t>NanoDrop</t> (circles), <t>BR-Qubit</t> (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line indicates the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. The detection limits of each measurement are described in Fig 1 . (B) Various lengths of the target sequence were amplified from Frozen- and FFPE-DNAs. The amplified products were electrophoresed on agarose gels. Lane 1, Frozen-H1; lane 2, Frozen-H2; lane 3, Frozen-H3; lane 4, FFPE-H1; lane 5, FFPE-H2; and lane 6, FFPE-H3.
    Qubit assay tubes are 500 µL thin-walled polypropylene tubes for use with the Qubit Fluorometer. 500 tubes per package.
    https://www.bioz.com/result/qubit/product/Thermo Fisher
    Average 99 stars, based on 178 article reviews
    Price from $9.99 to $1999.99
    qubit - by Bioz Stars, 2019-10
    99/100 stars

    Images

    1) Product Images from "Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions"

    Article Title: Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0150528

    Quantification and qualification of FFPE-DNA. (A) Each FFPE-DNA was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line indicates the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. The detection limits of each measurement are described in Fig 1 . (B) Various lengths of the target sequence were amplified from Frozen- and FFPE-DNAs. The amplified products were electrophoresed on agarose gels. Lane 1, Frozen-H1; lane 2, Frozen-H2; lane 3, Frozen-H3; lane 4, FFPE-H1; lane 5, FFPE-H2; and lane 6, FFPE-H3.
    Figure Legend Snippet: Quantification and qualification of FFPE-DNA. (A) Each FFPE-DNA was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line indicates the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. The detection limits of each measurement are described in Fig 1 . (B) Various lengths of the target sequence were amplified from Frozen- and FFPE-DNAs. The amplified products were electrophoresed on agarose gels. Lane 1, Frozen-H1; lane 2, Frozen-H2; lane 3, Frozen-H3; lane 4, FFPE-H1; lane 5, FFPE-H2; and lane 6, FFPE-H3.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Concentration Assay, Real-time Polymerase Chain Reaction, Sequencing, Amplification

    Dilution curves of Frozen-DNA diluted with distilled water as determined by NanoDrop, Qubit and qPCR. Each Frozen-DNA sample was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line shows the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution measured by NanoDrop is shown at the top right: dilution ratio = 1. Two additional concentrations are also shown in each graph. The detection limits of NanoDrop, BR-Qubit, HS-Qubit and qPCR are 2 ng/μl, 2 ng/μl, 0.2 ng/μl and 1 pg/μl, respectively.
    Figure Legend Snippet: Dilution curves of Frozen-DNA diluted with distilled water as determined by NanoDrop, Qubit and qPCR. Each Frozen-DNA sample was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line shows the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution measured by NanoDrop is shown at the top right: dilution ratio = 1. Two additional concentrations are also shown in each graph. The detection limits of NanoDrop, BR-Qubit, HS-Qubit and qPCR are 2 ng/μl, 2 ng/μl, 0.2 ng/μl and 1 pg/μl, respectively.

    Techniques Used: Real-time Polymerase Chain Reaction, Concentration Assay

    Quantification and qualification of Trizol-DNA. (A) Trizol-DNA was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line indicates the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. The detection limits of each measurement are described in Fig 1 . (B) Various lengths of the target sequence were amplified from Trizol-DNAs, and the amplified products were electrophoresed on an agarose gel. Lane 1, Frozen-H1; lane 2, Trizol-h1; lane 3, Trizol-h2; lane 4, Trizol-h3; lane 5, Trizol-h4; lane 6, Trizol-h5; lane 7, Trizol-h6; and lane 8, Trizol-h7.
    Figure Legend Snippet: Quantification and qualification of Trizol-DNA. (A) Trizol-DNA was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line indicates the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. The detection limits of each measurement are described in Fig 1 . (B) Various lengths of the target sequence were amplified from Trizol-DNAs, and the amplified products were electrophoresed on an agarose gel. Lane 1, Frozen-H1; lane 2, Trizol-h1; lane 3, Trizol-h2; lane 4, Trizol-h3; lane 5, Trizol-h4; lane 6, Trizol-h5; lane 7, Trizol-h6; and lane 8, Trizol-h7.

    Techniques Used: Concentration Assay, Real-time Polymerase Chain Reaction, Sequencing, Amplification, Agarose Gel Electrophoresis

    Quantification of Frozen-DNA diluted with various solutions by Qubit. (A) Frozen-R2 DNA was serially diluted with distilled water (black) or TE buffer (white), and the concentration of each diluent was measured by BR-Qubit (square) and HS-Qubit (diamond). (B) Eleven Frozen-DNAs were diluted with distilled water or TE buffer to approximately 20 ng/μl, as measured by NanoDrop, and the concentration of each diluent was measured by HS-Qubit. The ratios of the Qubit to NanoDrop values were determined for each diluent. (C, D) Frozen-R1 DNA was serially diluted with distilled water (closed diamonds), 0.01 mM NaCl (open diamonds), 0.1 mM NaCl (squares), 1 mM NaCl (triangles) or 10 mM NaCl (circles). The broken line shows the expected NanoDrop values. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. (D) The Q/E ratio was determined for each diluent, as shown in Fig 3C. (E) Frozen-R2 DNA was serially diluted with TE buffer (white) or distilled water (black), and a 0.1 volume of 100 mM Tris-HCl/10 mM EDTA was added to the latter diluent (gray). The expected NanoDrop values in parentheses indicate those diluted with distilled water. The detection limits of each measurement are described in Fig 1 .
    Figure Legend Snippet: Quantification of Frozen-DNA diluted with various solutions by Qubit. (A) Frozen-R2 DNA was serially diluted with distilled water (black) or TE buffer (white), and the concentration of each diluent was measured by BR-Qubit (square) and HS-Qubit (diamond). (B) Eleven Frozen-DNAs were diluted with distilled water or TE buffer to approximately 20 ng/μl, as measured by NanoDrop, and the concentration of each diluent was measured by HS-Qubit. The ratios of the Qubit to NanoDrop values were determined for each diluent. (C, D) Frozen-R1 DNA was serially diluted with distilled water (closed diamonds), 0.01 mM NaCl (open diamonds), 0.1 mM NaCl (squares), 1 mM NaCl (triangles) or 10 mM NaCl (circles). The broken line shows the expected NanoDrop values. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. (D) The Q/E ratio was determined for each diluent, as shown in Fig 3C. (E) Frozen-R2 DNA was serially diluted with TE buffer (white) or distilled water (black), and a 0.1 volume of 100 mM Tris-HCl/10 mM EDTA was added to the latter diluent (gray). The expected NanoDrop values in parentheses indicate those diluted with distilled water. The detection limits of each measurement are described in Fig 1 .

    Techniques Used: Concentration Assay

    2) Product Images from "DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples"

    Article Title: DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0062692

    Significant discrepancies in DNA quantification by NanoDrop and Qubit. A total of 100 ng of DNA based on NanoDrop (N, black bars) or Qubit (Q, grey bars) measurements was analyzed by electrophoresis on 0.8% agarose gel. Sample ID is indicated at the bottom. Lane L contains 200 ng of DNA as the reference for normalization. Densitometric analysis (bar chart) was performed by ImageJ software [20] . It is clear from the electrophoretic bands and their densitometric charts that NanoDrop overestimates DNA concentration.
    Figure Legend Snippet: Significant discrepancies in DNA quantification by NanoDrop and Qubit. A total of 100 ng of DNA based on NanoDrop (N, black bars) or Qubit (Q, grey bars) measurements was analyzed by electrophoresis on 0.8% agarose gel. Sample ID is indicated at the bottom. Lane L contains 200 ng of DNA as the reference for normalization. Densitometric analysis (bar chart) was performed by ImageJ software [20] . It is clear from the electrophoretic bands and their densitometric charts that NanoDrop overestimates DNA concentration.

    Techniques Used: Electrophoresis, Agarose Gel Electrophoresis, Software, Concentration Assay

    DNA qualification for next-generation sequencing applications. Effect of low-quality DNA on next-generation sequencing (NGS) workflow. Three FFPE samples were tested for construction of NGS amplicon libraries (Ion Torrent Ampliseq Cancer Panel). Qubit: 40 ng of DNA according to Qubit measurement were processed using the Ampliseq library construction kit (multiplex PCR amplification of 191 DNA regions from 46 cancer-related genes). NanoDrop: absorption spectra of samples showed different degrees of organic contamination (230 nm spike, A260/A230 ratio). Agilent: quality and quantity of the obtained libraries were evaluated by Agilent high sensitivity assay on-chip electrophoresis, where the library is represented by the large band between 150 and 200 bp. Fragments test: histogram showing length and abundance of produced sequences. Sample FFPE 5 did not produce a good library due to high organic contamination; this is revealed by the remarkable spike at 230 nm that concurs to the low 260/230 ratio, and explains the faint electrophoretic band and the almost flat fragments test histogram.
    Figure Legend Snippet: DNA qualification for next-generation sequencing applications. Effect of low-quality DNA on next-generation sequencing (NGS) workflow. Three FFPE samples were tested for construction of NGS amplicon libraries (Ion Torrent Ampliseq Cancer Panel). Qubit: 40 ng of DNA according to Qubit measurement were processed using the Ampliseq library construction kit (multiplex PCR amplification of 191 DNA regions from 46 cancer-related genes). NanoDrop: absorption spectra of samples showed different degrees of organic contamination (230 nm spike, A260/A230 ratio). Agilent: quality and quantity of the obtained libraries were evaluated by Agilent high sensitivity assay on-chip electrophoresis, where the library is represented by the large band between 150 and 200 bp. Fragments test: histogram showing length and abundance of produced sequences. Sample FFPE 5 did not produce a good library due to high organic contamination; this is revealed by the remarkable spike at 230 nm that concurs to the low 260/230 ratio, and explains the faint electrophoretic band and the almost flat fragments test histogram.

    Techniques Used: Next-Generation Sequencing, Formalin-fixed Paraffin-Embedded, Amplification, Multiplex Assay, Polymerase Chain Reaction, Sensitive Assay, Chromatin Immunoprecipitation, Electrophoresis, Produced

    Influence of RNA contamination on DNA quantification. DNA quantifications (n = 5) by NanoDrop and Qubit in the presence of RNA contamination. A DNA sample with a concentration of 38 ng/µl was mixed with different volumes of total RNA at 33 ng/µl extracted from the same tissue sample to obtain the indicated ratios; bars and brackets indicate mean and 95% confidence interval; asterisks show measurements significantly different from pure DNA (* p
    Figure Legend Snippet: Influence of RNA contamination on DNA quantification. DNA quantifications (n = 5) by NanoDrop and Qubit in the presence of RNA contamination. A DNA sample with a concentration of 38 ng/µl was mixed with different volumes of total RNA at 33 ng/µl extracted from the same tissue sample to obtain the indicated ratios; bars and brackets indicate mean and 95% confidence interval; asterisks show measurements significantly different from pure DNA (* p

    Techniques Used: Concentration Assay

    Cross-validation of DNA samples quantification by qPCR. Bland-Altman plots for inter-technology (NanoDrop or Qubit vs. qPCR) comparison of all samples (A), and according to the different sample sources, as indicated (B, C). A) Qubit measurements show high correlation (mean measured/expected ratio = 0.92; SD = 0.69; Wilcoxon signed rank test p = 0.07) with the measurements obtained by qPCR (x-axis), whereas NanoDrop measurements tend to overestimate samples concentration (mean measured/expected ratio = 3.8; SD = 6.4; Wilcoxon signed rank test p
    Figure Legend Snippet: Cross-validation of DNA samples quantification by qPCR. Bland-Altman plots for inter-technology (NanoDrop or Qubit vs. qPCR) comparison of all samples (A), and according to the different sample sources, as indicated (B, C). A) Qubit measurements show high correlation (mean measured/expected ratio = 0.92; SD = 0.69; Wilcoxon signed rank test p = 0.07) with the measurements obtained by qPCR (x-axis), whereas NanoDrop measurements tend to overestimate samples concentration (mean measured/expected ratio = 3.8; SD = 6.4; Wilcoxon signed rank test p

    Techniques Used: Real-time Polymerase Chain Reaction, Concentration Assay

    Intra- and inter-method accuracy and precision. Distribution of DNA sample concentration (dispersion chart) was estimated by both NanoDrop (black) and Qubit (gray) on repeated (n = 20) measurements of two commercial human genomic DNA preparations (Sample L 200 ng/µl; Sample G 5 ng/µl). For both samples, NanoDrop overestimated the DNA concentration (+8.8% for L and +24.0% for G, p
    Figure Legend Snippet: Intra- and inter-method accuracy and precision. Distribution of DNA sample concentration (dispersion chart) was estimated by both NanoDrop (black) and Qubit (gray) on repeated (n = 20) measurements of two commercial human genomic DNA preparations (Sample L 200 ng/µl; Sample G 5 ng/µl). For both samples, NanoDrop overestimated the DNA concentration (+8.8% for L and +24.0% for G, p

    Techniques Used: Concentration Assay

    3) Product Images from "Preanalytical blood sample workup for cell‐free DNA analysis using Droplet Digital PCR for future molecular cancer diagnostics"

    Article Title: Preanalytical blood sample workup for cell‐free DNA analysis using Droplet Digital PCR for future molecular cancer diagnostics

    Journal: Cancer Medicine

    doi: 10.1002/cam4.1184

    DNA quantification after isolation of EDTA samples using assay 3. In order to perform linear regression, all dd PCR results were adhered to NanoDrop and Qubit quantification results assuming 3.3 pg DNA /haploid genome ( x ‐axes) and depicted as ng/ μ L ( y ‐axis). In total, 38 samples were quantified by NanoDrop (A), of which five results were negative values and excluded from analysis. Seventy‐eight samples were quantified using Qubit (B). R 2 represents goodness‐of‐fit of DNA quantification methods for dd PCR .
    Figure Legend Snippet: DNA quantification after isolation of EDTA samples using assay 3. In order to perform linear regression, all dd PCR results were adhered to NanoDrop and Qubit quantification results assuming 3.3 pg DNA /haploid genome ( x ‐axes) and depicted as ng/ μ L ( y ‐axis). In total, 38 samples were quantified by NanoDrop (A), of which five results were negative values and excluded from analysis. Seventy‐eight samples were quantified using Qubit (B). R 2 represents goodness‐of‐fit of DNA quantification methods for dd PCR .

    Techniques Used: Isolation, Polymerase Chain Reaction

    4) Product Images from "DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples"

    Article Title: DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0062692

    Significant discrepancies in DNA quantification by NanoDrop and Qubit. A total of 100 ng of DNA based on NanoDrop (N, black bars) or Qubit (Q, grey bars) measurements was analyzed by electrophoresis on 0.8% agarose gel. Sample ID is indicated at the bottom. Lane L contains 200 ng of DNA as the reference for normalization. Densitometric analysis (bar chart) was performed by ImageJ software [20] . It is clear from the electrophoretic bands and their densitometric charts that NanoDrop overestimates DNA concentration.
    Figure Legend Snippet: Significant discrepancies in DNA quantification by NanoDrop and Qubit. A total of 100 ng of DNA based on NanoDrop (N, black bars) or Qubit (Q, grey bars) measurements was analyzed by electrophoresis on 0.8% agarose gel. Sample ID is indicated at the bottom. Lane L contains 200 ng of DNA as the reference for normalization. Densitometric analysis (bar chart) was performed by ImageJ software [20] . It is clear from the electrophoretic bands and their densitometric charts that NanoDrop overestimates DNA concentration.

    Techniques Used: Electrophoresis, Agarose Gel Electrophoresis, Software, Concentration Assay

    DNA qualification for next-generation sequencing applications. Effect of low-quality DNA on next-generation sequencing (NGS) workflow. Three FFPE samples were tested for construction of NGS amplicon libraries (Ion Torrent Ampliseq Cancer Panel). Qubit: 40 ng of DNA according to Qubit measurement were processed using the Ampliseq library construction kit (multiplex PCR amplification of 191 DNA regions from 46 cancer-related genes). NanoDrop: absorption spectra of samples showed different degrees of organic contamination (230 nm spike, A260/A230 ratio). Agilent: quality and quantity of the obtained libraries were evaluated by Agilent high sensitivity assay on-chip electrophoresis, where the library is represented by the large band between 150 and 200 bp. Fragments test: histogram showing length and abundance of produced sequences. Sample FFPE 5 did not produce a good library due to high organic contamination; this is revealed by the remarkable spike at 230 nm that concurs to the low 260/230 ratio, and explains the faint electrophoretic band and the almost flat fragments test histogram.
    Figure Legend Snippet: DNA qualification for next-generation sequencing applications. Effect of low-quality DNA on next-generation sequencing (NGS) workflow. Three FFPE samples were tested for construction of NGS amplicon libraries (Ion Torrent Ampliseq Cancer Panel). Qubit: 40 ng of DNA according to Qubit measurement were processed using the Ampliseq library construction kit (multiplex PCR amplification of 191 DNA regions from 46 cancer-related genes). NanoDrop: absorption spectra of samples showed different degrees of organic contamination (230 nm spike, A260/A230 ratio). Agilent: quality and quantity of the obtained libraries were evaluated by Agilent high sensitivity assay on-chip electrophoresis, where the library is represented by the large band between 150 and 200 bp. Fragments test: histogram showing length and abundance of produced sequences. Sample FFPE 5 did not produce a good library due to high organic contamination; this is revealed by the remarkable spike at 230 nm that concurs to the low 260/230 ratio, and explains the faint electrophoretic band and the almost flat fragments test histogram.

    Techniques Used: Next-Generation Sequencing, Formalin-fixed Paraffin-Embedded, Amplification, Multiplex Assay, Polymerase Chain Reaction, Sensitive Assay, Chromatin Immunoprecipitation, Electrophoresis, Produced

    Influence of RNA contamination on DNA quantification. DNA quantifications (n = 5) by NanoDrop and Qubit in the presence of RNA contamination. A DNA sample with a concentration of 38 ng/µl was mixed with different volumes of total RNA at 33 ng/µl extracted from the same tissue sample to obtain the indicated ratios; bars and brackets indicate mean and 95% confidence interval; asterisks show measurements significantly different from pure DNA (* p
    Figure Legend Snippet: Influence of RNA contamination on DNA quantification. DNA quantifications (n = 5) by NanoDrop and Qubit in the presence of RNA contamination. A DNA sample with a concentration of 38 ng/µl was mixed with different volumes of total RNA at 33 ng/µl extracted from the same tissue sample to obtain the indicated ratios; bars and brackets indicate mean and 95% confidence interval; asterisks show measurements significantly different from pure DNA (* p

    Techniques Used: Concentration Assay

    Cross-validation of DNA samples quantification by qPCR. Bland-Altman plots for inter-technology (NanoDrop or Qubit vs. qPCR) comparison of all samples (A), and according to the different sample sources, as indicated (B, C). A) Qubit measurements show high correlation (mean measured/expected ratio = 0.92; SD = 0.69; Wilcoxon signed rank test p = 0.07) with the measurements obtained by qPCR (x-axis), whereas NanoDrop measurements tend to overestimate samples concentration (mean measured/expected ratio = 3.8; SD = 6.4; Wilcoxon signed rank test p
    Figure Legend Snippet: Cross-validation of DNA samples quantification by qPCR. Bland-Altman plots for inter-technology (NanoDrop or Qubit vs. qPCR) comparison of all samples (A), and according to the different sample sources, as indicated (B, C). A) Qubit measurements show high correlation (mean measured/expected ratio = 0.92; SD = 0.69; Wilcoxon signed rank test p = 0.07) with the measurements obtained by qPCR (x-axis), whereas NanoDrop measurements tend to overestimate samples concentration (mean measured/expected ratio = 3.8; SD = 6.4; Wilcoxon signed rank test p

    Techniques Used: Real-time Polymerase Chain Reaction, Concentration Assay

    Intra- and inter-method accuracy and precision. Distribution of DNA sample concentration (dispersion chart) was estimated by both NanoDrop (black) and Qubit (gray) on repeated (n = 20) measurements of two commercial human genomic DNA preparations (Sample L 200 ng/µl; Sample G 5 ng/µl). For both samples, NanoDrop overestimated the DNA concentration (+8.8% for L and +24.0% for G, p
    Figure Legend Snippet: Intra- and inter-method accuracy and precision. Distribution of DNA sample concentration (dispersion chart) was estimated by both NanoDrop (black) and Qubit (gray) on repeated (n = 20) measurements of two commercial human genomic DNA preparations (Sample L 200 ng/µl; Sample G 5 ng/µl). For both samples, NanoDrop overestimated the DNA concentration (+8.8% for L and +24.0% for G, p

    Techniques Used: Concentration Assay

    5) Product Images from "Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing"

    Article Title: Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing

    Journal: Applied Microbiology and Biotechnology

    doi: 10.1007/s00253-012-4244-4

    The DNA yields and purity of the two AS samples with the seven kits. a DNA quantified with NanoDrop. b DNA quantified with Qubit. c DNA qualified by OD 260 /OD 280 with NanoDrop. The dashed line shows the ratio at 1.85, which is the index of optimal DNA purity
    Figure Legend Snippet: The DNA yields and purity of the two AS samples with the seven kits. a DNA quantified with NanoDrop. b DNA quantified with Qubit. c DNA qualified by OD 260 /OD 280 with NanoDrop. The dashed line shows the ratio at 1.85, which is the index of optimal DNA purity

    Techniques Used:

    6) Product Images from "DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples"

    Article Title: DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0062692

    Significant discrepancies in DNA quantification by NanoDrop and Qubit. A total of 100 ng of DNA based on NanoDrop (N, black bars) or Qubit (Q, grey bars) measurements was analyzed by electrophoresis on 0.8% agarose gel. Sample ID is indicated at the bottom. Lane L contains 200 ng of DNA as the reference for normalization. Densitometric analysis (bar chart) was performed by ImageJ software [20] . It is clear from the electrophoretic bands and their densitometric charts that NanoDrop overestimates DNA concentration.
    Figure Legend Snippet: Significant discrepancies in DNA quantification by NanoDrop and Qubit. A total of 100 ng of DNA based on NanoDrop (N, black bars) or Qubit (Q, grey bars) measurements was analyzed by electrophoresis on 0.8% agarose gel. Sample ID is indicated at the bottom. Lane L contains 200 ng of DNA as the reference for normalization. Densitometric analysis (bar chart) was performed by ImageJ software [20] . It is clear from the electrophoretic bands and their densitometric charts that NanoDrop overestimates DNA concentration.

    Techniques Used: Electrophoresis, Agarose Gel Electrophoresis, Software, Concentration Assay

    DNA qualification for next-generation sequencing applications. Effect of low-quality DNA on next-generation sequencing (NGS) workflow. Three FFPE samples were tested for construction of NGS amplicon libraries (Ion Torrent Ampliseq Cancer Panel). Qubit: 40 ng of DNA according to Qubit measurement were processed using the Ampliseq library construction kit (multiplex PCR amplification of 191 DNA regions from 46 cancer-related genes). NanoDrop: absorption spectra of samples showed different degrees of organic contamination (230 nm spike, A260/A230 ratio). Agilent: quality and quantity of the obtained libraries were evaluated by Agilent high sensitivity assay on-chip electrophoresis, where the library is represented by the large band between 150 and 200 bp. Fragments test: histogram showing length and abundance of produced sequences. Sample FFPE 5 did not produce a good library due to high organic contamination; this is revealed by the remarkable spike at 230 nm that concurs to the low 260/230 ratio, and explains the faint electrophoretic band and the almost flat fragments test histogram.
    Figure Legend Snippet: DNA qualification for next-generation sequencing applications. Effect of low-quality DNA on next-generation sequencing (NGS) workflow. Three FFPE samples were tested for construction of NGS amplicon libraries (Ion Torrent Ampliseq Cancer Panel). Qubit: 40 ng of DNA according to Qubit measurement were processed using the Ampliseq library construction kit (multiplex PCR amplification of 191 DNA regions from 46 cancer-related genes). NanoDrop: absorption spectra of samples showed different degrees of organic contamination (230 nm spike, A260/A230 ratio). Agilent: quality and quantity of the obtained libraries were evaluated by Agilent high sensitivity assay on-chip electrophoresis, where the library is represented by the large band between 150 and 200 bp. Fragments test: histogram showing length and abundance of produced sequences. Sample FFPE 5 did not produce a good library due to high organic contamination; this is revealed by the remarkable spike at 230 nm that concurs to the low 260/230 ratio, and explains the faint electrophoretic band and the almost flat fragments test histogram.

    Techniques Used: Next-Generation Sequencing, Formalin-fixed Paraffin-Embedded, Amplification, Multiplex Assay, Polymerase Chain Reaction, Sensitive Assay, Chromatin Immunoprecipitation, Electrophoresis, Produced

    Influence of RNA contamination on DNA quantification. DNA quantifications (n = 5) by NanoDrop and Qubit in the presence of RNA contamination. A DNA sample with a concentration of 38 ng/µl was mixed with different volumes of total RNA at 33 ng/µl extracted from the same tissue sample to obtain the indicated ratios; bars and brackets indicate mean and 95% confidence interval; asterisks show measurements significantly different from pure DNA (* p
    Figure Legend Snippet: Influence of RNA contamination on DNA quantification. DNA quantifications (n = 5) by NanoDrop and Qubit in the presence of RNA contamination. A DNA sample with a concentration of 38 ng/µl was mixed with different volumes of total RNA at 33 ng/µl extracted from the same tissue sample to obtain the indicated ratios; bars and brackets indicate mean and 95% confidence interval; asterisks show measurements significantly different from pure DNA (* p

    Techniques Used: Concentration Assay

    Cross-validation of DNA samples quantification by qPCR. Bland-Altman plots for inter-technology (NanoDrop or Qubit vs. qPCR) comparison of all samples (A), and according to the different sample sources, as indicated (B, C). A) Qubit measurements show high correlation (mean measured/expected ratio = 0.92; SD = 0.69; Wilcoxon signed rank test p = 0.07) with the measurements obtained by qPCR (x-axis), whereas NanoDrop measurements tend to overestimate samples concentration (mean measured/expected ratio = 3.8; SD = 6.4; Wilcoxon signed rank test p
    Figure Legend Snippet: Cross-validation of DNA samples quantification by qPCR. Bland-Altman plots for inter-technology (NanoDrop or Qubit vs. qPCR) comparison of all samples (A), and according to the different sample sources, as indicated (B, C). A) Qubit measurements show high correlation (mean measured/expected ratio = 0.92; SD = 0.69; Wilcoxon signed rank test p = 0.07) with the measurements obtained by qPCR (x-axis), whereas NanoDrop measurements tend to overestimate samples concentration (mean measured/expected ratio = 3.8; SD = 6.4; Wilcoxon signed rank test p

    Techniques Used: Real-time Polymerase Chain Reaction, Concentration Assay

    Intra- and inter-method accuracy and precision. Distribution of DNA sample concentration (dispersion chart) was estimated by both NanoDrop (black) and Qubit (gray) on repeated (n = 20) measurements of two commercial human genomic DNA preparations (Sample L 200 ng/µl; Sample G 5 ng/µl). For both samples, NanoDrop overestimated the DNA concentration (+8.8% for L and +24.0% for G, p
    Figure Legend Snippet: Intra- and inter-method accuracy and precision. Distribution of DNA sample concentration (dispersion chart) was estimated by both NanoDrop (black) and Qubit (gray) on repeated (n = 20) measurements of two commercial human genomic DNA preparations (Sample L 200 ng/µl; Sample G 5 ng/µl). For both samples, NanoDrop overestimated the DNA concentration (+8.8% for L and +24.0% for G, p

    Techniques Used: Concentration Assay

    7) Product Images from "Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs"

    Article Title: Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs

    Journal: Scientific Reports

    doi: 10.1038/s41598-017-08134-3

    Correlations between Nanoquant, Nanodrop and Qubit. Correlations between techniques using original and diluted plasma samples ( a – c ). Correlations between techniques using concentrated plasma samples ≥2 ng/µL ( d – f ). Regression lines (black) with their 95% confidence interval (dashed green) and 95% prediction interval (dashed blue) were generated from the correlation of n = 41 ( a – c ) and n = 15 ( d – f ) quantification values. Correlations were assessed with Spearman rank correlation coefficient (ρ) and linear regression R 2 . Concentrations are expressed in ng/µL.
    Figure Legend Snippet: Correlations between Nanoquant, Nanodrop and Qubit. Correlations between techniques using original and diluted plasma samples ( a – c ). Correlations between techniques using concentrated plasma samples ≥2 ng/µL ( d – f ). Regression lines (black) with their 95% confidence interval (dashed green) and 95% prediction interval (dashed blue) were generated from the correlation of n = 41 ( a – c ) and n = 15 ( d – f ) quantification values. Correlations were assessed with Spearman rank correlation coefficient (ρ) and linear regression R 2 . Concentrations are expressed in ng/µL.

    Techniques Used: Generated

    Quantification of miRNA-Ref samples at different normalized concentrations assessed by Nanoquant, Nanodrop, Qubit and Bio-PicoChip. Evaluation of the performance of the four quantification techniques in a series of five increasing miRNA-Ref concentrations prepared from the 10 ng/μL working solution. Data on the X axis are normalized to the lowest concentration (data in Supplementary Table S1 ). Values for all four platforms increased proportionally with increasing concentrations.
    Figure Legend Snippet: Quantification of miRNA-Ref samples at different normalized concentrations assessed by Nanoquant, Nanodrop, Qubit and Bio-PicoChip. Evaluation of the performance of the four quantification techniques in a series of five increasing miRNA-Ref concentrations prepared from the 10 ng/μL working solution. Data on the X axis are normalized to the lowest concentration (data in Supplementary Table S1 ). Values for all four platforms increased proportionally with increasing concentrations.

    Techniques Used: Concentration Assay

    Quantification of plasma samples at different normalized concentrations assessed by Nanoquant, Nanodrop, Qubit and Bio-PicoChip. Evaluation of the performance of the four quantification techniques in a series of five increasing concentrations prepared from the pooled plasma. Data on the X axis are normalized to the lowest concentration (data in Supplementary Table S3 ). Bio-PicoChip results showed high variability and did not increase proportionally with increasing concentrations.
    Figure Legend Snippet: Quantification of plasma samples at different normalized concentrations assessed by Nanoquant, Nanodrop, Qubit and Bio-PicoChip. Evaluation of the performance of the four quantification techniques in a series of five increasing concentrations prepared from the pooled plasma. Data on the X axis are normalized to the lowest concentration (data in Supplementary Table S3 ). Bio-PicoChip results showed high variability and did not increase proportionally with increasing concentrations.

    Techniques Used: Concentration Assay

    8) Product Images from "Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs"

    Article Title: Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs

    Journal: Scientific Reports

    doi: 10.1038/s41598-017-08134-3

    Correlations between Nanoquant, Nanodrop and Qubit. Correlations between techniques using original and diluted plasma samples ( a – c ). Correlations between techniques using concentrated plasma samples ≥2 ng/µL ( d – f ). Regression lines (black) with their 95% confidence interval (dashed green) and 95% prediction interval (dashed blue) were generated from the correlation of n = 41 ( a – c ) and n = 15 ( d – f ) quantification values. Correlations were assessed with Spearman rank correlation coefficient (ρ) and linear regression R 2 . Concentrations are expressed in ng/µL.
    Figure Legend Snippet: Correlations between Nanoquant, Nanodrop and Qubit. Correlations between techniques using original and diluted plasma samples ( a – c ). Correlations between techniques using concentrated plasma samples ≥2 ng/µL ( d – f ). Regression lines (black) with their 95% confidence interval (dashed green) and 95% prediction interval (dashed blue) were generated from the correlation of n = 41 ( a – c ) and n = 15 ( d – f ) quantification values. Correlations were assessed with Spearman rank correlation coefficient (ρ) and linear regression R 2 . Concentrations are expressed in ng/µL.

    Techniques Used: Generated

    Quantification of miRNA-Ref samples at different normalized concentrations assessed by Nanoquant, Nanodrop, Qubit and Bio-PicoChip. Evaluation of the performance of the four quantification techniques in a series of five increasing miRNA-Ref concentrations prepared from the 10 ng/μL working solution. Data on the X axis are normalized to the lowest concentration (data in Supplementary Table S1 ). Values for all four platforms increased proportionally with increasing concentrations.
    Figure Legend Snippet: Quantification of miRNA-Ref samples at different normalized concentrations assessed by Nanoquant, Nanodrop, Qubit and Bio-PicoChip. Evaluation of the performance of the four quantification techniques in a series of five increasing miRNA-Ref concentrations prepared from the 10 ng/μL working solution. Data on the X axis are normalized to the lowest concentration (data in Supplementary Table S1 ). Values for all four platforms increased proportionally with increasing concentrations.

    Techniques Used: Concentration Assay

    Quantification of plasma samples at different normalized concentrations assessed by Nanoquant, Nanodrop, Qubit and Bio-PicoChip. Evaluation of the performance of the four quantification techniques in a series of five increasing concentrations prepared from the pooled plasma. Data on the X axis are normalized to the lowest concentration (data in Supplementary Table S3 ). Bio-PicoChip results showed high variability and did not increase proportionally with increasing concentrations.
    Figure Legend Snippet: Quantification of plasma samples at different normalized concentrations assessed by Nanoquant, Nanodrop, Qubit and Bio-PicoChip. Evaluation of the performance of the four quantification techniques in a series of five increasing concentrations prepared from the pooled plasma. Data on the X axis are normalized to the lowest concentration (data in Supplementary Table S3 ). Bio-PicoChip results showed high variability and did not increase proportionally with increasing concentrations.

    Techniques Used: Concentration Assay

    9) Product Images from "Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs"

    Article Title: Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs

    Journal: Scientific Reports

    doi: 10.1038/s41598-017-08134-3

    Correlations between Nanoquant, Nanodrop and Qubit. Correlations between techniques using original and diluted plasma samples ( a – c ). Correlations between techniques using concentrated plasma samples ≥2 ng/µL ( d – f ). Regression lines (black) with their 95% confidence interval (dashed green) and 95% prediction interval (dashed blue) were generated from the correlation of n = 41 ( a – c ) and n = 15 ( d – f ) quantification values. Correlations were assessed with Spearman rank correlation coefficient (ρ) and linear regression R 2 . Concentrations are expressed in ng/µL.
    Figure Legend Snippet: Correlations between Nanoquant, Nanodrop and Qubit. Correlations between techniques using original and diluted plasma samples ( a – c ). Correlations between techniques using concentrated plasma samples ≥2 ng/µL ( d – f ). Regression lines (black) with their 95% confidence interval (dashed green) and 95% prediction interval (dashed blue) were generated from the correlation of n = 41 ( a – c ) and n = 15 ( d – f ) quantification values. Correlations were assessed with Spearman rank correlation coefficient (ρ) and linear regression R 2 . Concentrations are expressed in ng/µL.

    Techniques Used: Generated

    Quantification of miRNA-Ref samples at different normalized concentrations assessed by Nanoquant, Nanodrop, Qubit and Bio-PicoChip. Evaluation of the performance of the four quantification techniques in a series of five increasing miRNA-Ref concentrations prepared from the 10 ng/μL working solution. Data on the X axis are normalized to the lowest concentration (data in Supplementary Table S1 ). Values for all four platforms increased proportionally with increasing concentrations.
    Figure Legend Snippet: Quantification of miRNA-Ref samples at different normalized concentrations assessed by Nanoquant, Nanodrop, Qubit and Bio-PicoChip. Evaluation of the performance of the four quantification techniques in a series of five increasing miRNA-Ref concentrations prepared from the 10 ng/μL working solution. Data on the X axis are normalized to the lowest concentration (data in Supplementary Table S1 ). Values for all four platforms increased proportionally with increasing concentrations.

    Techniques Used: Concentration Assay

    Quantification of plasma samples at different normalized concentrations assessed by Nanoquant, Nanodrop, Qubit and Bio-PicoChip. Evaluation of the performance of the four quantification techniques in a series of five increasing concentrations prepared from the pooled plasma. Data on the X axis are normalized to the lowest concentration (data in Supplementary Table S3 ). Bio-PicoChip results showed high variability and did not increase proportionally with increasing concentrations.
    Figure Legend Snippet: Quantification of plasma samples at different normalized concentrations assessed by Nanoquant, Nanodrop, Qubit and Bio-PicoChip. Evaluation of the performance of the four quantification techniques in a series of five increasing concentrations prepared from the pooled plasma. Data on the X axis are normalized to the lowest concentration (data in Supplementary Table S3 ). Bio-PicoChip results showed high variability and did not increase proportionally with increasing concentrations.

    Techniques Used: Concentration Assay

    10) Product Images from "Quantification of massively parallel sequencing libraries – a comparative study of eight methods"

    Article Title: Quantification of massively parallel sequencing libraries – a comparative study of eight methods

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-19574-w

    Correlations between library concentration estimates and library coverage. A total of 35 Precision ID Ancestry Panel libraries were quantified prior to sequencing using the Qubit ( a ), TapeStation ( b ), or ABI7500 qPCR ( c ) instrument. The ABI7500 was used in combination with the IonLibQuant assay. Linear regression lines (black line) are plotted with 95% confidence interval (grey area). No correlation was observed between concentration estimates and coverage when using Qubit (R 2 = 7.4*10 −2 , p = 0.114) or TapeStation (R 2 = 6.7*10 −3 , p = 0.651), while the correlation obtained with qPCR was R 2 = 0.49 and p = 2.53*10 −6 .
    Figure Legend Snippet: Correlations between library concentration estimates and library coverage. A total of 35 Precision ID Ancestry Panel libraries were quantified prior to sequencing using the Qubit ( a ), TapeStation ( b ), or ABI7500 qPCR ( c ) instrument. The ABI7500 was used in combination with the IonLibQuant assay. Linear regression lines (black line) are plotted with 95% confidence interval (grey area). No correlation was observed between concentration estimates and coverage when using Qubit (R 2 = 7.4*10 −2 , p = 0.114) or TapeStation (R 2 = 6.7*10 −3 , p = 0.651), while the correlation obtained with qPCR was R 2 = 0.49 and p = 2.53*10 −6 .

    Techniques Used: Concentration Assay, Sequencing, Real-time Polymerase Chain Reaction

    Quantification of synthetic double-stranded oligos. Four dilutions of two synthetic double-stranded oligos consisting of either the Ion Torrent “A” and “P1” adapter sequences ( a ) or the Illumina “i7” and “i5” adapter sequences ( b ) were quantified in duplicate with the NanoDrop ( ), Qubit ( ), Bioanalyzer ( ), GX Touch ( ), TapeStation ( ), and Fragment Analyzer ( ). The mean of the measured oligo concentrations were plotted against the concentrations given by the oligo supplier.
    Figure Legend Snippet: Quantification of synthetic double-stranded oligos. Four dilutions of two synthetic double-stranded oligos consisting of either the Ion Torrent “A” and “P1” adapter sequences ( a ) or the Illumina “i7” and “i5” adapter sequences ( b ) were quantified in duplicate with the NanoDrop ( ), Qubit ( ), Bioanalyzer ( ), GX Touch ( ), TapeStation ( ), and Fragment Analyzer ( ). The mean of the measured oligo concentrations were plotted against the concentrations given by the oligo supplier.

    Techniques Used:

    11) Product Images from "Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq"

    Article Title: Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq

    Journal: Retrovirology

    doi: 10.1186/s12977-014-0122-8

    Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the Illumina MiSeq. (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.
    Figure Legend Snippet: Preparation and sequencing of samples. (A) Plasma is isolated from whole blood from up to 96 samples. (B) Viral RNA is isolated from up to 1 ml of plasma. (C) Viral RNA is used in a one-step RT-PCR amplification of a 2.8 kb region of the pol gene. When nested PCR is required, a 4.8 kb region is amplified as an external PCR followed by the 2.8 kb nested PCR of the pol gene. (D) PCR products are purified either by gel electrophoresis followed by gel extraction or through size-exclusion magnetic beads and then quantitated using the Qubit system. (E) Purified products are randomly fragmented and subjected to a limited cycle PCR to add sequencing adaptors and indices used for multiplexing samples. (F) Newly created libraries are purified by size-exclusion magnetic beads to remove short fragments. (G) The average size of the library fragments are calculated by bioanalysis and final concentration of the libraries calculated by Qubit are used to normalize each library and pool multiple libraries together at equimolar ratios. (H) Libraries are sequenced on the Illumina MiSeq. (I) Geneious Pro Software is used to trim sequencing reads based on quality scores and assemble the reads to a HXB2 reference sequence annotated with HIV drug resistance mutations. Geneious is used to identify variants within each sample relative to HXB2. Finally, variants associated with drug resistance mutations were extracted and their frequencies noted. Details about the analysis parameters are outlined in the Methods section.

    Techniques Used: Sequencing, Isolation, Reverse Transcription Polymerase Chain Reaction, Amplification, Nested PCR, Polymerase Chain Reaction, Purification, Nucleic Acid Electrophoresis, Gel Extraction, Magnetic Beads, Multiplexing, Concentration Assay, Software

    12) Product Images from "Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions"

    Article Title: Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0150528

    Quantification and qualification of FFPE-DNA. (A) Each FFPE-DNA was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line indicates the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. The detection limits of each measurement are described in Fig 1 . (B) Various lengths of the target sequence were amplified from Frozen- and FFPE-DNAs. The amplified products were electrophoresed on agarose gels. Lane 1, Frozen-H1; lane 2, Frozen-H2; lane 3, Frozen-H3; lane 4, FFPE-H1; lane 5, FFPE-H2; and lane 6, FFPE-H3.
    Figure Legend Snippet: Quantification and qualification of FFPE-DNA. (A) Each FFPE-DNA was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line indicates the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. The detection limits of each measurement are described in Fig 1 . (B) Various lengths of the target sequence were amplified from Frozen- and FFPE-DNAs. The amplified products were electrophoresed on agarose gels. Lane 1, Frozen-H1; lane 2, Frozen-H2; lane 3, Frozen-H3; lane 4, FFPE-H1; lane 5, FFPE-H2; and lane 6, FFPE-H3.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Concentration Assay, Real-time Polymerase Chain Reaction, Sequencing, Amplification

    Dilution curves of Frozen-DNA diluted with distilled water as determined by NanoDrop, Qubit and qPCR. Each Frozen-DNA sample was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line shows the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution measured by NanoDrop is shown at the top right: dilution ratio = 1. Two additional concentrations are also shown in each graph. The detection limits of NanoDrop, BR-Qubit, HS-Qubit and qPCR are 2 ng/μl, 2 ng/μl, 0.2 ng/μl and 1 pg/μl, respectively.
    Figure Legend Snippet: Dilution curves of Frozen-DNA diluted with distilled water as determined by NanoDrop, Qubit and qPCR. Each Frozen-DNA sample was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line shows the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution measured by NanoDrop is shown at the top right: dilution ratio = 1. Two additional concentrations are also shown in each graph. The detection limits of NanoDrop, BR-Qubit, HS-Qubit and qPCR are 2 ng/μl, 2 ng/μl, 0.2 ng/μl and 1 pg/μl, respectively.

    Techniques Used: Real-time Polymerase Chain Reaction, Concentration Assay

    Quantification and qualification of Trizol-DNA. (A) Trizol-DNA was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line indicates the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. The detection limits of each measurement are described in Fig 1 . (B) Various lengths of the target sequence were amplified from Trizol-DNAs, and the amplified products were electrophoresed on an agarose gel. Lane 1, Frozen-H1; lane 2, Trizol-h1; lane 3, Trizol-h2; lane 4, Trizol-h3; lane 5, Trizol-h4; lane 6, Trizol-h5; lane 7, Trizol-h6; and lane 8, Trizol-h7.
    Figure Legend Snippet: Quantification and qualification of Trizol-DNA. (A) Trizol-DNA was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line indicates the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. The detection limits of each measurement are described in Fig 1 . (B) Various lengths of the target sequence were amplified from Trizol-DNAs, and the amplified products were electrophoresed on an agarose gel. Lane 1, Frozen-H1; lane 2, Trizol-h1; lane 3, Trizol-h2; lane 4, Trizol-h3; lane 5, Trizol-h4; lane 6, Trizol-h5; lane 7, Trizol-h6; and lane 8, Trizol-h7.

    Techniques Used: Concentration Assay, Real-time Polymerase Chain Reaction, Sequencing, Amplification, Agarose Gel Electrophoresis

    Quantification of Frozen-DNA diluted with various solutions by Qubit. (A) Frozen-R2 DNA was serially diluted with distilled water (black) or TE buffer (white), and the concentration of each diluent was measured by BR-Qubit (square) and HS-Qubit (diamond). (B) Eleven Frozen-DNAs were diluted with distilled water or TE buffer to approximately 20 ng/μl, as measured by NanoDrop, and the concentration of each diluent was measured by HS-Qubit. The ratios of the Qubit to NanoDrop values were determined for each diluent. (C, D) Frozen-R1 DNA was serially diluted with distilled water (closed diamonds), 0.01 mM NaCl (open diamonds), 0.1 mM NaCl (squares), 1 mM NaCl (triangles) or 10 mM NaCl (circles). The broken line shows the expected NanoDrop values. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. (D) The Q/E ratio was determined for each diluent, as shown in Fig 3C. (E) Frozen-R2 DNA was serially diluted with TE buffer (white) or distilled water (black), and a 0.1 volume of 100 mM Tris-HCl/10 mM EDTA was added to the latter diluent (gray). The expected NanoDrop values in parentheses indicate those diluted with distilled water. The detection limits of each measurement are described in Fig 1 .
    Figure Legend Snippet: Quantification of Frozen-DNA diluted with various solutions by Qubit. (A) Frozen-R2 DNA was serially diluted with distilled water (black) or TE buffer (white), and the concentration of each diluent was measured by BR-Qubit (square) and HS-Qubit (diamond). (B) Eleven Frozen-DNAs were diluted with distilled water or TE buffer to approximately 20 ng/μl, as measured by NanoDrop, and the concentration of each diluent was measured by HS-Qubit. The ratios of the Qubit to NanoDrop values were determined for each diluent. (C, D) Frozen-R1 DNA was serially diluted with distilled water (closed diamonds), 0.01 mM NaCl (open diamonds), 0.1 mM NaCl (squares), 1 mM NaCl (triangles) or 10 mM NaCl (circles). The broken line shows the expected NanoDrop values. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. (D) The Q/E ratio was determined for each diluent, as shown in Fig 3C. (E) Frozen-R2 DNA was serially diluted with TE buffer (white) or distilled water (black), and a 0.1 volume of 100 mM Tris-HCl/10 mM EDTA was added to the latter diluent (gray). The expected NanoDrop values in parentheses indicate those diluted with distilled water. The detection limits of each measurement are described in Fig 1 .

    Techniques Used: Concentration Assay

    13) Product Images from "DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples"

    Article Title: DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0062692

    Significant discrepancies in DNA quantification by NanoDrop and Qubit. A total of 100 ng of DNA based on NanoDrop (N, black bars) or Qubit (Q, grey bars) measurements was analyzed by electrophoresis on 0.8% agarose gel. Sample ID is indicated at the bottom. Lane L contains 200 ng of DNA as the reference for normalization. Densitometric analysis (bar chart) was performed by ImageJ software [20] . It is clear from the electrophoretic bands and their densitometric charts that NanoDrop overestimates DNA concentration.
    Figure Legend Snippet: Significant discrepancies in DNA quantification by NanoDrop and Qubit. A total of 100 ng of DNA based on NanoDrop (N, black bars) or Qubit (Q, grey bars) measurements was analyzed by electrophoresis on 0.8% agarose gel. Sample ID is indicated at the bottom. Lane L contains 200 ng of DNA as the reference for normalization. Densitometric analysis (bar chart) was performed by ImageJ software [20] . It is clear from the electrophoretic bands and their densitometric charts that NanoDrop overestimates DNA concentration.

    Techniques Used: Electrophoresis, Agarose Gel Electrophoresis, Software, Concentration Assay

    DNA qualification for next-generation sequencing applications. Effect of low-quality DNA on next-generation sequencing (NGS) workflow. Three FFPE samples were tested for construction of NGS amplicon libraries (Ion Torrent Ampliseq Cancer Panel). Qubit: 40 ng of DNA according to Qubit measurement were processed using the Ampliseq library construction kit (multiplex PCR amplification of 191 DNA regions from 46 cancer-related genes). NanoDrop: absorption spectra of samples showed different degrees of organic contamination (230 nm spike, A260/A230 ratio). Agilent: quality and quantity of the obtained libraries were evaluated by Agilent high sensitivity assay on-chip electrophoresis, where the library is represented by the large band between 150 and 200 bp. Fragments test: histogram showing length and abundance of produced sequences. Sample FFPE 5 did not produce a good library due to high organic contamination; this is revealed by the remarkable spike at 230 nm that concurs to the low 260/230 ratio, and explains the faint electrophoretic band and the almost flat fragments test histogram.
    Figure Legend Snippet: DNA qualification for next-generation sequencing applications. Effect of low-quality DNA on next-generation sequencing (NGS) workflow. Three FFPE samples were tested for construction of NGS amplicon libraries (Ion Torrent Ampliseq Cancer Panel). Qubit: 40 ng of DNA according to Qubit measurement were processed using the Ampliseq library construction kit (multiplex PCR amplification of 191 DNA regions from 46 cancer-related genes). NanoDrop: absorption spectra of samples showed different degrees of organic contamination (230 nm spike, A260/A230 ratio). Agilent: quality and quantity of the obtained libraries were evaluated by Agilent high sensitivity assay on-chip electrophoresis, where the library is represented by the large band between 150 and 200 bp. Fragments test: histogram showing length and abundance of produced sequences. Sample FFPE 5 did not produce a good library due to high organic contamination; this is revealed by the remarkable spike at 230 nm that concurs to the low 260/230 ratio, and explains the faint electrophoretic band and the almost flat fragments test histogram.

    Techniques Used: Next-Generation Sequencing, Formalin-fixed Paraffin-Embedded, Amplification, Multiplex Assay, Polymerase Chain Reaction, Sensitive Assay, Chromatin Immunoprecipitation, Electrophoresis, Produced

    Influence of RNA contamination on DNA quantification. DNA quantifications (n = 5) by NanoDrop and Qubit in the presence of RNA contamination. A DNA sample with a concentration of 38 ng/µl was mixed with different volumes of total RNA at 33 ng/µl extracted from the same tissue sample to obtain the indicated ratios; bars and brackets indicate mean and 95% confidence interval; asterisks show measurements significantly different from pure DNA (* p
    Figure Legend Snippet: Influence of RNA contamination on DNA quantification. DNA quantifications (n = 5) by NanoDrop and Qubit in the presence of RNA contamination. A DNA sample with a concentration of 38 ng/µl was mixed with different volumes of total RNA at 33 ng/µl extracted from the same tissue sample to obtain the indicated ratios; bars and brackets indicate mean and 95% confidence interval; asterisks show measurements significantly different from pure DNA (* p

    Techniques Used: Concentration Assay

    Cross-validation of DNA samples quantification by qPCR. Bland-Altman plots for inter-technology (NanoDrop or Qubit vs. qPCR) comparison of all samples (A), and according to the different sample sources, as indicated (B, C). A) Qubit measurements show high correlation (mean measured/expected ratio = 0.92; SD = 0.69; Wilcoxon signed rank test p = 0.07) with the measurements obtained by qPCR (x-axis), whereas NanoDrop measurements tend to overestimate samples concentration (mean measured/expected ratio = 3.8; SD = 6.4; Wilcoxon signed rank test p
    Figure Legend Snippet: Cross-validation of DNA samples quantification by qPCR. Bland-Altman plots for inter-technology (NanoDrop or Qubit vs. qPCR) comparison of all samples (A), and according to the different sample sources, as indicated (B, C). A) Qubit measurements show high correlation (mean measured/expected ratio = 0.92; SD = 0.69; Wilcoxon signed rank test p = 0.07) with the measurements obtained by qPCR (x-axis), whereas NanoDrop measurements tend to overestimate samples concentration (mean measured/expected ratio = 3.8; SD = 6.4; Wilcoxon signed rank test p

    Techniques Used: Real-time Polymerase Chain Reaction, Concentration Assay

    Intra- and inter-method accuracy and precision. Distribution of DNA sample concentration (dispersion chart) was estimated by both NanoDrop (black) and Qubit (gray) on repeated (n = 20) measurements of two commercial human genomic DNA preparations (Sample L 200 ng/µl; Sample G 5 ng/µl). For both samples, NanoDrop overestimated the DNA concentration (+8.8% for L and +24.0% for G, p
    Figure Legend Snippet: Intra- and inter-method accuracy and precision. Distribution of DNA sample concentration (dispersion chart) was estimated by both NanoDrop (black) and Qubit (gray) on repeated (n = 20) measurements of two commercial human genomic DNA preparations (Sample L 200 ng/µl; Sample G 5 ng/µl). For both samples, NanoDrop overestimated the DNA concentration (+8.8% for L and +24.0% for G, p

    Techniques Used: Concentration Assay

    14) Product Images from "DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples"

    Article Title: DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0062692

    Significant discrepancies in DNA quantification by NanoDrop and Qubit. A total of 100 ng of DNA based on NanoDrop (N, black bars) or Qubit (Q, grey bars) measurements was analyzed by electrophoresis on 0.8% agarose gel. Sample ID is indicated at the bottom. Lane L contains 200 ng of DNA as the reference for normalization. Densitometric analysis (bar chart) was performed by ImageJ software [20] . It is clear from the electrophoretic bands and their densitometric charts that NanoDrop overestimates DNA concentration.
    Figure Legend Snippet: Significant discrepancies in DNA quantification by NanoDrop and Qubit. A total of 100 ng of DNA based on NanoDrop (N, black bars) or Qubit (Q, grey bars) measurements was analyzed by electrophoresis on 0.8% agarose gel. Sample ID is indicated at the bottom. Lane L contains 200 ng of DNA as the reference for normalization. Densitometric analysis (bar chart) was performed by ImageJ software [20] . It is clear from the electrophoretic bands and their densitometric charts that NanoDrop overestimates DNA concentration.

    Techniques Used: Electrophoresis, Agarose Gel Electrophoresis, Software, Concentration Assay

    DNA qualification for next-generation sequencing applications. Effect of low-quality DNA on next-generation sequencing (NGS) workflow. Three FFPE samples were tested for construction of NGS amplicon libraries (Ion Torrent Ampliseq Cancer Panel). Qubit: 40 ng of DNA according to Qubit measurement were processed using the Ampliseq library construction kit (multiplex PCR amplification of 191 DNA regions from 46 cancer-related genes). NanoDrop: absorption spectra of samples showed different degrees of organic contamination (230 nm spike, A260/A230 ratio). Agilent: quality and quantity of the obtained libraries were evaluated by Agilent high sensitivity assay on-chip electrophoresis, where the library is represented by the large band between 150 and 200 bp. Fragments test: histogram showing length and abundance of produced sequences. Sample FFPE 5 did not produce a good library due to high organic contamination; this is revealed by the remarkable spike at 230 nm that concurs to the low 260/230 ratio, and explains the faint electrophoretic band and the almost flat fragments test histogram.
    Figure Legend Snippet: DNA qualification for next-generation sequencing applications. Effect of low-quality DNA on next-generation sequencing (NGS) workflow. Three FFPE samples were tested for construction of NGS amplicon libraries (Ion Torrent Ampliseq Cancer Panel). Qubit: 40 ng of DNA according to Qubit measurement were processed using the Ampliseq library construction kit (multiplex PCR amplification of 191 DNA regions from 46 cancer-related genes). NanoDrop: absorption spectra of samples showed different degrees of organic contamination (230 nm spike, A260/A230 ratio). Agilent: quality and quantity of the obtained libraries were evaluated by Agilent high sensitivity assay on-chip electrophoresis, where the library is represented by the large band between 150 and 200 bp. Fragments test: histogram showing length and abundance of produced sequences. Sample FFPE 5 did not produce a good library due to high organic contamination; this is revealed by the remarkable spike at 230 nm that concurs to the low 260/230 ratio, and explains the faint electrophoretic band and the almost flat fragments test histogram.

    Techniques Used: Next-Generation Sequencing, Formalin-fixed Paraffin-Embedded, Amplification, Multiplex Assay, Polymerase Chain Reaction, Sensitive Assay, Chromatin Immunoprecipitation, Electrophoresis, Produced

    Influence of RNA contamination on DNA quantification. DNA quantifications (n = 5) by NanoDrop and Qubit in the presence of RNA contamination. A DNA sample with a concentration of 38 ng/µl was mixed with different volumes of total RNA at 33 ng/µl extracted from the same tissue sample to obtain the indicated ratios; bars and brackets indicate mean and 95% confidence interval; asterisks show measurements significantly different from pure DNA (* p
    Figure Legend Snippet: Influence of RNA contamination on DNA quantification. DNA quantifications (n = 5) by NanoDrop and Qubit in the presence of RNA contamination. A DNA sample with a concentration of 38 ng/µl was mixed with different volumes of total RNA at 33 ng/µl extracted from the same tissue sample to obtain the indicated ratios; bars and brackets indicate mean and 95% confidence interval; asterisks show measurements significantly different from pure DNA (* p

    Techniques Used: Concentration Assay

    Cross-validation of DNA samples quantification by qPCR. Bland-Altman plots for inter-technology (NanoDrop or Qubit vs. qPCR) comparison of all samples (A), and according to the different sample sources, as indicated (B, C). A) Qubit measurements show high correlation (mean measured/expected ratio = 0.92; SD = 0.69; Wilcoxon signed rank test p = 0.07) with the measurements obtained by qPCR (x-axis), whereas NanoDrop measurements tend to overestimate samples concentration (mean measured/expected ratio = 3.8; SD = 6.4; Wilcoxon signed rank test p
    Figure Legend Snippet: Cross-validation of DNA samples quantification by qPCR. Bland-Altman plots for inter-technology (NanoDrop or Qubit vs. qPCR) comparison of all samples (A), and according to the different sample sources, as indicated (B, C). A) Qubit measurements show high correlation (mean measured/expected ratio = 0.92; SD = 0.69; Wilcoxon signed rank test p = 0.07) with the measurements obtained by qPCR (x-axis), whereas NanoDrop measurements tend to overestimate samples concentration (mean measured/expected ratio = 3.8; SD = 6.4; Wilcoxon signed rank test p

    Techniques Used: Real-time Polymerase Chain Reaction, Concentration Assay

    Intra- and inter-method accuracy and precision. Distribution of DNA sample concentration (dispersion chart) was estimated by both NanoDrop (black) and Qubit (gray) on repeated (n = 20) measurements of two commercial human genomic DNA preparations (Sample L 200 ng/µl; Sample G 5 ng/µl). For both samples, NanoDrop overestimated the DNA concentration (+8.8% for L and +24.0% for G, p
    Figure Legend Snippet: Intra- and inter-method accuracy and precision. Distribution of DNA sample concentration (dispersion chart) was estimated by both NanoDrop (black) and Qubit (gray) on repeated (n = 20) measurements of two commercial human genomic DNA preparations (Sample L 200 ng/µl; Sample G 5 ng/µl). For both samples, NanoDrop overestimated the DNA concentration (+8.8% for L and +24.0% for G, p

    Techniques Used: Concentration Assay

    15) Product Images from "Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions"

    Article Title: Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0150528

    Quantification and qualification of FFPE-DNA. (A) Each FFPE-DNA was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line indicates the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. The detection limits of each measurement are described in Fig 1 . (B) Various lengths of the target sequence were amplified from Frozen- and FFPE-DNAs. The amplified products were electrophoresed on agarose gels. Lane 1, Frozen-H1; lane 2, Frozen-H2; lane 3, Frozen-H3; lane 4, FFPE-H1; lane 5, FFPE-H2; and lane 6, FFPE-H3.
    Figure Legend Snippet: Quantification and qualification of FFPE-DNA. (A) Each FFPE-DNA was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line indicates the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. The detection limits of each measurement are described in Fig 1 . (B) Various lengths of the target sequence were amplified from Frozen- and FFPE-DNAs. The amplified products were electrophoresed on agarose gels. Lane 1, Frozen-H1; lane 2, Frozen-H2; lane 3, Frozen-H3; lane 4, FFPE-H1; lane 5, FFPE-H2; and lane 6, FFPE-H3.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Concentration Assay, Real-time Polymerase Chain Reaction, Sequencing, Amplification

    Dilution curves of Frozen-DNA diluted with distilled water as determined by NanoDrop, Qubit and qPCR. Each Frozen-DNA sample was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line shows the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution measured by NanoDrop is shown at the top right: dilution ratio = 1. Two additional concentrations are also shown in each graph. The detection limits of NanoDrop, BR-Qubit, HS-Qubit and qPCR are 2 ng/μl, 2 ng/μl, 0.2 ng/μl and 1 pg/μl, respectively.
    Figure Legend Snippet: Dilution curves of Frozen-DNA diluted with distilled water as determined by NanoDrop, Qubit and qPCR. Each Frozen-DNA sample was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line shows the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution measured by NanoDrop is shown at the top right: dilution ratio = 1. Two additional concentrations are also shown in each graph. The detection limits of NanoDrop, BR-Qubit, HS-Qubit and qPCR are 2 ng/μl, 2 ng/μl, 0.2 ng/μl and 1 pg/μl, respectively.

    Techniques Used: Real-time Polymerase Chain Reaction, Concentration Assay

    Quantification and qualification of Trizol-DNA. (A) Trizol-DNA was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line indicates the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. The detection limits of each measurement are described in Fig 1 . (B) Various lengths of the target sequence were amplified from Trizol-DNAs, and the amplified products were electrophoresed on an agarose gel. Lane 1, Frozen-H1; lane 2, Trizol-h1; lane 3, Trizol-h2; lane 4, Trizol-h3; lane 5, Trizol-h4; lane 6, Trizol-h5; lane 7, Trizol-h6; and lane 8, Trizol-h7.
    Figure Legend Snippet: Quantification and qualification of Trizol-DNA. (A) Trizol-DNA was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line indicates the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. The detection limits of each measurement are described in Fig 1 . (B) Various lengths of the target sequence were amplified from Trizol-DNAs, and the amplified products were electrophoresed on an agarose gel. Lane 1, Frozen-H1; lane 2, Trizol-h1; lane 3, Trizol-h2; lane 4, Trizol-h3; lane 5, Trizol-h4; lane 6, Trizol-h5; lane 7, Trizol-h6; and lane 8, Trizol-h7.

    Techniques Used: Concentration Assay, Real-time Polymerase Chain Reaction, Sequencing, Amplification, Agarose Gel Electrophoresis

    Quantification of Frozen-DNA diluted with various solutions by Qubit. (A) Frozen-R2 DNA was serially diluted with distilled water (black) or TE buffer (white), and the concentration of each diluent was measured by BR-Qubit (square) and HS-Qubit (diamond). (B) Eleven Frozen-DNAs were diluted with distilled water or TE buffer to approximately 20 ng/μl, as measured by NanoDrop, and the concentration of each diluent was measured by HS-Qubit. The ratios of the Qubit to NanoDrop values were determined for each diluent. (C, D) Frozen-R1 DNA was serially diluted with distilled water (closed diamonds), 0.01 mM NaCl (open diamonds), 0.1 mM NaCl (squares), 1 mM NaCl (triangles) or 10 mM NaCl (circles). The broken line shows the expected NanoDrop values. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. (D) The Q/E ratio was determined for each diluent, as shown in Fig 3C. (E) Frozen-R2 DNA was serially diluted with TE buffer (white) or distilled water (black), and a 0.1 volume of 100 mM Tris-HCl/10 mM EDTA was added to the latter diluent (gray). The expected NanoDrop values in parentheses indicate those diluted with distilled water. The detection limits of each measurement are described in Fig 1 .
    Figure Legend Snippet: Quantification of Frozen-DNA diluted with various solutions by Qubit. (A) Frozen-R2 DNA was serially diluted with distilled water (black) or TE buffer (white), and the concentration of each diluent was measured by BR-Qubit (square) and HS-Qubit (diamond). (B) Eleven Frozen-DNAs were diluted with distilled water or TE buffer to approximately 20 ng/μl, as measured by NanoDrop, and the concentration of each diluent was measured by HS-Qubit. The ratios of the Qubit to NanoDrop values were determined for each diluent. (C, D) Frozen-R1 DNA was serially diluted with distilled water (closed diamonds), 0.01 mM NaCl (open diamonds), 0.1 mM NaCl (squares), 1 mM NaCl (triangles) or 10 mM NaCl (circles). The broken line shows the expected NanoDrop values. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. (D) The Q/E ratio was determined for each diluent, as shown in Fig 3C. (E) Frozen-R2 DNA was serially diluted with TE buffer (white) or distilled water (black), and a 0.1 volume of 100 mM Tris-HCl/10 mM EDTA was added to the latter diluent (gray). The expected NanoDrop values in parentheses indicate those diluted with distilled water. The detection limits of each measurement are described in Fig 1 .

    Techniques Used: Concentration Assay

    16) Product Images from "Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions"

    Article Title: Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0150528

    Quantification and qualification of FFPE-DNA. (A) Each FFPE-DNA was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line indicates the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. The detection limits of each measurement are described in Fig 1 . (B) Various lengths of the target sequence were amplified from Frozen- and FFPE-DNAs. The amplified products were electrophoresed on agarose gels. Lane 1, Frozen-H1; lane 2, Frozen-H2; lane 3, Frozen-H3; lane 4, FFPE-H1; lane 5, FFPE-H2; and lane 6, FFPE-H3.
    Figure Legend Snippet: Quantification and qualification of FFPE-DNA. (A) Each FFPE-DNA was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line indicates the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. The detection limits of each measurement are described in Fig 1 . (B) Various lengths of the target sequence were amplified from Frozen- and FFPE-DNAs. The amplified products were electrophoresed on agarose gels. Lane 1, Frozen-H1; lane 2, Frozen-H2; lane 3, Frozen-H3; lane 4, FFPE-H1; lane 5, FFPE-H2; and lane 6, FFPE-H3.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Concentration Assay, Real-time Polymerase Chain Reaction, Sequencing, Amplification

    Dilution curves of Frozen-DNA diluted with distilled water as determined by NanoDrop, Qubit and qPCR. Each Frozen-DNA sample was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line shows the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution measured by NanoDrop is shown at the top right: dilution ratio = 1. Two additional concentrations are also shown in each graph. The detection limits of NanoDrop, BR-Qubit, HS-Qubit and qPCR are 2 ng/μl, 2 ng/μl, 0.2 ng/μl and 1 pg/μl, respectively.
    Figure Legend Snippet: Dilution curves of Frozen-DNA diluted with distilled water as determined by NanoDrop, Qubit and qPCR. Each Frozen-DNA sample was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line shows the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution measured by NanoDrop is shown at the top right: dilution ratio = 1. Two additional concentrations are also shown in each graph. The detection limits of NanoDrop, BR-Qubit, HS-Qubit and qPCR are 2 ng/μl, 2 ng/μl, 0.2 ng/μl and 1 pg/μl, respectively.

    Techniques Used: Real-time Polymerase Chain Reaction, Concentration Assay

    Quantification and qualification of Trizol-DNA. (A) Trizol-DNA was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line indicates the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. The detection limits of each measurement are described in Fig 1 . (B) Various lengths of the target sequence were amplified from Trizol-DNAs, and the amplified products were electrophoresed on an agarose gel. Lane 1, Frozen-H1; lane 2, Trizol-h1; lane 3, Trizol-h2; lane 4, Trizol-h3; lane 5, Trizol-h4; lane 6, Trizol-h5; lane 7, Trizol-h6; and lane 8, Trizol-h7.
    Figure Legend Snippet: Quantification and qualification of Trizol-DNA. (A) Trizol-DNA was serially diluted with distilled water, and the concentration of each diluent was measured by NanoDrop (circles), BR-Qubit (squares), HS-Qubit (diamonds) and qPCR (triangles). The broken line indicates the expected NanoDrop value. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. The detection limits of each measurement are described in Fig 1 . (B) Various lengths of the target sequence were amplified from Trizol-DNAs, and the amplified products were electrophoresed on an agarose gel. Lane 1, Frozen-H1; lane 2, Trizol-h1; lane 3, Trizol-h2; lane 4, Trizol-h3; lane 5, Trizol-h4; lane 6, Trizol-h5; lane 7, Trizol-h6; and lane 8, Trizol-h7.

    Techniques Used: Concentration Assay, Real-time Polymerase Chain Reaction, Sequencing, Amplification, Agarose Gel Electrophoresis

    Quantification of Frozen-DNA diluted with various solutions by Qubit. (A) Frozen-R2 DNA was serially diluted with distilled water (black) or TE buffer (white), and the concentration of each diluent was measured by BR-Qubit (square) and HS-Qubit (diamond). (B) Eleven Frozen-DNAs were diluted with distilled water or TE buffer to approximately 20 ng/μl, as measured by NanoDrop, and the concentration of each diluent was measured by HS-Qubit. The ratios of the Qubit to NanoDrop values were determined for each diluent. (C, D) Frozen-R1 DNA was serially diluted with distilled water (closed diamonds), 0.01 mM NaCl (open diamonds), 0.1 mM NaCl (squares), 1 mM NaCl (triangles) or 10 mM NaCl (circles). The broken line shows the expected NanoDrop values. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. (D) The Q/E ratio was determined for each diluent, as shown in Fig 3C. (E) Frozen-R2 DNA was serially diluted with TE buffer (white) or distilled water (black), and a 0.1 volume of 100 mM Tris-HCl/10 mM EDTA was added to the latter diluent (gray). The expected NanoDrop values in parentheses indicate those diluted with distilled water. The detection limits of each measurement are described in Fig 1 .
    Figure Legend Snippet: Quantification of Frozen-DNA diluted with various solutions by Qubit. (A) Frozen-R2 DNA was serially diluted with distilled water (black) or TE buffer (white), and the concentration of each diluent was measured by BR-Qubit (square) and HS-Qubit (diamond). (B) Eleven Frozen-DNAs were diluted with distilled water or TE buffer to approximately 20 ng/μl, as measured by NanoDrop, and the concentration of each diluent was measured by HS-Qubit. The ratios of the Qubit to NanoDrop values were determined for each diluent. (C, D) Frozen-R1 DNA was serially diluted with distilled water (closed diamonds), 0.01 mM NaCl (open diamonds), 0.1 mM NaCl (squares), 1 mM NaCl (triangles) or 10 mM NaCl (circles). The broken line shows the expected NanoDrop values. The concentration (ng/μl) of each original DNA solution, as measured by NanoDrop, is shown at the top right: dilution ratio = 1. (D) The Q/E ratio was determined for each diluent, as shown in Fig 3C. (E) Frozen-R2 DNA was serially diluted with TE buffer (white) or distilled water (black), and a 0.1 volume of 100 mM Tris-HCl/10 mM EDTA was added to the latter diluent (gray). The expected NanoDrop values in parentheses indicate those diluted with distilled water. The detection limits of each measurement are described in Fig 1 .

    Techniques Used: Concentration Assay

    17) Product Images from "Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?"

    Article Title: Nucleic acid extraction from formalin-fixed paraffin-embedded cancer cell line samples: a trade off between quantity and quality?

    Journal: BMC Clinical Pathology

    doi: 10.1186/s12907-016-0039-3

    Comparison of Qubit RNA yields obtained using four off the shelf extraction kits: Geometric mean RNA yield and associated geometric standard error of mean for the four extraction kits tested in this study, n = 30 for each method. P-values show the statistical significance of the difference in yield between each method
    Figure Legend Snippet: Comparison of Qubit RNA yields obtained using four off the shelf extraction kits: Geometric mean RNA yield and associated geometric standard error of mean for the four extraction kits tested in this study, n = 30 for each method. P-values show the statistical significance of the difference in yield between each method

    Techniques Used:

    18) Product Images from "Variation in pre-PCR processing of FFPE samples leads to discrepancies in BRAF and EGFR mutation detection: a diagnostic RING trial"

    Article Title: Variation in pre-PCR processing of FFPE samples leads to discrepancies in BRAF and EGFR mutation detection: a diagnostic RING trial

    Journal: Journal of Clinical Pathology

    doi: 10.1136/jclinpath-2014-202644

    Average Nanodrop:Qubit ratio for each laboratory as well as the average and median ratio for the entire cohort.
    Figure Legend Snippet: Average Nanodrop:Qubit ratio for each laboratory as well as the average and median ratio for the entire cohort.

    Techniques Used:

    Related Articles

    Centrifugation:

    Article Title: CXCL12 methylation-mediated epigenetic regulation of gene expression in papillary thyroid carcinoma
    Article Snippet: The prepared tube was then placed into another 1.5 mL centrifuge tube and we added 80–200 μL ddH2O into the center of the membrane and incubated at room temperature for 2 min. Genomic DNA was eluted after centrifugation at 12,000 × g for 1 min. Quantifications were performed using a NanoDrop (Thermo Fisher Scientific). .. PCR enrichment and Qubit Instruments (Invitrogen, Carlsbad, CA, USA) quantitative library were performed.

    Article Title: Multiplex mutagenesis of four clustered CrRLK1L with CRISPR/Cas9 exposes their growth regulatory roles in response to metal ions
    Article Snippet: RNA in the supernatant was precipitated with 250 µL 10 M LiCl at 4 °C for more than 1.5 h. After centrifugation and EtOH washes the pellet was dissolved in 20 µL RNase free water and stored at −80 °C. .. RNA was quantified with Qubit (Invitrogen) and NanoDrop (Peqlab) systems. cDNA was synthesized from 2.5 µg RNA after RNAse free DNase I digestion (Fermentas) with the M-MuLV H PLUS reverse transcriptase (Peqlab) as described .

    Amplification:

    Article Title: The Gene tia, Harbored by the Subtilase-Encoding Pathogenicity Island, Is Involved in the Ability of Locus of Enterocyte Effacement-Negative Shiga Toxin-Producing Escherichia coli Strains To Invade Monolayers of Epithelial Cells
    Article Snippet: The expression of tia in this strain and in the ED32 wild-type strain was evaluated by the extraction of total RNA, followed by PCR amplification of the gene tia using cDNA as a template. .. One hundred nanograms of cDNA, quantified with a Qubit (version 3.0) fluorometer (Thermo Fisher Scientific, Waltham, MA, USA), was used as the template for a PCR with primers tia UP and tia LO ( ).

    Article Title: Characterization of MHC class I in a long distance migratory wader, the Icelandic black-tailed godwit
    Article Snippet: Twenty-five microliters PCR reaction volume were prepared containing 12.5 μl 2X Phusion High-Fidelity PCR Master Mix (ThermoFisher Scientific, Waltham, USA), 3 μl of each index primers, and 2 μl of cleaned PCR amplicon product. .. Equimolar quantities of every sample were pooled, and these pools were then quantified with Qubit (ThermoFisher Scientific, Waltham, USA) and run on a Bioanalyzer DNA 2100 chip for quality and size validation.

    Article Title: Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions
    Article Snippet: In this respect, Qubit is superior to NanoDrop for quantifying FFPE-DNA. .. In contrast, the ratio of the qPCR quantity to the ex-ND value (qPCR/ex-ND) was different for each FFPE-DNA as follows: 0.1 in FFPE-H1, 0.3 in FFPE-H2 and 0.2 in FFPE-H3.

    Article Title: Automated serial extraction of DNA and RNA from biobanked tissue specimens
    Article Snippet: The concentration of double stranded DNA measured by the fluorometric Qubit method, proved to be a more useful measurement of amplifiable DNA, and compared well with real time PCR amplification of LINE1 elements (data not shown) [ ]. .. The differences between Qubit and Nanodrop measurements may be explained by the fact that the Nanodrop instrument measures both single and double stranded DNA, as well as single nucleotides, giving an overall higher DNA yield than the Qubit method [ ].

    Article Title: Mutations in AP2S1 cause familial hypocalciuric hypercalcemia type 3
    Article Snippet: Leukocyte DNA was prepared from venous blood , , and quantified using the High Sensitivity Qubit system (Invitrogen) and assessed for integrity using an agarose gel. .. Leukocyte DNA was prepared from venous blood , , and quantified using the High Sensitivity Qubit system (Invitrogen) and assessed for integrity using an agarose gel.

    Article Title: Recurrent homozygous deletion of DROSHA and microduplication of PDE4DIP in pineoblastoma
    Article Snippet: Barcoded libraries were prepared using the Kapa Low-Throughput Library Preparation Kit Standard (Kapa Biosystems), amplified using the KAPA HiFi Library Amplification kit (Kapa Biosystems) (eight cycles) and quantified using Qubit Fluorimetric Quantitation (Invitrogen) and Agilent Bioanalyzer. .. The pooled capture library was quantified by Qubit (Invitrogen) and Bioanalyzer (Agilent), and sequenced on an Illumina HiSeq 2500 using a paired end, 100 nucleotides in length run mode to achieve an average of 100× coverage.

    Synthesized:

    Article Title: Multiplex mutagenesis of four clustered CrRLK1L with CRISPR/Cas9 exposes their growth regulatory roles in response to metal ions
    Article Snippet: RNA in the supernatant was precipitated with 250 µL 10 M LiCl at 4 °C for more than 1.5 h. After centrifugation and EtOH washes the pellet was dissolved in 20 µL RNase free water and stored at −80 °C. .. RNA was quantified with Qubit (Invitrogen) and NanoDrop (Peqlab) systems. cDNA was synthesized from 2.5 µg RNA after RNAse free DNase I digestion (Fermentas) with the M-MuLV H PLUS reverse transcriptase (Peqlab) as described . .. RT-qPCR expression analysis was performed using the Hot FirePol EvaGreen qPCR Mastermix (Solis Biodyne) with a Rotorgene 3000 (Qiagen).

    Picogreen Assay:

    Article Title: Characterization of MHC class I in a long distance migratory wader, the Icelandic black-tailed godwit
    Article Snippet: Cleaned PCR products were then checked on a 2% agarose gel, and the concentration was measured with Quant-iT PicoGreen dsDNA Assay Kit (ThermoFisher Scientific/Invitrogen, Waltham, USA) modified for a 96-well plate. .. Equimolar quantities of every sample were pooled, and these pools were then quantified with Qubit (ThermoFisher Scientific, Waltham, USA) and run on a Bioanalyzer DNA 2100 chip for quality and size validation.

    Quantitative RT-PCR:

    Article Title: Mutations in AP2S1 cause familial hypocalciuric hypercalcemia type 3
    Article Snippet: Leukocyte DNA was prepared from venous blood , , and quantified using the High Sensitivity Qubit system (Invitrogen) and assessed for integrity using an agarose gel. .. Fragmented DNA was amplified using universal adapter sequences and the amplified library hybridized to the SureSelect oligos before additional rounds of amplification.

    Article Title: Multiplex mutagenesis of four clustered CrRLK1L with CRISPR/Cas9 exposes their growth regulatory roles in response to metal ions
    Article Snippet: RNA was quantified with Qubit (Invitrogen) and NanoDrop (Peqlab) systems. cDNA was synthesized from 2.5 µg RNA after RNAse free DNase I digestion (Fermentas) with the M-MuLV H PLUS reverse transcriptase (Peqlab) as described . .. RNA was quantified with Qubit (Invitrogen) and NanoDrop (Peqlab) systems. cDNA was synthesized from 2.5 µg RNA after RNAse free DNase I digestion (Fermentas) with the M-MuLV H PLUS reverse transcriptase (Peqlab) as described .

    Real-time Polymerase Chain Reaction:

    Article Title: Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions
    Article Snippet: Paragraph title: Quantification of FFPE-DNA by NanoDrop, Qubit and qPCR ... In this respect, Qubit is superior to NanoDrop for quantifying FFPE-DNA.

    Article Title: Automated serial extraction of DNA and RNA from biobanked tissue specimens
    Article Snippet: The concentration of double stranded DNA measured by the fluorometric Qubit method, proved to be a more useful measurement of amplifiable DNA, and compared well with real time PCR amplification of LINE1 elements (data not shown) [ ]. .. The differences between Qubit and Nanodrop measurements may be explained by the fact that the Nanodrop instrument measures both single and double stranded DNA, as well as single nucleotides, giving an overall higher DNA yield than the Qubit method [ ].

    Article Title: Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms
    Article Snippet: We quantified eDNA concentrations prior to addition thereof to the experimental systems using a Qubit (2.0) fluorometer (Life Technologies, Carlsbad, USA) for each species resulting in 5.45 ng/μL (5.45E6 ng/L) for D. magna , 7.33 ng/μL (7.33E6 ng/L) for E. danica , and 1.75 ng/μL (1.75E6 ng/L) for A. anguilla . .. We quantified eDNA concentrations prior to addition thereof to the experimental systems using a Qubit (2.0) fluorometer (Life Technologies, Carlsbad, USA) for each species resulting in 5.45 ng/μL (5.45E6 ng/L) for D. magna , 7.33 ng/μL (7.33E6 ng/L) for E. danica , and 1.75 ng/μL (1.75E6 ng/L) for A. anguilla .

    Article Title: Multiplex mutagenesis of four clustered CrRLK1L with CRISPR/Cas9 exposes their growth regulatory roles in response to metal ions
    Article Snippet: Paragraph title: Expression analysis by quantitative real-time PCR ... RNA was quantified with Qubit (Invitrogen) and NanoDrop (Peqlab) systems. cDNA was synthesized from 2.5 µg RNA after RNAse free DNase I digestion (Fermentas) with the M-MuLV H PLUS reverse transcriptase (Peqlab) as described .

    Microarray:

    Article Title: Automated serial extraction of DNA and RNA from biobanked tissue specimens
    Article Snippet: The differences between Qubit and Nanodrop measurements may be explained by the fact that the Nanodrop instrument measures both single and double stranded DNA, as well as single nucleotides, giving an overall higher DNA yield than the Qubit method [ ]. .. The differences between Qubit and Nanodrop measurements may be explained by the fact that the Nanodrop instrument measures both single and double stranded DNA, as well as single nucleotides, giving an overall higher DNA yield than the Qubit method [ ].

    Incubation:

    Article Title: CXCL12 methylation-mediated epigenetic regulation of gene expression in papillary thyroid carcinoma
    Article Snippet: The prepared tube was then placed into another 1.5 mL centrifuge tube and we added 80–200 μL ddH2O into the center of the membrane and incubated at room temperature for 2 min. Genomic DNA was eluted after centrifugation at 12,000 × g for 1 min. Quantifications were performed using a NanoDrop (Thermo Fisher Scientific). .. PCR enrichment and Qubit Instruments (Invitrogen, Carlsbad, CA, USA) quantitative library were performed.

    Article Title: Whole genome sequencing reveals within-host genetic changes in paired meningococcal carriage isolates from Ethiopia
    Article Snippet: Cultures were incubated overnight on blood agar plates at 37 °C in an atmosphere of 5% CO2 . .. DNA quantity was assessed using the Qubit device (Invitrogen, Thermo Fisher Scientific Inc, Waltham, MA, US).

    Article Title: Anterograde trafficking of neurotrophin-3 in the adult olfactory system in vivo
    Article Snippet: Collection membranes were removed from caps, placed in 50 μl of RNA extraction buffer (Arcturus), and incubated at 42°C for 30 min. Membranes were removed and samples were stored in extraction buffer at -80°C prior to isolation of total RNA using the Arcturus PicoPure procedure with DNase treatment according to kit instructions. .. RNA concentration and quality was assessed by Qubit assay (Invitrogen, Carlsbad, CA), and by Pico Chip assay (Agilent Technologies, Santa Clara, CA) using the Agilent 2100 Bioanalyzer.

    Formalin-fixed Paraffin-Embedded:

    Article Title: Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions
    Article Snippet: These results indicate that the divergence of the Qubit quantity of FFPE-DNA is likely due to a deterioration in DNA quality such as the degradation and modification characteristics of FFPE-DNA itself. .. In this respect, Qubit is superior to NanoDrop for quantifying FFPE-DNA. .. Three measurements of FFPE-DNA indicated another issue.

    Activity Assay:

    Article Title: Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms
    Article Snippet: We quantified eDNA concentrations prior to addition thereof to the experimental systems using a Qubit (2.0) fluorometer (Life Technologies, Carlsbad, USA) for each species resulting in 5.45 ng/μL (5.45E6 ng/L) for D. magna , 7.33 ng/μL (7.33E6 ng/L) for E. danica , and 1.75 ng/μL (1.75E6 ng/L) for A. anguilla . .. We quantified eDNA concentrations prior to addition thereof to the experimental systems using a Qubit (2.0) fluorometer (Life Technologies, Carlsbad, USA) for each species resulting in 5.45 ng/μL (5.45E6 ng/L) for D. magna , 7.33 ng/μL (7.33E6 ng/L) for E. danica , and 1.75 ng/μL (1.75E6 ng/L) for A. anguilla .

    Expressing:

    Article Title: The Gene tia, Harbored by the Subtilase-Encoding Pathogenicity Island, Is Involved in the Ability of Locus of Enterocyte Effacement-Negative Shiga Toxin-Producing Escherichia coli Strains To Invade Monolayers of Epithelial Cells
    Article Snippet: Paragraph title: Expression of tia in JM109 competent cells. ... One hundred nanograms of cDNA, quantified with a Qubit (version 3.0) fluorometer (Thermo Fisher Scientific, Waltham, MA, USA), was used as the template for a PCR with primers tia UP and tia LO ( ).

    Article Title: Multiplex mutagenesis of four clustered CrRLK1L with CRISPR/Cas9 exposes their growth regulatory roles in response to metal ions
    Article Snippet: Paragraph title: Expression analysis by quantitative real-time PCR ... RNA was quantified with Qubit (Invitrogen) and NanoDrop (Peqlab) systems. cDNA was synthesized from 2.5 µg RNA after RNAse free DNase I digestion (Fermentas) with the M-MuLV H PLUS reverse transcriptase (Peqlab) as described .

    Modification:

    Article Title: Characterization of MHC class I in a long distance migratory wader, the Icelandic black-tailed godwit
    Article Snippet: Cleaned PCR products were then checked on a 2% agarose gel, and the concentration was measured with Quant-iT PicoGreen dsDNA Assay Kit (ThermoFisher Scientific/Invitrogen, Waltham, USA) modified for a 96-well plate. .. Equimolar quantities of every sample were pooled, and these pools were then quantified with Qubit (ThermoFisher Scientific, Waltham, USA) and run on a Bioanalyzer DNA 2100 chip for quality and size validation.

    Article Title: Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions
    Article Snippet: These results indicate that the divergence of the Qubit quantity of FFPE-DNA is likely due to a deterioration in DNA quality such as the degradation and modification characteristics of FFPE-DNA itself. .. In this respect, Qubit is superior to NanoDrop for quantifying FFPE-DNA.

    Generated:

    Article Title: CXCL12 methylation-mediated epigenetic regulation of gene expression in papillary thyroid carcinoma
    Article Snippet: PCR enrichment and Qubit Instruments (Invitrogen, Carlsbad, CA, USA) quantitative library were performed. .. The methylation data was obtained using Illumina Hiseq2500 sequencing.

    Polymerase Chain Reaction:

    Article Title: The Gene tia, Harbored by the Subtilase-Encoding Pathogenicity Island, Is Involved in the Ability of Locus of Enterocyte Effacement-Negative Shiga Toxin-Producing Escherichia coli Strains To Invade Monolayers of Epithelial Cells
    Article Snippet: A DNA wipeout kit (Qiagen, Chatsworth, CA, USA) was used to remove genomic DNA from a total of 1 μg of total RNA, which was retrotranscribed into cDNA with a QuantiTect reverse transcription kit (Qiagen, Chatsworth, CA, USA) according to the manufacturer's instructions. .. One hundred nanograms of cDNA, quantified with a Qubit (version 3.0) fluorometer (Thermo Fisher Scientific, Waltham, MA, USA), was used as the template for a PCR with primers tia UP and tia LO ( ). .. To verify that the amount of cDNA was the same in the two strains, 10 ng of the same cDNA was used to amplify a 215-bp fragment of the constitutive gene gapA , coding for glyceraldehyde-3-phosphate dehydrogenase, using the primers gapA F and gapA R ( ).

    Article Title: Characterization of MHC class I in a long distance migratory wader, the Icelandic black-tailed godwit
    Article Snippet: Cleaned PCR products were then checked on a 2% agarose gel, and the concentration was measured with Quant-iT PicoGreen dsDNA Assay Kit (ThermoFisher Scientific/Invitrogen, Waltham, USA) modified for a 96-well plate. .. Equimolar quantities of every sample were pooled, and these pools were then quantified with Qubit (ThermoFisher Scientific, Waltham, USA) and run on a Bioanalyzer DNA 2100 chip for quality and size validation.

    Article Title: CXCL12 methylation-mediated epigenetic regulation of gene expression in papillary thyroid carcinoma
    Article Snippet: Finally, 150–175 or 175–225 bp fragments were screened by 2% agarose gel electrophoresis and DNA was reclaimed using QIAGEN gel extraction kits (Hilden, Germany) according to the manufacturer’s recommendations. .. PCR enrichment and Qubit Instruments (Invitrogen, Carlsbad, CA, USA) quantitative library were performed. .. The methylation data was obtained using Illumina Hiseq2500 sequencing.

    Article Title: Congenital Proprotein Convertase 1/3 Deficiency Causes Malabsorptive Diarrhea and other Endocrinopathies in a Pediatric Cohort
    Article Snippet: Paragraph title: Genomic DNA Isolation, PCR and Sequencing ... Genomic DNA was extracted from blood or saliva by standard procedures, and measured by Qubit (Invitrogen).

    Article Title: Multiplex mutagenesis of four clustered CrRLK1L with CRISPR/Cas9 exposes their growth regulatory roles in response to metal ions
    Article Snippet: RNA was quantified with Qubit (Invitrogen) and NanoDrop (Peqlab) systems. cDNA was synthesized from 2.5 µg RNA after RNAse free DNase I digestion (Fermentas) with the M-MuLV H PLUS reverse transcriptase (Peqlab) as described . .. RNA was quantified with Qubit (Invitrogen) and NanoDrop (Peqlab) systems. cDNA was synthesized from 2.5 µg RNA after RNAse free DNase I digestion (Fermentas) with the M-MuLV H PLUS reverse transcriptase (Peqlab) as described .

    DNA Sequencing:

    Article Title: Mutations in AP2S1 cause familial hypocalciuric hypercalcemia type 3
    Article Snippet: Paragraph title: Exome capture and DNA sequencing ... Leukocyte DNA was prepared from venous blood , , and quantified using the High Sensitivity Qubit system (Invitrogen) and assessed for integrity using an agarose gel.

    Protein Concentration:

    Article Title: Fibroblast growth factor receptor 3 effects on proliferation and telomerase activity in sheep growth plate chondrocytes
    Article Snippet: DNA, RNA, and protein were isolated from the remaining aliquot of the cell lysate (All Prep™ kit, Qiagen, Germantown, MD). .. A Qubit fluorometer based Quant-it assay (Invitrogen, Molecular Probes Inc., Eugene, OR) was used to determine the DNA, RNA, and protein concentration of each well sample; all wells were replicated in triplicate under each treatment. .. Chondrocyte proliferation was determined by quantifying DNA concentration of chondrocyte cultures at 3, 5, and 7 days post siRNA transfection [ ].

    Sequencing:

    Article Title: Characterization of MHC class I in a long distance migratory wader, the Icelandic black-tailed godwit
    Article Snippet: Paragraph title: Illumina MiSeq sequencing of MHC-I exon 3 ... Equimolar quantities of every sample were pooled, and these pools were then quantified with Qubit (ThermoFisher Scientific, Waltham, USA) and run on a Bioanalyzer DNA 2100 chip for quality and size validation.

    Article Title: CXCL12 methylation-mediated epigenetic regulation of gene expression in papillary thyroid carcinoma
    Article Snippet: Paragraph title: RRBS library preparation, sequencing and data processing ... PCR enrichment and Qubit Instruments (Invitrogen, Carlsbad, CA, USA) quantitative library were performed.

    Article Title: Noninvasive prenatal diagnosis of 21-Hydroxylase deficiency using target capture sequencing of maternal plasma DNA
    Article Snippet: Paragraph title: Role of fetal DNA fraction and sequencing depth in NIPT ... After quantification using Qubit (Invitrogen by Life Technologies), fetal gDNA and maternal gDNA were combined to create artificial plasma samples of 1%, 2%, 3%, 4%, and 10% fetal DNA fractions (w/w).

    Article Title: Congenital Proprotein Convertase 1/3 Deficiency Causes Malabsorptive Diarrhea and other Endocrinopathies in a Pediatric Cohort
    Article Snippet: Paragraph title: Genomic DNA Isolation, PCR and Sequencing ... Genomic DNA was extracted from blood or saliva by standard procedures, and measured by Qubit (Invitrogen).

    Article Title: Whole genome sequencing reveals within-host genetic changes in paired meningococcal carriage isolates from Ethiopia
    Article Snippet: Paragraph title: Genome sequencing ... DNA quantity was assessed using the Qubit device (Invitrogen, Thermo Fisher Scientific Inc, Waltham, MA, US).

    Article Title: Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets
    Article Snippet: Pellets were dissolved with 40 μl of 8 M urea 0.5 M tetraethylammonium bicarbonate (TEAB) and quantified by Qubit (Invitrogen) according to manufacturer instructions. .. Samples were then reduced with 50 mM Tris-(2-carboxyethyl) phosphine at 37 °C for 180 min, alkylated with 100 mM methylmethanethiosulfonate for 10 min, and urea concentration was lowered to less than 2 M with 500 mM TEAB.

    Article Title: Recurrent homozygous deletion of DROSHA and microduplication of PDE4DIP in pineoblastoma
    Article Snippet: Paragraph title: Whole-exome and whole-genome sequencing and analysis ... The pooled capture library was quantified by Qubit (Invitrogen) and Bioanalyzer (Agilent), and sequenced on an Illumina HiSeq 2500 using a paired end, 100 nucleotides in length run mode to achieve an average of 100× coverage.

    Injection:

    Article Title: Lymphocyte activation gene 3 (Lag3) expression is increased in prion infections but does not modify disease progression
    Article Snippet: RNA sequencing on hippocampal and cerebellar tissues of mice intracerebrally injected with RML6 or NBH was performed as previously described , . .. Briefly, total RNA was extracted using the RNeasy Plus universal mini kit (QIAGEN) and subjected to quality control using Bioanalyzer 2100 (Agilent Technologies) and Qubit (1.0) Fluorometer (Life Technologies).

    DNA Extraction:

    Article Title: A pilot study of ultra-deep targeted sequencing of plasma DNA identifies driver mutations in hepatocellular carcinoma
    Article Snippet: Paragraph title: DNA extraction, quality control and quantification ... The purified plasma DNA was run on a 2100 Bioanalyzer Instrument (Agilent) for size estimation, and its concentration was measured by fluorometric quantitation using Qubit (ThermoFisher).

    Article Title: Congenital Proprotein Convertase 1/3 Deficiency Causes Malabsorptive Diarrhea and other Endocrinopathies in a Pediatric Cohort
    Article Snippet: Paragraph title: Genomic DNA Isolation, PCR and Sequencing ... Genomic DNA was extracted from blood or saliva by standard procedures, and measured by Qubit (Invitrogen).

    Nucleic Acid Electrophoresis:

    Article Title: Genomic sequence analysis of a plant-associated Photobacterium halotolerans MELD1: from marine to terrestrial environment?
    Article Snippet: The genomic DNA was extracted by WelPrep DNA kit (Welgene Biotech, Cat No.D001). .. The size, purity and DNA concentration was measured by running pulse field gel electrophoresis, ratio of absorbance values at OD 260/280 in the range 1.8 ~ 2.0, and quantity ratio by Qubit versus NanoDrop over 0.7. .. DNA was sequenced using Illumina Solexa technology.

    RNA Sequencing Assay:

    Article Title: Lymphocyte activation gene 3 (Lag3) expression is increased in prion infections but does not modify disease progression
    Article Snippet: Paragraph title: RNA sequencing ... Briefly, total RNA was extracted using the RNeasy Plus universal mini kit (QIAGEN) and subjected to quality control using Bioanalyzer 2100 (Agilent Technologies) and Qubit (1.0) Fluorometer (Life Technologies).

    Isolation:

    Article Title: A pilot study of ultra-deep targeted sequencing of plasma DNA identifies driver mutations in hepatocellular carcinoma
    Article Snippet: Germline DNA was isolated from PBMC using the QIAamp DNA Mini Kit (Qiagen). .. The purified plasma DNA was run on a 2100 Bioanalyzer Instrument (Agilent) for size estimation, and its concentration was measured by fluorometric quantitation using Qubit (ThermoFisher).

    Article Title: Whole genome sequencing reveals within-host genetic changes in paired meningococcal carriage isolates from Ethiopia
    Article Snippet: DNA was extracted using an automated MagNAPure isolation station and MagNAPure 96 DNA and Viral NA Small Volume Kit (Roche, Basel, Switzerland), according to the manufacturer's instructions. .. DNA quantity was assessed using the Qubit device (Invitrogen, Thermo Fisher Scientific Inc, Waltham, MA, US).

    Article Title: Fibroblast growth factor receptor 3 effects on proliferation and telomerase activity in sheep growth plate chondrocytes
    Article Snippet: Paragraph title: Isolation and quantification of DNA, RNA, and protein ... A Qubit fluorometer based Quant-it assay (Invitrogen, Molecular Probes Inc., Eugene, OR) was used to determine the DNA, RNA, and protein concentration of each well sample; all wells were replicated in triplicate under each treatment.

    Article Title: Anterograde trafficking of neurotrophin-3 in the adult olfactory system in vivo
    Article Snippet: Paragraph title: Laser Capture Microdissection and RNA isolation ... RNA concentration and quality was assessed by Qubit assay (Invitrogen, Carlsbad, CA), and by Pico Chip assay (Agilent Technologies, Santa Clara, CA) using the Agilent 2100 Bioanalyzer.

    Article Title: Multiplex mutagenesis of four clustered CrRLK1L with CRISPR/Cas9 exposes their growth regulatory roles in response to metal ions
    Article Snippet: Total RNA of snap-frozen seedlings grown on MS2.5 supplemented with 1% (w/v) agar (Duchefa), rosette leaves, cauline leaves, or flowers was isolated using a LiCl/CTAB method. .. RNA was quantified with Qubit (Invitrogen) and NanoDrop (Peqlab) systems. cDNA was synthesized from 2.5 µg RNA after RNAse free DNase I digestion (Fermentas) with the M-MuLV H PLUS reverse transcriptase (Peqlab) as described .

    Purification:

    Article Title: A pilot study of ultra-deep targeted sequencing of plasma DNA identifies driver mutations in hepatocellular carcinoma
    Article Snippet: Extracted DNA was immediately aliquoted and stored at −20°C. .. The purified plasma DNA was run on a 2100 Bioanalyzer Instrument (Agilent) for size estimation, and its concentration was measured by fluorometric quantitation using Qubit (ThermoFisher). .. Ultra-deep DNA sequencing was performed for all exons of a panel of 58 genes ( ) selected based on 2 main criteria: 1) high prevalence of mutations in previous HCC studies , and 2) evidence of druggability .

    Article Title: Characterization of MHC class I in a long distance migratory wader, the Icelandic black-tailed godwit
    Article Snippet: The PCR products were checked on a 2% agarose gel and cleaned with Agencourt AMPure XP-PCR Purification kit (Beckman Coulter, Indianapolis, USA). .. Equimolar quantities of every sample were pooled, and these pools were then quantified with Qubit (ThermoFisher Scientific, Waltham, USA) and run on a Bioanalyzer DNA 2100 chip for quality and size validation.

    Article Title: Multiplex mutagenesis of four clustered CrRLK1L with CRISPR/Cas9 exposes their growth regulatory roles in response to metal ions
    Article Snippet: RNA was quantified with Qubit (Invitrogen) and NanoDrop (Peqlab) systems. cDNA was synthesized from 2.5 µg RNA after RNAse free DNase I digestion (Fermentas) with the M-MuLV H PLUS reverse transcriptase (Peqlab) as described . .. RNA was quantified with Qubit (Invitrogen) and NanoDrop (Peqlab) systems. cDNA was synthesized from 2.5 µg RNA after RNAse free DNase I digestion (Fermentas) with the M-MuLV H PLUS reverse transcriptase (Peqlab) as described .

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Automated serial extraction of DNA and RNA from biobanked tissue specimens
    Article Snippet: The differences between Qubit and Nanodrop measurements may be explained by the fact that the Nanodrop instrument measures both single and double stranded DNA, as well as single nucleotides, giving an overall higher DNA yield than the Qubit method [ ]. .. The differences between Qubit and Nanodrop measurements may be explained by the fact that the Nanodrop instrument measures both single and double stranded DNA, as well as single nucleotides, giving an overall higher DNA yield than the Qubit method [ ].

    Gel Extraction:

    Article Title: CXCL12 methylation-mediated epigenetic regulation of gene expression in papillary thyroid carcinoma
    Article Snippet: Finally, 150–175 or 175–225 bp fragments were screened by 2% agarose gel electrophoresis and DNA was reclaimed using QIAGEN gel extraction kits (Hilden, Germany) according to the manufacturer’s recommendations. .. PCR enrichment and Qubit Instruments (Invitrogen, Carlsbad, CA, USA) quantitative library were performed.

    Mouse Assay:

    Article Title: Lymphocyte activation gene 3 (Lag3) expression is increased in prion infections but does not modify disease progression
    Article Snippet: RNA sequencing on hippocampal and cerebellar tissues of mice intracerebrally injected with RML6 or NBH was performed as previously described , . .. Briefly, total RNA was extracted using the RNeasy Plus universal mini kit (QIAGEN) and subjected to quality control using Bioanalyzer 2100 (Agilent Technologies) and Qubit (1.0) Fluorometer (Life Technologies).

    Chromatin Immunoprecipitation:

    Article Title: Characterization of MHC class I in a long distance migratory wader, the Icelandic black-tailed godwit
    Article Snippet: Cleaned PCR products were then checked on a 2% agarose gel, and the concentration was measured with Quant-iT PicoGreen dsDNA Assay Kit (ThermoFisher Scientific/Invitrogen, Waltham, USA) modified for a 96-well plate. .. Equimolar quantities of every sample were pooled, and these pools were then quantified with Qubit (ThermoFisher Scientific, Waltham, USA) and run on a Bioanalyzer DNA 2100 chip for quality and size validation. .. Lastly, equimolar quantities of all pools were taken together to create a final 4 nM library that was sent for 300 bp paired-end Illumina MiSeq sequencing (Illumina Inc., San Diego, CA, USA) at the DNA sequencing facility Department of Biology, Faculty of Science, Lund University.

    Article Title: Anterograde trafficking of neurotrophin-3 in the adult olfactory system in vivo
    Article Snippet: RNA from dissected hippocampus was isolated using Qiagen's RNeasy Plus kit (Qiagen, Valencia, CA). .. RNA concentration and quality was assessed by Qubit assay (Invitrogen, Carlsbad, CA), and by Pico Chip assay (Agilent Technologies, Santa Clara, CA) using the Agilent 2100 Bioanalyzer. .. The resulting electropherograms were examined and samples with RNA integrity numbers (RIN) lower than 6.0 were excluded from further analysis.

    Plasmid Preparation:

    Article Title: The Gene tia, Harbored by the Subtilase-Encoding Pathogenicity Island, Is Involved in the Ability of Locus of Enterocyte Effacement-Negative Shiga Toxin-Producing Escherichia coli Strains To Invade Monolayers of Epithelial Cells
    Article Snippet: The insertion of the expected 973-bp fragment in the plasmid pGEM-T Easy resulted in an amplification product of 1,292 bp. .. One hundred nanograms of cDNA, quantified with a Qubit (version 3.0) fluorometer (Thermo Fisher Scientific, Waltham, MA, USA), was used as the template for a PCR with primers tia UP and tia LO ( ).

    Software:

    Article Title: Whole genome sequencing reveals within-host genetic changes in paired meningococcal carriage isolates from Ethiopia
    Article Snippet: DNA quantity was assessed using the Qubit device (Invitrogen, Thermo Fisher Scientific Inc, Waltham, MA, US). .. DNA quantity was assessed using the Qubit device (Invitrogen, Thermo Fisher Scientific Inc, Waltham, MA, US).

    RNA Extraction:

    Article Title: The Gene tia, Harbored by the Subtilase-Encoding Pathogenicity Island, Is Involved in the Ability of Locus of Enterocyte Effacement-Negative Shiga Toxin-Producing Escherichia coli Strains To Invade Monolayers of Epithelial Cells
    Article Snippet: Briefly, total RNA was extracted from the ED32 wild-type strain and strain JM109/pGEM_ tia using a total RNA extraction kit (Norgen Biotek Corp., Thorold, ON, Canada) according to the manufacturer's instructions. .. One hundred nanograms of cDNA, quantified with a Qubit (version 3.0) fluorometer (Thermo Fisher Scientific, Waltham, MA, USA), was used as the template for a PCR with primers tia UP and tia LO ( ).

    Article Title: Anterograde trafficking of neurotrophin-3 in the adult olfactory system in vivo
    Article Snippet: Collection membranes were removed from caps, placed in 50 μl of RNA extraction buffer (Arcturus), and incubated at 42°C for 30 min. Membranes were removed and samples were stored in extraction buffer at -80°C prior to isolation of total RNA using the Arcturus PicoPure procedure with DNase treatment according to kit instructions. .. RNA concentration and quality was assessed by Qubit assay (Invitrogen, Carlsbad, CA), and by Pico Chip assay (Agilent Technologies, Santa Clara, CA) using the Agilent 2100 Bioanalyzer.

    Article Title: Multiplex mutagenesis of four clustered CrRLK1L with CRISPR/Cas9 exposes their growth regulatory roles in response to metal ions
    Article Snippet: After grinding roughly 100 mg frozen tissue, 1 mL of pre-heated RNA extraction buffer (2% [w/v] hexadecyltrimethylammonium bromide, CTAB; 2% [w/v] polyvinylpyrrolidone, PVP; 100 mM Tris/HCl pH 8.0; 25 mM EDTA; 2 M NaCl; 0.5 g/L spermidine and 2.7% [v/v] 2-mercaptoethanol) was added, mixed and incubated at 65 °C for 5 min. CTAB was removed through two extractions with 1 mL of ice-cold chloroform: isoamylalcohol (24:1) and centrifugation at 4 °C. .. RNA was quantified with Qubit (Invitrogen) and NanoDrop (Peqlab) systems. cDNA was synthesized from 2.5 µg RNA after RNAse free DNase I digestion (Fermentas) with the M-MuLV H PLUS reverse transcriptase (Peqlab) as described .

    Selection:

    Article Title: Noninvasive prenatal diagnosis of 21-Hydroxylase deficiency using target capture sequencing of maternal plasma DNA
    Article Snippet: Double size selection of fragments was performed using SPRIselect beads (Beckman Coulter Genomics, Danvers, MA, USA) to recover fragment size 100–300 bp according to the manufacturer’s protocol. .. After quantification using Qubit (Invitrogen by Life Technologies), fetal gDNA and maternal gDNA were combined to create artificial plasma samples of 1%, 2%, 3%, 4%, and 10% fetal DNA fractions (w/w).

    Agarose Gel Electrophoresis:

    Article Title: Characterization of MHC class I in a long distance migratory wader, the Icelandic black-tailed godwit
    Article Snippet: Cleaned PCR products were then checked on a 2% agarose gel, and the concentration was measured with Quant-iT PicoGreen dsDNA Assay Kit (ThermoFisher Scientific/Invitrogen, Waltham, USA) modified for a 96-well plate. .. Equimolar quantities of every sample were pooled, and these pools were then quantified with Qubit (ThermoFisher Scientific, Waltham, USA) and run on a Bioanalyzer DNA 2100 chip for quality and size validation.

    Article Title: CXCL12 methylation-mediated epigenetic regulation of gene expression in papillary thyroid carcinoma
    Article Snippet: Finally, 150–175 or 175–225 bp fragments were screened by 2% agarose gel electrophoresis and DNA was reclaimed using QIAGEN gel extraction kits (Hilden, Germany) according to the manufacturer’s recommendations. .. PCR enrichment and Qubit Instruments (Invitrogen, Carlsbad, CA, USA) quantitative library were performed.

    Article Title: Mutations in AP2S1 cause familial hypocalciuric hypercalcemia type 3
    Article Snippet: Clinical details of the two FHH3 kindreds - and the FHH patients without CaSR mutations have been reported . .. Leukocyte DNA was prepared from venous blood , , and quantified using the High Sensitivity Qubit system (Invitrogen) and assessed for integrity using an agarose gel. .. Three μg of DNA were fragmented, and libraries prepared using the SureSelect Human All Exon v2 Kit (Agilent Technologies, Santa Clara, CA), as follows .

    Cross-linking Immunoprecipitation:

    Article Title: Whole genome sequencing reveals within-host genetic changes in paired meningococcal carriage isolates from Ethiopia
    Article Snippet: DNA quantity was assessed using the Qubit device (Invitrogen, Thermo Fisher Scientific Inc, Waltham, MA, US). .. Sequencing was performed on the Illumina MiSeq platform with MiSeq Reagent Kits v2 500-cycles (Illumina Inc., San Diego, CA, US) with 250 bp paired-end run modes.

    Laser Capture Microdissection:

    Article Title: Anterograde trafficking of neurotrophin-3 in the adult olfactory system in vivo
    Article Snippet: Paragraph title: Laser Capture Microdissection and RNA isolation ... RNA concentration and quality was assessed by Qubit assay (Invitrogen, Carlsbad, CA), and by Pico Chip assay (Agilent Technologies, Santa Clara, CA) using the Agilent 2100 Bioanalyzer.

    Quantitation Assay:

    Article Title: A pilot study of ultra-deep targeted sequencing of plasma DNA identifies driver mutations in hepatocellular carcinoma
    Article Snippet: Extracted DNA was immediately aliquoted and stored at −20°C. .. The purified plasma DNA was run on a 2100 Bioanalyzer Instrument (Agilent) for size estimation, and its concentration was measured by fluorometric quantitation using Qubit (ThermoFisher). .. Ultra-deep DNA sequencing was performed for all exons of a panel of 58 genes ( ) selected based on 2 main criteria: 1) high prevalence of mutations in previous HCC studies , and 2) evidence of druggability .

    Article Title: Recurrent homozygous deletion of DROSHA and microduplication of PDE4DIP in pineoblastoma
    Article Snippet: Barcoded libraries were prepared using the Kapa Low-Throughput Library Preparation Kit Standard (Kapa Biosystems), amplified using the KAPA HiFi Library Amplification kit (Kapa Biosystems) (eight cycles) and quantified using Qubit Fluorimetric Quantitation (Invitrogen) and Agilent Bioanalyzer. .. The pooled capture library was quantified by Qubit (Invitrogen) and Bioanalyzer (Agilent), and sequenced on an Illumina HiSeq 2500 using a paired end, 100 nucleotides in length run mode to achieve an average of 100× coverage.

    Sampling:

    Article Title: Noninvasive prenatal diagnosis of 21-Hydroxylase deficiency using target capture sequencing of maternal plasma DNA
    Article Snippet: After quantification using Qubit (Invitrogen by Life Technologies), fetal gDNA and maternal gDNA were combined to create artificial plasma samples of 1%, 2%, 3%, 4%, and 10% fetal DNA fractions (w/w). .. After quantification using Qubit (Invitrogen by Life Technologies), fetal gDNA and maternal gDNA were combined to create artificial plasma samples of 1%, 2%, 3%, 4%, and 10% fetal DNA fractions (w/w).

    Concentration Assay:

    Article Title: A pilot study of ultra-deep targeted sequencing of plasma DNA identifies driver mutations in hepatocellular carcinoma
    Article Snippet: Extracted DNA was immediately aliquoted and stored at −20°C. .. The purified plasma DNA was run on a 2100 Bioanalyzer Instrument (Agilent) for size estimation, and its concentration was measured by fluorometric quantitation using Qubit (ThermoFisher). .. Ultra-deep DNA sequencing was performed for all exons of a panel of 58 genes ( ) selected based on 2 main criteria: 1) high prevalence of mutations in previous HCC studies , and 2) evidence of druggability .

    Article Title: Characterization of MHC class I in a long distance migratory wader, the Icelandic black-tailed godwit
    Article Snippet: Cleaned PCR products were then checked on a 2% agarose gel, and the concentration was measured with Quant-iT PicoGreen dsDNA Assay Kit (ThermoFisher Scientific/Invitrogen, Waltham, USA) modified for a 96-well plate. .. Equimolar quantities of every sample were pooled, and these pools were then quantified with Qubit (ThermoFisher Scientific, Waltham, USA) and run on a Bioanalyzer DNA 2100 chip for quality and size validation.

    Article Title: Genomic sequence analysis of a plant-associated Photobacterium halotolerans MELD1: from marine to terrestrial environment?
    Article Snippet: The genomic DNA was extracted by WelPrep DNA kit (Welgene Biotech, Cat No.D001). .. The size, purity and DNA concentration was measured by running pulse field gel electrophoresis, ratio of absorbance values at OD 260/280 in the range 1.8 ~ 2.0, and quantity ratio by Qubit versus NanoDrop over 0.7. .. DNA was sequenced using Illumina Solexa technology.

    Article Title: Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions
    Article Snippet: The Qubit and qPCR values were proportional to the dilution ratios and were significantly lower than the ex-ND values (p = 0.01 and 0.003, respectively), even at the highest concentration. .. In this respect, Qubit is superior to NanoDrop for quantifying FFPE-DNA.

    Article Title: Anterograde trafficking of neurotrophin-3 in the adult olfactory system in vivo
    Article Snippet: RNA from dissected hippocampus was isolated using Qiagen's RNeasy Plus kit (Qiagen, Valencia, CA). .. RNA concentration and quality was assessed by Qubit assay (Invitrogen, Carlsbad, CA), and by Pico Chip assay (Agilent Technologies, Santa Clara, CA) using the Agilent 2100 Bioanalyzer. .. The resulting electropherograms were examined and samples with RNA integrity numbers (RIN) lower than 6.0 were excluded from further analysis.

    Article Title: Automated serial extraction of DNA and RNA from biobanked tissue specimens
    Article Snippet: The concentration of double stranded DNA measured by the fluorometric Qubit method, proved to be a more useful measurement of amplifiable DNA, and compared well with real time PCR amplification of LINE1 elements (data not shown) [ ]. .. The differences between Qubit and Nanodrop measurements may be explained by the fact that the Nanodrop instrument measures both single and double stranded DNA, as well as single nucleotides, giving an overall higher DNA yield than the Qubit method [ ].

    Article Title: Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs
    Article Snippet: Correlation results are depicted in Fig. . .. At the original plasma concentration or in diluted samples, although Nanoquant and Nanodrop kept good correlation with one another (ρ = 0.901 and R2 = 0.879) (Fig. ), both displayed only a modest correlation with Qubit: ρ = 0.725 and R2 = 0.290 for Qubit versus Nanoquant (Fig. ) and ρ = 0.781 and R2 = 0.333 for Qubit versus Nanodrop (Fig. ). .. Nevertheless, in more concentrated samples ( > 2 ng/μL by Qubit) correlation between the three techniques was very good: ρ = 0.945 and R2 = 0.941 for Nanoquant versus Nanodrop (Fig. ), ρ = 0.967 and R2 = 0.935 for Qubit versus Nanoquant (Fig. ) and ρ = 0.956 and R2 = 0.961 for Qubit versus Nanodrop (Fig. ).

    Article Title: Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms
    Article Snippet: The reduced volume for E. danica was due to higher eDNA concentration in the holding tanks. .. We quantified eDNA concentrations prior to addition thereof to the experimental systems using a Qubit (2.0) fluorometer (Life Technologies, Carlsbad, USA) for each species resulting in 5.45 ng/μL (5.45E6 ng/L) for D. magna , 7.33 ng/μL (7.33E6 ng/L) for E. danica , and 1.75 ng/μL (1.75E6 ng/L) for A. anguilla .

    Article Title: Under control: how a dietary additive can restore the gut microbiome and proteomic profile, and improve disease resilience in a marine teleostean fish fed vegetable diets
    Article Snippet: Pellets were dissolved with 40 μl of 8 M urea 0.5 M tetraethylammonium bicarbonate (TEAB) and quantified by Qubit (Invitrogen) according to manufacturer instructions. .. Pellets were dissolved with 40 μl of 8 M urea 0.5 M tetraethylammonium bicarbonate (TEAB) and quantified by Qubit (Invitrogen) according to manufacturer instructions.

    Article Title: Multiplex mutagenesis of four clustered CrRLK1L with CRISPR/Cas9 exposes their growth regulatory roles in response to metal ions
    Article Snippet: RNA was quantified with Qubit (Invitrogen) and NanoDrop (Peqlab) systems. cDNA was synthesized from 2.5 µg RNA after RNAse free DNase I digestion (Fermentas) with the M-MuLV H PLUS reverse transcriptase (Peqlab) as described . .. RNA was quantified with Qubit (Invitrogen) and NanoDrop (Peqlab) systems. cDNA was synthesized from 2.5 µg RNA after RNAse free DNase I digestion (Fermentas) with the M-MuLV H PLUS reverse transcriptase (Peqlab) as described .

    Lysis:

    Article Title: Fibroblast growth factor receptor 3 effects on proliferation and telomerase activity in sheep growth plate chondrocytes
    Article Snippet: Approximately 10% of the cell lysate volume was removed, diluted 1:10 in CHAPS lysis buffer, snap frozen in liquid nitrogen, and stored at −80°C. .. A Qubit fluorometer based Quant-it assay (Invitrogen, Molecular Probes Inc., Eugene, OR) was used to determine the DNA, RNA, and protein concentration of each well sample; all wells were replicated in triplicate under each treatment.

    Article Title: Automated serial extraction of DNA and RNA from biobanked tissue specimens
    Article Snippet: This is inherent to methods using chaotropic lysis buffers. .. The differences between Qubit and Nanodrop measurements may be explained by the fact that the Nanodrop instrument measures both single and double stranded DNA, as well as single nucleotides, giving an overall higher DNA yield than the Qubit method [ ].

    Fluorescence In Situ Hybridization:

    Article Title: Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms
    Article Snippet: Prior to collection, the water from the Cynrig Fish Culture Unit was subjected to ultraviolet light due to water treatment protocols. .. We quantified eDNA concentrations prior to addition thereof to the experimental systems using a Qubit (2.0) fluorometer (Life Technologies, Carlsbad, USA) for each species resulting in 5.45 ng/μL (5.45E6 ng/L) for D. magna , 7.33 ng/μL (7.33E6 ng/L) for E. danica , and 1.75 ng/μL (1.75E6 ng/L) for A. anguilla .

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    Thermo Fisher qubit 3 fluorometer
    Qubit 3 Fluorometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/qubit 3 fluorometer/product/Thermo Fisher
    Average 99 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    qubit 3 fluorometer - by Bioz Stars, 2019-10
    99/100 stars
      Buy from Supplier

    Image Search Results