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Thermo Fisher qubit
Quantification of ssDNA by <t>ssDNA-Qubit</t> and dsDNA-Qubit. <t>Frozen-R1</t> and Trizol-h3 diluted with TE buffer or distilled water in 20 ng/μl were measured with ssDNA-Qubit and dsDNA-Qubit. The amounts of dsDNA (black) and ssDNA (white) were determined using the standard curve shown in S1 Fig .
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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 of ssDNA by ssDNA-Qubit and dsDNA-Qubit. Frozen-R1 and Trizol-h3 diluted with TE buffer or distilled water in 20 ng/μl were measured with ssDNA-Qubit and dsDNA-Qubit. The amounts of dsDNA (black) and ssDNA (white) were determined using the standard curve shown in S1 Fig .
Figure Legend Snippet: Quantification of ssDNA by ssDNA-Qubit and dsDNA-Qubit. Frozen-R1 and Trizol-h3 diluted with TE buffer or distilled water in 20 ng/μl were measured with ssDNA-Qubit and dsDNA-Qubit. The amounts of dsDNA (black) and ssDNA (white) were determined using the standard curve shown in S1 Fig .

Techniques Used:

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 "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:

3) 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

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

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 "Protocol Improvements for Low Concentration DNA-Based Bioaerosol Sampling and Analysis"

Article Title: Protocol Improvements for Low Concentration DNA-Based Bioaerosol Sampling and Analysis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0141158

Improving DNA yield with additional heat and sonication lysis. Additional sonication and thermal lysis show improved DNA yield for (a)—AHU filter samples and (b)–ambient air samples as measured by the Qubit fluorometer for total DNA (left bar, left axis) and by qPCR for bacterial (middle bar, right axis) and fungal (right bar, right axis) DNA ( N = 4).
Figure Legend Snippet: Improving DNA yield with additional heat and sonication lysis. Additional sonication and thermal lysis show improved DNA yield for (a)—AHU filter samples and (b)–ambient air samples as measured by the Qubit fluorometer for total DNA (left bar, left axis) and by qPCR for bacterial (middle bar, right axis) and fungal (right bar, right axis) DNA ( N = 4).

Techniques Used: Sonication, Lysis, Real-time Polymerase Chain Reaction

Comparison of two sampling approaches. Comparison of a sampling approach utilizing a single filter continuously sampled for 24 h (grey bar) and a combined series of three filters, each operated for 8 h (black bar) expressed in terms of total DNA (left bar, left axis) measured by Qubit and in terms of bacterial (middle bar, right axis) and fungal (right bar, right axis) DNA measured by qPCR ( N = 3).
Figure Legend Snippet: Comparison of two sampling approaches. Comparison of a sampling approach utilizing a single filter continuously sampled for 24 h (grey bar) and a combined series of three filters, each operated for 8 h (black bar) expressed in terms of total DNA (left bar, left axis) measured by Qubit and in terms of bacterial (middle bar, right axis) and fungal (right bar, right axis) DNA measured by qPCR ( N = 3).

Techniques Used: Sampling, Real-time Polymerase Chain Reaction

6) 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

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:

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

7) 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

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 "Automated Workflow for Somatic and Germline Next Generation Sequencing Analysis in Routine Clinical Cancer Diagnostics"

Article Title: Automated Workflow for Somatic and Germline Next Generation Sequencing Analysis in Routine Clinical Cancer Diagnostics

Journal: Cancers

doi: 10.3390/cancers11111691

Comparison of the three manual DNA extraction systems (MM, PC and GR). Mean of DNA concentration (ng/μL) and total DNA (ng) as measured by the NanoDrop D-1000 spectrophotometer ( A ) and Qubit 3.0 fluorometer ( B ) . Total DNA amount (ng) measured by the NanoDrop D-1000 spectrophotometer ( E ) and Qubit 3.0 fluorometer ( F ) and DNA concentration (ng/μL) measured by the NanoDrop D-1000 spectrophotometer ( C ) and Qubit 3.0 fluorometer ( D ) for the 24N, 24T, 48N, 48T, 72N, and 72T samples. * p
Figure Legend Snippet: Comparison of the three manual DNA extraction systems (MM, PC and GR). Mean of DNA concentration (ng/μL) and total DNA (ng) as measured by the NanoDrop D-1000 spectrophotometer ( A ) and Qubit 3.0 fluorometer ( B ) . Total DNA amount (ng) measured by the NanoDrop D-1000 spectrophotometer ( E ) and Qubit 3.0 fluorometer ( F ) and DNA concentration (ng/μL) measured by the NanoDrop D-1000 spectrophotometer ( C ) and Qubit 3.0 fluorometer ( D ) for the 24N, 24T, 48N, 48T, 72N, and 72T samples. * p

Techniques Used: DNA Extraction, Concentration Assay, Spectrophotometry

Comparison of two automatic DNA extraction systems (OMNIA Prima and King Fisher Duo). DNA concentration (ng/μL) measured by the NanoDrop D-1000 spectrophotometer ( A ) and Qubit 3.0 fluorometer ( B ). DNA (ng/μL) measured by the NanoDrop D-1000 spectrophotometer ( C ) and Qubit 3.0 fluorometer ( D ) for the 24N, 24T, 48N, 48T, 72N, and 72T samples. Total DNA amount (ng) measured by the NanoDrop D-1000 spectrophotometer ( E ) and Qubit 3.0 fluorometer ( F ) for the 24N, 24T, 48N, 48T, 72N, and 72T samples. * p
Figure Legend Snippet: Comparison of two automatic DNA extraction systems (OMNIA Prima and King Fisher Duo). DNA concentration (ng/μL) measured by the NanoDrop D-1000 spectrophotometer ( A ) and Qubit 3.0 fluorometer ( B ). DNA (ng/μL) measured by the NanoDrop D-1000 spectrophotometer ( C ) and Qubit 3.0 fluorometer ( D ) for the 24N, 24T, 48N, 48T, 72N, and 72T samples. Total DNA amount (ng) measured by the NanoDrop D-1000 spectrophotometer ( E ) and Qubit 3.0 fluorometer ( F ) for the 24N, 24T, 48N, 48T, 72N, and 72T samples. * p

Techniques Used: DNA Extraction, Concentration Assay, Spectrophotometry

10) 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

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

11) Product Images from "Chromatin regulates IL-33 release and extracellular cytokine activity"

Article Title: Chromatin regulates IL-33 release and extracellular cytokine activity

Journal: Nature Communications

doi: 10.1038/s41467-018-05485-x

IL-33 is released in complex with histones. TE-7 pools with stable, Dox-inducible overexpression of wild-type (WT) or truncated (Trunc) IL-33 were subjected to cryoshock, and the presence of high molecular weight IL-33 species in the supernatants was subsequently determined by size-exclusion chromatography. a IL-33 protein levels in different fractions as determined by ELISA, with normalization to the fraction with the highest amount of IL-33. Dashed arrow indicates where WT IL-33 is predicted to elute based off of a previously generated protein standard curve. b Proportion of IL-33 present in indicated fractions from a . c High molecular weight (corresponding to 35–39 mL retention volume, H) and low molecular weight (corresponding to 55–59 mL retention volumes, L) were pooled, concentrated by acetone precipitation, and subjected to western blot analysis for IL-33 and histone H2B. d DNA concentration in indicated fractions (high molecular weight [H], low molecular weight [L]) as determined by Qubit. a , c , e depict a representative example of three independent experiments. b , d depict mean and standard error of the mean of cumulative data from three independent experiments. e TE-7 pools with stable, Dox-inducible overexpression of WT IL-33 were subjected to cryoshock, and then co-immunoprecipitation with anti-histone H2B antibody (αH2B), isotype control (IgG1), or Protein A/G beads alone (Beads) was performed. Protein expression in eluates of IL-33 and histone H2B was assessed by western blot analysis. Black dashed arrows indicate bands corresponding to IL-33 and H2B. f Supernatants from pools of TE-7 cells with stable, Dox-inducible overexpression of WT IL-33 subjected to cryoshock were concentrated with a centrifugal filter with a 100 kDa molecular weight exclusion. HMC-1 mast cells that had been pre-treated with anti-ST2 or control IgG for 1 h were then treated with dilutions of either the input or concentrate as indicated. Depicted is mean and standard error of the mean of a representative example of two independent experiments. **, p
Figure Legend Snippet: IL-33 is released in complex with histones. TE-7 pools with stable, Dox-inducible overexpression of wild-type (WT) or truncated (Trunc) IL-33 were subjected to cryoshock, and the presence of high molecular weight IL-33 species in the supernatants was subsequently determined by size-exclusion chromatography. a IL-33 protein levels in different fractions as determined by ELISA, with normalization to the fraction with the highest amount of IL-33. Dashed arrow indicates where WT IL-33 is predicted to elute based off of a previously generated protein standard curve. b Proportion of IL-33 present in indicated fractions from a . c High molecular weight (corresponding to 35–39 mL retention volume, H) and low molecular weight (corresponding to 55–59 mL retention volumes, L) were pooled, concentrated by acetone precipitation, and subjected to western blot analysis for IL-33 and histone H2B. d DNA concentration in indicated fractions (high molecular weight [H], low molecular weight [L]) as determined by Qubit. a , c , e depict a representative example of three independent experiments. b , d depict mean and standard error of the mean of cumulative data from three independent experiments. e TE-7 pools with stable, Dox-inducible overexpression of WT IL-33 were subjected to cryoshock, and then co-immunoprecipitation with anti-histone H2B antibody (αH2B), isotype control (IgG1), or Protein A/G beads alone (Beads) was performed. Protein expression in eluates of IL-33 and histone H2B was assessed by western blot analysis. Black dashed arrows indicate bands corresponding to IL-33 and H2B. f Supernatants from pools of TE-7 cells with stable, Dox-inducible overexpression of WT IL-33 subjected to cryoshock were concentrated with a centrifugal filter with a 100 kDa molecular weight exclusion. HMC-1 mast cells that had been pre-treated with anti-ST2 or control IgG for 1 h were then treated with dilutions of either the input or concentrate as indicated. Depicted is mean and standard error of the mean of a representative example of two independent experiments. **, p

Techniques Used: Over Expression, Molecular Weight, Size-exclusion Chromatography, Enzyme-linked Immunosorbent Assay, Generated, Western Blot, Concentration Assay, Immunoprecipitation, Expressing

12) 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

13) 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

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

14) 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:

Variance in DNA recovered by the different extraction methods was calculated using Qubit measurements for engineered samples 1–4. It should be noted that one of the laboratories used a modified version of RecoverAll; however, for the purpose of the analysis, these were treated the same. N refers to the number of laboratories using each method.
Figure Legend Snippet: Variance in DNA recovered by the different extraction methods was calculated using Qubit measurements for engineered samples 1–4. It should be noted that one of the laboratories used a modified version of RecoverAll; however, for the purpose of the analysis, these were treated the same. N refers to the number of laboratories using each method.

Techniques Used: Modification

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 of ssDNA by ssDNA-Qubit and dsDNA-Qubit. Frozen-R1 and Trizol-h3 diluted with TE buffer or distilled water in 20 ng/μl were measured with ssDNA-Qubit and dsDNA-Qubit. The amounts of dsDNA (black) and ssDNA (white) were determined using the standard curve shown in S1 Fig .
Figure Legend Snippet: Quantification of ssDNA by ssDNA-Qubit and dsDNA-Qubit. Frozen-R1 and Trizol-h3 diluted with TE buffer or distilled water in 20 ng/μl were measured with ssDNA-Qubit and dsDNA-Qubit. The amounts of dsDNA (black) and ssDNA (white) were determined using the standard curve shown in S1 Fig .

Techniques Used:

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 of ssDNA by ssDNA-Qubit and dsDNA-Qubit. Frozen-R1 and Trizol-h3 diluted with TE buffer or distilled water in 20 ng/μl were measured with ssDNA-Qubit and dsDNA-Qubit. The amounts of dsDNA (black) and ssDNA (white) were determined using the standard curve shown in S1 Fig .
Figure Legend Snippet: Quantification of ssDNA by ssDNA-Qubit and dsDNA-Qubit. Frozen-R1 and Trizol-h3 diluted with TE buffer or distilled water in 20 ng/μl were measured with ssDNA-Qubit and dsDNA-Qubit. The amounts of dsDNA (black) and ssDNA (white) were determined using the standard curve shown in S1 Fig .

Techniques Used:

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 "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

18) 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

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

19) 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:

20) 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

21) 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:

22) Product Images from "Biases during DNA extraction affect bacterial and archaeal community profile of anaerobic digestion samples"

Article Title: Biases during DNA extraction affect bacterial and archaeal community profile of anaerobic digestion samples

Journal: 3 Biotech

doi: 10.1007/s13205-017-1009-x

Yield and quality of DNA extracted from samples obtained from the inlet, digester and slurry using various methods of DNA extraction. a DNA quantified with Qubit. b DNA quantified with NanoDrop. c DNA quality determined by A260/A280 ratio. d DNA quality
Figure Legend Snippet: Yield and quality of DNA extracted from samples obtained from the inlet, digester and slurry using various methods of DNA extraction. a DNA quantified with Qubit. b DNA quantified with NanoDrop. c DNA quality determined by A260/A280 ratio. d DNA quality

Techniques Used: DNA Extraction

23) 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

24) 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

25) 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

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

26) 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

27) 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:

Variance in DNA recovered by the different extraction methods was calculated using Qubit measurements for engineered samples 1–4. It should be noted that one of the laboratories used a modified version of RecoverAll; however, for the purpose of the analysis, these were treated the same. N refers to the number of laboratories using each method.
Figure Legend Snippet: Variance in DNA recovered by the different extraction methods was calculated using Qubit measurements for engineered samples 1–4. It should be noted that one of the laboratories used a modified version of RecoverAll; however, for the purpose of the analysis, these were treated the same. N refers to the number of laboratories using each method.

Techniques Used: Modification

28) 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 of ssDNA by ssDNA-Qubit and dsDNA-Qubit. Frozen-R1 and Trizol-h3 diluted with TE buffer or distilled water in 20 ng/μl were measured with ssDNA-Qubit and dsDNA-Qubit. The amounts of dsDNA (black) and ssDNA (white) were determined using the standard curve shown in S1 Fig .
Figure Legend Snippet: Quantification of ssDNA by ssDNA-Qubit and dsDNA-Qubit. Frozen-R1 and Trizol-h3 diluted with TE buffer or distilled water in 20 ng/μl were measured with ssDNA-Qubit and dsDNA-Qubit. The amounts of dsDNA (black) and ssDNA (white) were determined using the standard curve shown in S1 Fig .

Techniques Used:

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

29) 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

30) 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

31) Product Images from "Maintaining Breast Cancer Specimen Integrity and Individual or Simultaneous Extraction of Quality DNA, RNA, and Proteins from Allprotect-Stabilized and Nonstabilized Tissue Samples"

Article Title: Maintaining Breast Cancer Specimen Integrity and Individual or Simultaneous Extraction of Quality DNA, RNA, and Proteins from Allprotect-Stabilized and Nonstabilized Tissue Samples

Journal: Biopreservation and Biobanking

doi: 10.1089/bio.2011.0034

Bland-Altman Plot of Difference (Qubit-Nanodrop) (ng/μL) vs. average DNA yield (mean of Qubit and Nanodrop).
Figure Legend Snippet: Bland-Altman Plot of Difference (Qubit-Nanodrop) (ng/μL) vs. average DNA yield (mean of Qubit and Nanodrop).

Techniques Used:

32) Product Images from "Biases during DNA extraction affect bacterial and archaeal community profile of anaerobic digestion samples"

Article Title: Biases during DNA extraction affect bacterial and archaeal community profile of anaerobic digestion samples

Journal: 3 Biotech

doi: 10.1007/s13205-017-1009-x

Yield and quality of DNA extracted from samples obtained from the inlet, digester and slurry using various methods of DNA extraction. a DNA quantified with Qubit. b DNA quantified with NanoDrop. c DNA quality determined by A260/A280 ratio. d DNA quality
Figure Legend Snippet: Yield and quality of DNA extracted from samples obtained from the inlet, digester and slurry using various methods of DNA extraction. a DNA quantified with Qubit. b DNA quantified with NanoDrop. c DNA quality determined by A260/A280 ratio. d DNA quality

Techniques Used: DNA Extraction

33) 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:

34) 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

35) 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

36) 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

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:

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

37) 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

Related Articles

Concentration Assay:

Article Title: MicroRNA-130a Contributes to Type-2 Classical DC-activation in Sjögren's Syndrome by Targeting Mitogen- and Stress-Activated Protein Kinase-1
Article Snippet: .. RNA concentration was assessed with Qubit RNA Kit (Thermo Fisher Scientific). ..

Article Title: Ammonia-induced miRNA expression changes in cultured rat astrocytes
Article Snippet: .. Total RNA was quality controlled on Agilent Bioanalyzer, quantification was carried out using Invitrogen Qubit RNA (Invitrogen™, Life Technologies, Darmstadt, Germany) and the RNA concentration was normalized to 200 ng input. .. The one-color (Cy3) labeling reaction was carried using Agilent miRNA labeling kit as per protocol of the manufacturer, except that DMSO was not purified on column and samples were speed-vac concentrated after labeling.

Article Title: A Novel Enzyme Portfolio for Red Algal Polysaccharide Degradation in the Marine Bacterium Paraglaciecola hydrolytica S66T Encoded in a Sizeable Polysaccharide Utilization Locus
Article Snippet: .. RNA purity and concentration were determined using a Qubit® RNA HR Assay Kit (Invitrogen) and RNA quality was assessed by agarose gel electrophoresis. .. Contaminating DNA was removed using the DNA-freeTM DNA removal kit (Ambion) according to the manufacturer’s instructions.

Chromatin Immunoprecipitation:

Article Title: Activity of Bdellovibrio Hit Locus Proteins, Bd0108 and Bd0109, Links Type IVa Pilus Extrusion/Retraction Status to Prey-Independent Growth Signalling
Article Snippet: .. The rRNA removal was confirmed with a Pico chip run on the Agilent Bioanalyser 2100 and the quantity measured with the Qubit RNA kit and Qubit fluorometer (Invitrogen). .. The resulting ribosomal depleted RNA was then fragmented for 8 minutes at 94°C using the Elute, Fragment, Prime buffer from Illumina TruSeq RNA kit.

Article Title: Characterizing the Key Metabolic Pathways of the Neonatal Mouse Heart Using a Quantitative Combinatorial Omics Approach
Article Snippet: .. Agilent Bioanalyzer RNA pico chip (Agilent) was used to evaluate the integrity of RNA and Qubit RNA-kit (Life Technologies) to quantitate RNA. .. From each sample, a 1.5 μg of total RNA was collected, ribodepleted and further prepared to RNA-seq library by using ScriptSeq v2™ Complete kit (Illumina, Inc., San Diego, CA, USA).

Article Title: Aggressive natural killer-cell leukemia mutational landscape and drug profiling highlight JAK-STAT signaling as therapeutic target
Article Snippet: .. Agilent Bioanalyzer RNApico chip (Agilent) was used to evaluate the integrity of RNA and Qubit RNA kit (Life Technologies) to quantitate RNA in samples. .. 1.5 µg of total RNA was used for ScriptSeq v2™ Complete kit for human/mouse/rat (Illumina) to ribodeplete rRNA and further for RNA-seq library preparation.

Agarose Gel Electrophoresis:

Article Title: A Novel Enzyme Portfolio for Red Algal Polysaccharide Degradation in the Marine Bacterium Paraglaciecola hydrolytica S66T Encoded in a Sizeable Polysaccharide Utilization Locus
Article Snippet: .. RNA purity and concentration were determined using a Qubit® RNA HR Assay Kit (Invitrogen) and RNA quality was assessed by agarose gel electrophoresis. .. Contaminating DNA was removed using the DNA-freeTM DNA removal kit (Ambion) according to the manufacturer’s instructions.

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    Thermo Fisher rna br assay kit
    Monocyte differentiation with IFN-λ3 drives a pro-inflammatory macrophage phenotype. Monocytes were cultured with M- or GM-CSF ± IFN-λ3 for 7 days to examine the effect of IFN-λ3 on Mϕ differentiation, followed by phenotypic and functional characterization (A) . <t>RNA</t> sequencing ( n = 3/treatment) demonstrated that GM-CSF Mϕs were significantly more responsive to IFN-λ3, as demonstrated by smear plot and Venn diagram of genes regulated above 2-fold (B) . GM-CSF Mϕ ISG induction was significantly stronger, as demonstrated by heat map of gene log 2-fold change (logFC) (C) . IFN-λ3 increased transcript abundance of numerous ISGs and transcription factors (TFs) in both Mϕ sets, as well as numerous chemokines, cytokines, and genes responsible for antigen (Ag) presentation and co-stimulation, particularly in GM-CSF Mϕs (D) . IFN-λ3 stimulated genes were confirmed by qPCR, using IFN-α differentiated Mϕs as a comparison (E) ( n = 8). Quantitative <t>PCR</t> data are representative of three independent experiments. Paired t -test * /# p
    Rna Br Assay Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher qubit fluorometric quantitation
    Single-cell whole genome amplification and sequencing of the U-2 OS cell line. (A) Bar diagram displaying the WGA <t>DNA</t> yields from the individual U-2 OS cells and the respective controls, as measured by <t>Qubit</t> ™ . (B) Agarose gel illustrating the differently sized products of the LINE1 multiplex PCR that was performed on the WGA DNA of the individual U-2 OS cells. (C) Exemplary sequencing chromatograms of the SLC34A2 and TET2 gene mutations in the cell bulk and individual cells. (D) Conclusions on the occurrence of allelic dropout (ADO) through sequencing of single nucleotide polymorphisms (SNPs). SNPs rs1391438 and rs7655890 are located in close genomic proximity to the TET2 mutation and show heterozygous patterns in the cell bulk (left). In the single U-2 OS cells B8 and C10, wild-type only is detected at the TET2 mutation site. The heterozygous patterns of the SNPs in B8 suggest true wild-type in TET2 , while the detection of only one allele of both SNPs in C10 suggest loss of the genomic region due to ADO. NTC: no-template control, PTC: positive control.
    Qubit Fluorometric Quantitation, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 223 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher qubit fluorometer
    Mean (±SEM) <t>DNA</t> concentration (nM) of PCR products, measured by <t>Qubit</t> fluorometer, of the six template categories (Mammalia, Aves, Reptilia, Amphibia, Mosquito, negative control [No DNA]) by three primer combinations (Mod_RepCOI_F + Mod_RepCOI_R, VertCOI_7194_F + Mod_RepCOI_R, Mod_RepCOI_F + VertCOI_7216_R). Tukey’s HSD test detected pairwise differences between mean DNA concentration for each primer combination and host class. Significant differences between groups are indicated by letters. Mean DNA concentration of groups that have the same letter are not significantly different from each other, while mean DNA concentration of groups that do not share a common letter are significantly different. Comparisons were considered significant if P
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    Monocyte differentiation with IFN-λ3 drives a pro-inflammatory macrophage phenotype. Monocytes were cultured with M- or GM-CSF ± IFN-λ3 for 7 days to examine the effect of IFN-λ3 on Mϕ differentiation, followed by phenotypic and functional characterization (A) . RNA sequencing ( n = 3/treatment) demonstrated that GM-CSF Mϕs were significantly more responsive to IFN-λ3, as demonstrated by smear plot and Venn diagram of genes regulated above 2-fold (B) . GM-CSF Mϕ ISG induction was significantly stronger, as demonstrated by heat map of gene log 2-fold change (logFC) (C) . IFN-λ3 increased transcript abundance of numerous ISGs and transcription factors (TFs) in both Mϕ sets, as well as numerous chemokines, cytokines, and genes responsible for antigen (Ag) presentation and co-stimulation, particularly in GM-CSF Mϕs (D) . IFN-λ3 stimulated genes were confirmed by qPCR, using IFN-α differentiated Mϕs as a comparison (E) ( n = 8). Quantitative PCR data are representative of three independent experiments. Paired t -test * /# p

    Journal: Frontiers in Immunology

    Article Title: Macrophage Coordination of the Interferon Lambda Immune Response

    doi: 10.3389/fimmu.2019.02674

    Figure Lengend Snippet: Monocyte differentiation with IFN-λ3 drives a pro-inflammatory macrophage phenotype. Monocytes were cultured with M- or GM-CSF ± IFN-λ3 for 7 days to examine the effect of IFN-λ3 on Mϕ differentiation, followed by phenotypic and functional characterization (A) . RNA sequencing ( n = 3/treatment) demonstrated that GM-CSF Mϕs were significantly more responsive to IFN-λ3, as demonstrated by smear plot and Venn diagram of genes regulated above 2-fold (B) . GM-CSF Mϕ ISG induction was significantly stronger, as demonstrated by heat map of gene log 2-fold change (logFC) (C) . IFN-λ3 increased transcript abundance of numerous ISGs and transcription factors (TFs) in both Mϕ sets, as well as numerous chemokines, cytokines, and genes responsible for antigen (Ag) presentation and co-stimulation, particularly in GM-CSF Mϕs (D) . IFN-λ3 stimulated genes were confirmed by qPCR, using IFN-α differentiated Mϕs as a comparison (E) ( n = 8). Quantitative PCR data are representative of three independent experiments. Paired t -test * /# p

    Article Snippet: Digital Droplet PCR (ddPCR) Immune cell RNA was quantified using the Qubit fluorometer and RNA BR assay kit (Thermo Fisher), and cDNA was synthesized from ≥10 ng of RNA per sample using qScript cDNA supermix (Quantabio). cDNA was combined with ddPCR supermix and droplet generation oil for probes (Bio-Rad), and droplets were generated using the Bio-Rad QX200 Droplet Generator.

    Techniques: Cell Culture, Functional Assay, RNA Sequencing Assay, Real-time Polymerase Chain Reaction

    Single-cell whole genome amplification and sequencing of the U-2 OS cell line. (A) Bar diagram displaying the WGA DNA yields from the individual U-2 OS cells and the respective controls, as measured by Qubit ™ . (B) Agarose gel illustrating the differently sized products of the LINE1 multiplex PCR that was performed on the WGA DNA of the individual U-2 OS cells. (C) Exemplary sequencing chromatograms of the SLC34A2 and TET2 gene mutations in the cell bulk and individual cells. (D) Conclusions on the occurrence of allelic dropout (ADO) through sequencing of single nucleotide polymorphisms (SNPs). SNPs rs1391438 and rs7655890 are located in close genomic proximity to the TET2 mutation and show heterozygous patterns in the cell bulk (left). In the single U-2 OS cells B8 and C10, wild-type only is detected at the TET2 mutation site. The heterozygous patterns of the SNPs in B8 suggest true wild-type in TET2 , while the detection of only one allele of both SNPs in C10 suggest loss of the genomic region due to ADO. NTC: no-template control, PTC: positive control.

    Journal: PLoS ONE

    Article Title: Molecular Genetic Characterization of Individual Cancer Cells Isolated via Single-Cell Printing

    doi: 10.1371/journal.pone.0163455

    Figure Lengend Snippet: Single-cell whole genome amplification and sequencing of the U-2 OS cell line. (A) Bar diagram displaying the WGA DNA yields from the individual U-2 OS cells and the respective controls, as measured by Qubit ™ . (B) Agarose gel illustrating the differently sized products of the LINE1 multiplex PCR that was performed on the WGA DNA of the individual U-2 OS cells. (C) Exemplary sequencing chromatograms of the SLC34A2 and TET2 gene mutations in the cell bulk and individual cells. (D) Conclusions on the occurrence of allelic dropout (ADO) through sequencing of single nucleotide polymorphisms (SNPs). SNPs rs1391438 and rs7655890 are located in close genomic proximity to the TET2 mutation and show heterozygous patterns in the cell bulk (left). In the single U-2 OS cells B8 and C10, wild-type only is detected at the TET2 mutation site. The heterozygous patterns of the SNPs in B8 suggest true wild-type in TET2 , while the detection of only one allele of both SNPs in C10 suggest loss of the genomic region due to ADO. NTC: no-template control, PTC: positive control.

    Article Snippet: The DNA yield was assessed by Qubit fluorometric quantitation (Thermo Fisher Scientific) according to the manufacturer’s protocol.

    Techniques: Whole Genome Amplification, Sequencing, Agarose Gel Electrophoresis, Multiplex Assay, Polymerase Chain Reaction, Mutagenesis, Positive Control

    Mean (±SEM) DNA concentration (nM) of PCR products, measured by Qubit fluorometer, of the six template categories (Mammalia, Aves, Reptilia, Amphibia, Mosquito, negative control [No DNA]) by three primer combinations (Mod_RepCOI_F + Mod_RepCOI_R, VertCOI_7194_F + Mod_RepCOI_R, Mod_RepCOI_F + VertCOI_7216_R). Tukey’s HSD test detected pairwise differences between mean DNA concentration for each primer combination and host class. Significant differences between groups are indicated by letters. Mean DNA concentration of groups that have the same letter are not significantly different from each other, while mean DNA concentration of groups that do not share a common letter are significantly different. Comparisons were considered significant if P

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Barcoding blood meals: New vertebrate-specific primer sets for assigning taxonomic identities to host DNA from mosquito blood meals

    doi: 10.1371/journal.pntd.0006767

    Figure Lengend Snippet: Mean (±SEM) DNA concentration (nM) of PCR products, measured by Qubit fluorometer, of the six template categories (Mammalia, Aves, Reptilia, Amphibia, Mosquito, negative control [No DNA]) by three primer combinations (Mod_RepCOI_F + Mod_RepCOI_R, VertCOI_7194_F + Mod_RepCOI_R, Mod_RepCOI_F + VertCOI_7216_R). Tukey’s HSD test detected pairwise differences between mean DNA concentration for each primer combination and host class. Significant differences between groups are indicated by letters. Mean DNA concentration of groups that have the same letter are not significantly different from each other, while mean DNA concentration of groups that do not share a common letter are significantly different. Comparisons were considered significant if P

    Article Snippet: For each PCR product, the remaining volume was sent to the University of Florida, Interdisciplinary Center for Biotechnology Research (ICBR) for DNA quantification by Qubit fluorometer (Thermo Fisher Scientific, Waltham, MA).

    Techniques: Concentration Assay, Polymerase Chain Reaction, Negative Control, IF-P

    IL-33 is released in complex with histones. TE-7 pools with stable, Dox-inducible overexpression of wild-type (WT) or truncated (Trunc) IL-33 were subjected to cryoshock, and the presence of high molecular weight IL-33 species in the supernatants was subsequently determined by size-exclusion chromatography. a IL-33 protein levels in different fractions as determined by ELISA, with normalization to the fraction with the highest amount of IL-33. Dashed arrow indicates where WT IL-33 is predicted to elute based off of a previously generated protein standard curve. b Proportion of IL-33 present in indicated fractions from a . c High molecular weight (corresponding to 35–39 mL retention volume, H) and low molecular weight (corresponding to 55–59 mL retention volumes, L) were pooled, concentrated by acetone precipitation, and subjected to western blot analysis for IL-33 and histone H2B. d DNA concentration in indicated fractions (high molecular weight [H], low molecular weight [L]) as determined by Qubit. a , c , e depict a representative example of three independent experiments. b , d depict mean and standard error of the mean of cumulative data from three independent experiments. e TE-7 pools with stable, Dox-inducible overexpression of WT IL-33 were subjected to cryoshock, and then co-immunoprecipitation with anti-histone H2B antibody (αH2B), isotype control (IgG1), or Protein A/G beads alone (Beads) was performed. Protein expression in eluates of IL-33 and histone H2B was assessed by western blot analysis. Black dashed arrows indicate bands corresponding to IL-33 and H2B. f Supernatants from pools of TE-7 cells with stable, Dox-inducible overexpression of WT IL-33 subjected to cryoshock were concentrated with a centrifugal filter with a 100 kDa molecular weight exclusion. HMC-1 mast cells that had been pre-treated with anti-ST2 or control IgG for 1 h were then treated with dilutions of either the input or concentrate as indicated. Depicted is mean and standard error of the mean of a representative example of two independent experiments. **, p

    Journal: Nature Communications

    Article Title: Chromatin regulates IL-33 release and extracellular cytokine activity

    doi: 10.1038/s41467-018-05485-x

    Figure Lengend Snippet: IL-33 is released in complex with histones. TE-7 pools with stable, Dox-inducible overexpression of wild-type (WT) or truncated (Trunc) IL-33 were subjected to cryoshock, and the presence of high molecular weight IL-33 species in the supernatants was subsequently determined by size-exclusion chromatography. a IL-33 protein levels in different fractions as determined by ELISA, with normalization to the fraction with the highest amount of IL-33. Dashed arrow indicates where WT IL-33 is predicted to elute based off of a previously generated protein standard curve. b Proportion of IL-33 present in indicated fractions from a . c High molecular weight (corresponding to 35–39 mL retention volume, H) and low molecular weight (corresponding to 55–59 mL retention volumes, L) were pooled, concentrated by acetone precipitation, and subjected to western blot analysis for IL-33 and histone H2B. d DNA concentration in indicated fractions (high molecular weight [H], low molecular weight [L]) as determined by Qubit. a , c , e depict a representative example of three independent experiments. b , d depict mean and standard error of the mean of cumulative data from three independent experiments. e TE-7 pools with stable, Dox-inducible overexpression of WT IL-33 were subjected to cryoshock, and then co-immunoprecipitation with anti-histone H2B antibody (αH2B), isotype control (IgG1), or Protein A/G beads alone (Beads) was performed. Protein expression in eluates of IL-33 and histone H2B was assessed by western blot analysis. Black dashed arrows indicate bands corresponding to IL-33 and H2B. f Supernatants from pools of TE-7 cells with stable, Dox-inducible overexpression of WT IL-33 subjected to cryoshock were concentrated with a centrifugal filter with a 100 kDa molecular weight exclusion. HMC-1 mast cells that had been pre-treated with anti-ST2 or control IgG for 1 h were then treated with dilutions of either the input or concentrate as indicated. Depicted is mean and standard error of the mean of a representative example of two independent experiments. **, p

    Article Snippet: In separate experiments, double-stranded DNA concentration in fractions was quantitated by Qubit ( , Thermo Scientific) following the manufacturer’s instructions.

    Techniques: Over Expression, Molecular Weight, Size-exclusion Chromatography, Enzyme-linked Immunosorbent Assay, Generated, Western Blot, Concentration Assay, Immunoprecipitation, Expressing