2100 bioanalyzer system  (Agilent technologies)

 
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  • 99
    Name:
    2100 Electrophoresis Bioanalyzer Instrument
    Description:

    Catalog Number:
    G2939AA
    Price:
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    Score:
    85
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    Structured Review

    Agilent technologies 2100 bioanalyzer system
    Data from <t>2100</t> <t>Bioanalyzer</t> analysis.Upper left: Electropherograms from a representative normal subject (blue line) and a dry eye (DE) patient (red line) are here aligned and overlapped. Recognized peaks of interest are numbered 1 through 11. Upper right: The virtual gel images related to both samples are here compared showing different intensity of corresponding bands between normal subject and DE patient. Bands are here also numbered 1 through 11. Table at the bottom summarizes for each peak the following parameters: recognized molecular weight in kDa, name of the protein assigned on the basis of the validation process [ 13 ], concentration of each protein expressed in ng/microliter, percentage of each protein versus total protein content for both (N) normal subject and (DE) patient. The last line of this table reports total protein concentration expressed in ng/microliter

    https://www.bioz.com/result/2100 bioanalyzer system/product/Agilent technologies
    Average 99 stars, based on 194 article reviews
    Price from $9.99 to $1999.99
    2100 bioanalyzer system - by Bioz Stars, 2019-12
    99/100 stars

    Images

    1) Product Images from "Diagnostic performance of a tear protein panel in early dry eye"

    Article Title: Diagnostic performance of a tear protein panel in early dry eye

    Journal: Molecular Vision

    doi:

    Data from 2100 Bioanalyzer analysis.Upper left: Electropherograms from a representative normal subject (blue line) and a dry eye (DE) patient (red line) are here aligned and overlapped. Recognized peaks of interest are numbered 1 through 11. Upper right: The virtual gel images related to both samples are here compared showing different intensity of corresponding bands between normal subject and DE patient. Bands are here also numbered 1 through 11. Table at the bottom summarizes for each peak the following parameters: recognized molecular weight in kDa, name of the protein assigned on the basis of the validation process [ 13 ], concentration of each protein expressed in ng/microliter, percentage of each protein versus total protein content for both (N) normal subject and (DE) patient. The last line of this table reports total protein concentration expressed in ng/microliter
    Figure Legend Snippet: Data from 2100 Bioanalyzer analysis.Upper left: Electropherograms from a representative normal subject (blue line) and a dry eye (DE) patient (red line) are here aligned and overlapped. Recognized peaks of interest are numbered 1 through 11. Upper right: The virtual gel images related to both samples are here compared showing different intensity of corresponding bands between normal subject and DE patient. Bands are here also numbered 1 through 11. Table at the bottom summarizes for each peak the following parameters: recognized molecular weight in kDa, name of the protein assigned on the basis of the validation process [ 13 ], concentration of each protein expressed in ng/microliter, percentage of each protein versus total protein content for both (N) normal subject and (DE) patient. The last line of this table reports total protein concentration expressed in ng/microliter

    Techniques Used: Molecular Weight, Concentration Assay, Protein Concentration

    2) Product Images from "Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing"

    Article Title: Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing

    Journal: Standards in Genomic Sciences

    doi: 10.1186/s40793-017-0239-1

    Appearance of DNA libraries from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of DNA libraries sizes prepared for sequencing with the PacBio SMRTbell 10 kb Template Preparation Kit on the Agilent NGS Workstation. A typical electropherogram using the Agilent bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The DNA libraries and the upper marker co-elutes with each other, the sharper peak is the upper marker, shown in red on the gel image. The average library sizes are: Campylobacter ( green , 9.1 kb), Listeria ( blue , 9.5 kb), Vibrio ( aqua , 10 kb), and Salmonella ( red , 15 kb)
    Figure Legend Snippet: Appearance of DNA libraries from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of DNA libraries sizes prepared for sequencing with the PacBio SMRTbell 10 kb Template Preparation Kit on the Agilent NGS Workstation. A typical electropherogram using the Agilent bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The DNA libraries and the upper marker co-elutes with each other, the sharper peak is the upper marker, shown in red on the gel image. The average library sizes are: Campylobacter ( green , 9.1 kb), Listeria ( blue , 9.5 kb), Vibrio ( aqua , 10 kb), and Salmonella ( red , 15 kb)

    Techniques Used: Generated, Sequencing, Next-Generation Sequencing, Marker

    Appearance of sheared DNA from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) are used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of sheared bacterial genomic DNA with average shearing size for Campylobacter ( green , 10 kb), Listeria ( blue , 13.5 kb), Vibrio ( aqua ,11.6 kb), and Salmonella ( red , 17 kb). Peaks near 35 are the lower marker internal standard for the DNA 12000 kit. A typical electropherogram using the Agilent Bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The sheared DNA and the red upper marker, seen in the gel image, co-elute together
    Figure Legend Snippet: Appearance of sheared DNA from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) are used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of sheared bacterial genomic DNA with average shearing size for Campylobacter ( green , 10 kb), Listeria ( blue , 13.5 kb), Vibrio ( aqua ,11.6 kb), and Salmonella ( red , 17 kb). Peaks near 35 are the lower marker internal standard for the DNA 12000 kit. A typical electropherogram using the Agilent Bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The sheared DNA and the red upper marker, seen in the gel image, co-elute together

    Techniques Used: Generated, Marker

    3) Product Images from "Upregulation of APP, ADAM10 and ADAM17 in the Denervated Mouse Dentate Gyrus"

    Article Title: Upregulation of APP, ADAM10 and ADAM17 in the Denervated Mouse Dentate Gyrus

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0084962

    Laser microdissection of dentate subregions. Hippocampal section (coronal plane, dorsal part of the hippocampus, cresyl violet staining) before (A) and after (B) laser microdissection (LMD) of the granule cell layer (gcl) and the outer molecular layer (oml). (C) RNA integrity analysis of total RNA isolated from the dissected granule cell layer (gcl, red) and from the outer molecular layer (oml, blue) demonstrating highly intact RNA (RIN-values: 8.15-8.3; Agilent 2100 Bioanalyzer). hf: hippocampal fissure; iml: inner molecular layer; h: hilar region. Scale bar: 200 µm.
    Figure Legend Snippet: Laser microdissection of dentate subregions. Hippocampal section (coronal plane, dorsal part of the hippocampus, cresyl violet staining) before (A) and after (B) laser microdissection (LMD) of the granule cell layer (gcl) and the outer molecular layer (oml). (C) RNA integrity analysis of total RNA isolated from the dissected granule cell layer (gcl, red) and from the outer molecular layer (oml, blue) demonstrating highly intact RNA (RIN-values: 8.15-8.3; Agilent 2100 Bioanalyzer). hf: hippocampal fissure; iml: inner molecular layer; h: hilar region. Scale bar: 200 µm.

    Techniques Used: Laser Capture Microdissection, Staining, Isolation

    4) Product Images from "Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing"

    Article Title: Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing

    Journal: Standards in Genomic Sciences

    doi: 10.1186/s40793-017-0239-1

    Appearance of DNA libraries from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of DNA libraries sizes prepared for sequencing with the PacBio SMRTbell 10 kb Template Preparation Kit on the Agilent NGS Workstation. A typical electropherogram using the Agilent bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The DNA libraries and the upper marker co-elutes with each other, the sharper peak is the upper marker, shown in red on the gel image. The average library sizes are: Campylobacter ( green , 9.1 kb), Listeria ( blue , 9.5 kb), Vibrio ( aqua , 10 kb), and Salmonella ( red , 15 kb)
    Figure Legend Snippet: Appearance of DNA libraries from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of DNA libraries sizes prepared for sequencing with the PacBio SMRTbell 10 kb Template Preparation Kit on the Agilent NGS Workstation. A typical electropherogram using the Agilent bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The DNA libraries and the upper marker co-elutes with each other, the sharper peak is the upper marker, shown in red on the gel image. The average library sizes are: Campylobacter ( green , 9.1 kb), Listeria ( blue , 9.5 kb), Vibrio ( aqua , 10 kb), and Salmonella ( red , 15 kb)

    Techniques Used: Generated, Sequencing, Next-Generation Sequencing, Marker

    Appearance of sheared DNA from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) are used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of sheared bacterial genomic DNA with average shearing size for Campylobacter ( green , 10 kb), Listeria ( blue , 13.5 kb), Vibrio ( aqua ,11.6 kb), and Salmonella ( red , 17 kb). Peaks near 35 are the lower marker internal standard for the DNA 12000 kit. A typical electropherogram using the Agilent Bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The sheared DNA and the red upper marker, seen in the gel image, co-elute together
    Figure Legend Snippet: Appearance of sheared DNA from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) are used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of sheared bacterial genomic DNA with average shearing size for Campylobacter ( green , 10 kb), Listeria ( blue , 13.5 kb), Vibrio ( aqua ,11.6 kb), and Salmonella ( red , 17 kb). Peaks near 35 are the lower marker internal standard for the DNA 12000 kit. A typical electropherogram using the Agilent Bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The sheared DNA and the red upper marker, seen in the gel image, co-elute together

    Techniques Used: Generated, Marker

    5) Product Images from "Region-Specific Differences in Amyloid Precursor Protein Expression in the Mouse Hippocampus"

    Article Title: Region-Specific Differences in Amyloid Precursor Protein Expression in the Mouse Hippocampus

    Journal: Frontiers in Molecular Neuroscience

    doi: 10.3389/fnmol.2016.00134

    Quantitative App mRNA expression in hippocampal subregions. (A,B) LMD of hippocampal subregions, i.e., CA1 pcl and gcl of the DG. Representative section of the dorsal hippocampus (coronal plane, cresyl violet staining) before (A) and after (B) LMD is shown. Scale bar: 250 μm. (C) RNA integrity analysis of total RNA isolated from the dissected gcl (red) and from pcl (blue) demonstrating highly intact RNA (RIN-values: ~9; Agilent 2100 Bioanalyzer). (D,E) Average expression stability values ( M ) and evaluation of the optimum number of candidate reference genes for CA1 pcl and for DG gcl according to geNorm software. Pairwise variation (V) of candidate reference genes indicates that the use of the two most stable genes is sufficient to obtain an accurate normalization index for quantitative PCR (qPCR) analysis. (F) A significantly higher gene expression for App (1.5- to 1.7-fold) was detected in CA1 pcl relative to DG gcl using two different App -specific TaqMan assays ( A : Mm_01344172_m1, B : Mm_00431830_m1) after normalization to a reference gene index calculated by geNorm. (G,H) Gene expression stability values ( S ) and accumulated SD analysis using NormFinder. The minimal number of reference genes required for effective normalization is highlighted. (I) Comparable to the results obtained by geNorm algorithm, a significantly higher App expression (1.6- to 1.7-fold) was detected in CA1 pcl relative to DG gcl after normalization to the reference gene index estimated by NormFinder. Data ( N = 5–6 mice) were tested for statistical significance using one-way ANOVA followed by Bonferroni post hoc test to correct for multiple comparisons, * p ≤ 0.05.
    Figure Legend Snippet: Quantitative App mRNA expression in hippocampal subregions. (A,B) LMD of hippocampal subregions, i.e., CA1 pcl and gcl of the DG. Representative section of the dorsal hippocampus (coronal plane, cresyl violet staining) before (A) and after (B) LMD is shown. Scale bar: 250 μm. (C) RNA integrity analysis of total RNA isolated from the dissected gcl (red) and from pcl (blue) demonstrating highly intact RNA (RIN-values: ~9; Agilent 2100 Bioanalyzer). (D,E) Average expression stability values ( M ) and evaluation of the optimum number of candidate reference genes for CA1 pcl and for DG gcl according to geNorm software. Pairwise variation (V) of candidate reference genes indicates that the use of the two most stable genes is sufficient to obtain an accurate normalization index for quantitative PCR (qPCR) analysis. (F) A significantly higher gene expression for App (1.5- to 1.7-fold) was detected in CA1 pcl relative to DG gcl using two different App -specific TaqMan assays ( A : Mm_01344172_m1, B : Mm_00431830_m1) after normalization to a reference gene index calculated by geNorm. (G,H) Gene expression stability values ( S ) and accumulated SD analysis using NormFinder. The minimal number of reference genes required for effective normalization is highlighted. (I) Comparable to the results obtained by geNorm algorithm, a significantly higher App expression (1.6- to 1.7-fold) was detected in CA1 pcl relative to DG gcl after normalization to the reference gene index estimated by NormFinder. Data ( N = 5–6 mice) were tested for statistical significance using one-way ANOVA followed by Bonferroni post hoc test to correct for multiple comparisons, * p ≤ 0.05.

    Techniques Used: Expressing, Laser Capture Microdissection, Staining, Isolation, Software, Real-time Polymerase Chain Reaction, Mouse Assay

    6) Product Images from "Region-Specific Differences in Amyloid Precursor Protein Expression in the Mouse Hippocampus"

    Article Title: Region-Specific Differences in Amyloid Precursor Protein Expression in the Mouse Hippocampus

    Journal: Frontiers in Molecular Neuroscience

    doi: 10.3389/fnmol.2016.00134

    Quantitative App mRNA expression in hippocampal subregions. (A,B) LMD of hippocampal subregions, i.e., CA1 pcl and gcl of the DG. Representative section of the dorsal hippocampus (coronal plane, cresyl violet staining) before (A) and after (B) LMD is shown. Scale bar: 250 μm. (C) RNA integrity analysis of total RNA isolated from the dissected gcl (red) and from pcl (blue) demonstrating highly intact RNA (RIN-values: ~9; Agilent 2100 Bioanalyzer). (D,E) Average expression stability values ( M ) and evaluation of the optimum number of candidate reference genes for CA1 pcl and for DG gcl according to geNorm software. Pairwise variation (V) of candidate reference genes indicates that the use of the two most stable genes is sufficient to obtain an accurate normalization index for quantitative PCR (qPCR) analysis. (F) A significantly higher gene expression for App (1.5- to 1.7-fold) was detected in CA1 pcl relative to DG gcl using two different App -specific TaqMan assays ( A : Mm_01344172_m1, B : Mm_00431830_m1) after normalization to a reference gene index calculated by geNorm. (G,H) Gene expression stability values ( S ) and accumulated SD analysis using NormFinder. The minimal number of reference genes required for effective normalization is highlighted. (I) Comparable to the results obtained by geNorm algorithm, a significantly higher App expression (1.6- to 1.7-fold) was detected in CA1 pcl relative to DG gcl after normalization to the reference gene index estimated by NormFinder. Data ( N = 5–6 mice) were tested for statistical significance using one-way ANOVA followed by Bonferroni post hoc test to correct for multiple comparisons, * p ≤ 0.05.
    Figure Legend Snippet: Quantitative App mRNA expression in hippocampal subregions. (A,B) LMD of hippocampal subregions, i.e., CA1 pcl and gcl of the DG. Representative section of the dorsal hippocampus (coronal plane, cresyl violet staining) before (A) and after (B) LMD is shown. Scale bar: 250 μm. (C) RNA integrity analysis of total RNA isolated from the dissected gcl (red) and from pcl (blue) demonstrating highly intact RNA (RIN-values: ~9; Agilent 2100 Bioanalyzer). (D,E) Average expression stability values ( M ) and evaluation of the optimum number of candidate reference genes for CA1 pcl and for DG gcl according to geNorm software. Pairwise variation (V) of candidate reference genes indicates that the use of the two most stable genes is sufficient to obtain an accurate normalization index for quantitative PCR (qPCR) analysis. (F) A significantly higher gene expression for App (1.5- to 1.7-fold) was detected in CA1 pcl relative to DG gcl using two different App -specific TaqMan assays ( A : Mm_01344172_m1, B : Mm_00431830_m1) after normalization to a reference gene index calculated by geNorm. (G,H) Gene expression stability values ( S ) and accumulated SD analysis using NormFinder. The minimal number of reference genes required for effective normalization is highlighted. (I) Comparable to the results obtained by geNorm algorithm, a significantly higher App expression (1.6- to 1.7-fold) was detected in CA1 pcl relative to DG gcl after normalization to the reference gene index estimated by NormFinder. Data ( N = 5–6 mice) were tested for statistical significance using one-way ANOVA followed by Bonferroni post hoc test to correct for multiple comparisons, * p ≤ 0.05.

    Techniques Used: Expressing, Laser Capture Microdissection, Staining, Isolation, Software, Real-time Polymerase Chain Reaction, Mouse Assay

    7) Product Images from "Analysis of the complementarity determining regions β-chain genomic rearrangement using high-throughput sequencing in periphery cytotoxic T lymphocytes of patients with chronic hepatitis B"

    Article Title: Analysis of the complementarity determining regions β-chain genomic rearrangement using high-throughput sequencing in periphery cytotoxic T lymphocytes of patients with chronic hepatitis B

    Journal: Molecular Medicine Reports

    doi: 10.3892/mmr.2016.5329

    Mimic diagram of size distribution of polymerase chain reaction products with Agilent 2100 Bioanalyzer system analysis.
    Figure Legend Snippet: Mimic diagram of size distribution of polymerase chain reaction products with Agilent 2100 Bioanalyzer system analysis.

    Techniques Used: Polymerase Chain Reaction

    Agilent 2100 Bioanalyzer system analyzed data from samples of one patient (prior and subsequent to treatment). (A) Blank control. Size distribution was measured and polymerase chain reaction product quality was tested with Agilent 2100 Bioanalyzer analysis (B) prior to and (C) following treatment.
    Figure Legend Snippet: Agilent 2100 Bioanalyzer system analyzed data from samples of one patient (prior and subsequent to treatment). (A) Blank control. Size distribution was measured and polymerase chain reaction product quality was tested with Agilent 2100 Bioanalyzer analysis (B) prior to and (C) following treatment.

    Techniques Used: Polymerase Chain Reaction

    8) Product Images from "A de novo transcriptome assembly of the zebra bullhead shark, Heterodontus zebra"

    Article Title: A de novo transcriptome assembly of the zebra bullhead shark, Heterodontus zebra

    Journal: Scientific Data

    doi: 10.1038/sdata.2018.197

    The zebra bullhead shark and sample preparation. ( a ) Juvnile zebra bullhead sharks. ( b ) A schematic diagram of a zebra bullhead shark embryo. Dashed lines, dissected positions; pctr, pectoral fins; plv, pelvic fins. ( c-e ) RNA length distribution analysis of head ( c ), trunk ( d ), and tail ( e ) samples on the 2100 Bioanalyzer, respectively. ( f ) DNA length distribution analysis of prepared libraries on the 2100 Bioanalyzer.
    Figure Legend Snippet: The zebra bullhead shark and sample preparation. ( a ) Juvnile zebra bullhead sharks. ( b ) A schematic diagram of a zebra bullhead shark embryo. Dashed lines, dissected positions; pctr, pectoral fins; plv, pelvic fins. ( c-e ) RNA length distribution analysis of head ( c ), trunk ( d ), and tail ( e ) samples on the 2100 Bioanalyzer, respectively. ( f ) DNA length distribution analysis of prepared libraries on the 2100 Bioanalyzer.

    Techniques Used: Sample Prep

    9) Product Images from "A rapid standardized quantitative microfluidic system approach for evaluating human tear proteins"

    Article Title: A rapid standardized quantitative microfluidic system approach for evaluating human tear proteins

    Journal: Molecular Vision

    doi:

    Analysis of tear proteins obtained by running aliquots from the same samples in parallel. Tear samples (one to eight) were runned through the 2100 Bioanalyzer (upper part of the figure, Protein 230 kit, gel-like view), and the 1D SDS–PAGE (lower part of the figure). The corresponding molecular weight in kDa is reported on the left of the ladder L : and of the prestained protein standard S : The same profiles were obtained for each sample in the two analytical methods.
    Figure Legend Snippet: Analysis of tear proteins obtained by running aliquots from the same samples in parallel. Tear samples (one to eight) were runned through the 2100 Bioanalyzer (upper part of the figure, Protein 230 kit, gel-like view), and the 1D SDS–PAGE (lower part of the figure). The corresponding molecular weight in kDa is reported on the left of the ladder L : and of the prestained protein standard S : The same profiles were obtained for each sample in the two analytical methods.

    Techniques Used: SDS Page, Molecular Weight

    Inter-practitioner (Techn1 and Techn2) measurement variability (reproducibility) for the Agilent 2100 Bioanalyzer is shown. A : The tear lysozyme measurements (mg/ml) performed by Techn1 (y-axis) and by Techn 2 (x-axis) on the same tear samples are graphed. B : The Bland–Altman plot for various tear samples analyzed for lysozyme content, performed by two different laboratory technicians (Techn 1 and Techn 2), is shown. The x-axis indicates the mean of the lysozyme content in mg/ml obtained by Techn 1 and Techn 2. The y-axis indicates the difference in measurement between the two technicians. The mean difference of the technicians is 0.01, with an upper specification limit of 0.23 and a lower specification limit of 0.20. C : The concordance correlation coefficients calculated for the two technicians are shown; all values demonstrated the high reproducibility of the Bioanalyzer method.
    Figure Legend Snippet: Inter-practitioner (Techn1 and Techn2) measurement variability (reproducibility) for the Agilent 2100 Bioanalyzer is shown. A : The tear lysozyme measurements (mg/ml) performed by Techn1 (y-axis) and by Techn 2 (x-axis) on the same tear samples are graphed. B : The Bland–Altman plot for various tear samples analyzed for lysozyme content, performed by two different laboratory technicians (Techn 1 and Techn 2), is shown. The x-axis indicates the mean of the lysozyme content in mg/ml obtained by Techn 1 and Techn 2. The y-axis indicates the difference in measurement between the two technicians. The mean difference of the technicians is 0.01, with an upper specification limit of 0.23 and a lower specification limit of 0.20. C : The concordance correlation coefficients calculated for the two technicians are shown; all values demonstrated the high reproducibility of the Bioanalyzer method.

    Techniques Used:

    Degree of agreement between measurements conducted on replicate specimens. The same tear samples were runned with two methods: monodimensional sodium dodecyl sulfate-polyacrylamide lectrophoresis (1D SDS–PAGE) electrophoresis and the 2100 Agilent Bioanalyzer (Protein 230 kit). A : The measurements obtained with 1D-SDS–PAGE electrophoresis (y-axis) and the 2100 Agilent Bioanalyzer (x-axis) are graphed. B : The Bland–Altman plot for various samples of tears analyzed for lysozyme content, performed with the two methods, is shown. The x-axis indicates the mean of the lysozyme content in mg/ml obtained with 1D SDS–PAGE electrophoresis and the 2100 Agilent Bioanalyzer. The y-axis indicates the difference in measurement between the two methods. The mean difference is 0.08, with an upper specification limit of 0.28 and a lower specification limit of 0.43. C : The concordance correlation coefficients calculated for the two methods are shown; all values demonstrated high correlation between the two methods.
    Figure Legend Snippet: Degree of agreement between measurements conducted on replicate specimens. The same tear samples were runned with two methods: monodimensional sodium dodecyl sulfate-polyacrylamide lectrophoresis (1D SDS–PAGE) electrophoresis and the 2100 Agilent Bioanalyzer (Protein 230 kit). A : The measurements obtained with 1D-SDS–PAGE electrophoresis (y-axis) and the 2100 Agilent Bioanalyzer (x-axis) are graphed. B : The Bland–Altman plot for various samples of tears analyzed for lysozyme content, performed with the two methods, is shown. The x-axis indicates the mean of the lysozyme content in mg/ml obtained with 1D SDS–PAGE electrophoresis and the 2100 Agilent Bioanalyzer. The y-axis indicates the difference in measurement between the two methods. The mean difference is 0.08, with an upper specification limit of 0.28 and a lower specification limit of 0.43. C : The concordance correlation coefficients calculated for the two methods are shown; all values demonstrated high correlation between the two methods.

    Techniques Used: SDS Page, Electrophoresis

    Inter-session (session 1 and session 2) measurement variability (repeatability) for the Agilent 2100 Bioanalyzer is shown. A : The tear lysozyme measurements (mg/ml) performed during session 1 (y-axis) and session 2 (x-axis) on the same tear samples are graphed. B : The Bland–Altman plot for various tear samples analyzed for lysozyme content, performed in two sessions, is shown. The x-axis indicates the mean of the lysozyme content in mg/ml obtained in session 1 and session 2. The y-axis indicates the difference in measurement between the two sessions. The mean difference of both sessions is 0.04, with an upper specification limit of 0.24 and a lower specification limit of 0.16. C : The concordance correlation coefficients calculated for the two sessions are shown; all values demonstrated the high repeatability of the Bioanalyzer method.
    Figure Legend Snippet: Inter-session (session 1 and session 2) measurement variability (repeatability) for the Agilent 2100 Bioanalyzer is shown. A : The tear lysozyme measurements (mg/ml) performed during session 1 (y-axis) and session 2 (x-axis) on the same tear samples are graphed. B : The Bland–Altman plot for various tear samples analyzed for lysozyme content, performed in two sessions, is shown. The x-axis indicates the mean of the lysozyme content in mg/ml obtained in session 1 and session 2. The y-axis indicates the difference in measurement between the two sessions. The mean difference of both sessions is 0.04, with an upper specification limit of 0.24 and a lower specification limit of 0.16. C : The concordance correlation coefficients calculated for the two sessions are shown; all values demonstrated the high repeatability of the Bioanalyzer method.

    Techniques Used:

    10) Product Images from "Frequencies of genetic polymorphisms related to triptans metabolism in chronic migraine"

    Article Title: Frequencies of genetic polymorphisms related to triptans metabolism in chronic migraine

    Journal: The Journal of Headache and Pain

    doi: 10.1007/s10194-010-0202-7

    Comparison between classic agarose gel electrophoresis and chip technology for resolution and accuracy. The same samples were analyzed by electrophoresis onto 3% agarose gel ( a ) and Bioanalyzer 2100 ( b ). The molecular weight of the upper band in the S1 line of the agarose gel is not unambiguously assignable. b Gel-like image and electropherograms of samples S1 and S2 obtained by Bioanalyzer 2100 analysis. The exact length of the longer fragment is easily determined ( Mk molecular weight marker)
    Figure Legend Snippet: Comparison between classic agarose gel electrophoresis and chip technology for resolution and accuracy. The same samples were analyzed by electrophoresis onto 3% agarose gel ( a ) and Bioanalyzer 2100 ( b ). The molecular weight of the upper band in the S1 line of the agarose gel is not unambiguously assignable. b Gel-like image and electropherograms of samples S1 and S2 obtained by Bioanalyzer 2100 analysis. The exact length of the longer fragment is easily determined ( Mk molecular weight marker)

    Techniques Used: Agarose Gel Electrophoresis, Electrophoresis, Chromatin Immunoprecipitation, Molecular Weight, Marker

    11) Product Images from "Upregulation of APP, ADAM10 and ADAM17 in the Denervated Mouse Dentate Gyrus"

    Article Title: Upregulation of APP, ADAM10 and ADAM17 in the Denervated Mouse Dentate Gyrus

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0084962

    Laser microdissection of dentate subregions. Hippocampal section (coronal plane, dorsal part of the hippocampus, cresyl violet staining) before (A) and after (B) laser microdissection (LMD) of the granule cell layer (gcl) and the outer molecular layer (oml). (C) RNA integrity analysis of total RNA isolated from the dissected granule cell layer (gcl, red) and from the outer molecular layer (oml, blue) demonstrating highly intact RNA (RIN-values: 8.15-8.3; Agilent 2100 Bioanalyzer). hf: hippocampal fissure; iml: inner molecular layer; h: hilar region. Scale bar: 200 µm.
    Figure Legend Snippet: Laser microdissection of dentate subregions. Hippocampal section (coronal plane, dorsal part of the hippocampus, cresyl violet staining) before (A) and after (B) laser microdissection (LMD) of the granule cell layer (gcl) and the outer molecular layer (oml). (C) RNA integrity analysis of total RNA isolated from the dissected granule cell layer (gcl, red) and from the outer molecular layer (oml, blue) demonstrating highly intact RNA (RIN-values: 8.15-8.3; Agilent 2100 Bioanalyzer). hf: hippocampal fissure; iml: inner molecular layer; h: hilar region. Scale bar: 200 µm.

    Techniques Used: Laser Capture Microdissection, Staining, Isolation

    12) Product Images from "Upregulation of APP, ADAM10 and ADAM17 in the Denervated Mouse Dentate Gyrus"

    Article Title: Upregulation of APP, ADAM10 and ADAM17 in the Denervated Mouse Dentate Gyrus

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0084962

    Laser microdissection of dentate subregions. Hippocampal section (coronal plane, dorsal part of the hippocampus, cresyl violet staining) before (A) and after (B) laser microdissection (LMD) of the granule cell layer (gcl) and the outer molecular layer (oml). (C) RNA integrity analysis of total RNA isolated from the dissected granule cell layer (gcl, red) and from the outer molecular layer (oml, blue) demonstrating highly intact RNA (RIN-values: 8.15-8.3; Agilent 2100 Bioanalyzer). hf: hippocampal fissure; iml: inner molecular layer; h: hilar region. Scale bar: 200 µm.
    Figure Legend Snippet: Laser microdissection of dentate subregions. Hippocampal section (coronal plane, dorsal part of the hippocampus, cresyl violet staining) before (A) and after (B) laser microdissection (LMD) of the granule cell layer (gcl) and the outer molecular layer (oml). (C) RNA integrity analysis of total RNA isolated from the dissected granule cell layer (gcl, red) and from the outer molecular layer (oml, blue) demonstrating highly intact RNA (RIN-values: 8.15-8.3; Agilent 2100 Bioanalyzer). hf: hippocampal fissure; iml: inner molecular layer; h: hilar region. Scale bar: 200 µm.

    Techniques Used: Laser Capture Microdissection, Staining, Isolation

    13) Product Images from "Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read ( > 11 kb), single molecule, real-time sequencing"

    Article Title: Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read ( > 11 kb), single molecule, real-time sequencing

    Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

    doi: 10.1093/dnares/dsw022

    Comparison of SMRTbell library preparation efficiency from P. falciparum genomic DNA purified using three different methods. (A) High molecular weight P. falciparum genomic DNA prepared from an asynchronous culture using the Genomic tip kit was purified by three different methods: (i) AMPure PB magnetic bead-based clean up (Lanes 1 2), (ii) electrophoretic DNA extraction using the Aurora System (Lanes 3 4) or (iii) phenol-chloroform extraction (Lanes 5 6), and sheared as described in Materials and Methods. Quality and size distribution of the sheared DNA (140 ng) was assessed using field-inversion gel electrophoresis (Pippin Pulse System, Sage Science). Size markers included CHEF 8-48 kb DNA Size Standard (Bio-Rad) and 2.5 kb Molecular Ruler (Bio-Rad). (B) SMRTbell libraries prepared using the indicated amount of purified genomic DNA was subjected to size selection on the BluePippin System using a 15 kb cut-off. The DNA yield and % recovery of various steps, library preparation efficiency and size-selection distribution (based on Fig. 2C) of the three DNA purification methods were compared. (C) Size, quantity and quality of SMRTbell libraries before and after size-selection were assessed using the Agilent DNA 12000 kit on the Agilent 2100 Bioanalyzer System.
    Figure Legend Snippet: Comparison of SMRTbell library preparation efficiency from P. falciparum genomic DNA purified using three different methods. (A) High molecular weight P. falciparum genomic DNA prepared from an asynchronous culture using the Genomic tip kit was purified by three different methods: (i) AMPure PB magnetic bead-based clean up (Lanes 1 2), (ii) electrophoretic DNA extraction using the Aurora System (Lanes 3 4) or (iii) phenol-chloroform extraction (Lanes 5 6), and sheared as described in Materials and Methods. Quality and size distribution of the sheared DNA (140 ng) was assessed using field-inversion gel electrophoresis (Pippin Pulse System, Sage Science). Size markers included CHEF 8-48 kb DNA Size Standard (Bio-Rad) and 2.5 kb Molecular Ruler (Bio-Rad). (B) SMRTbell libraries prepared using the indicated amount of purified genomic DNA was subjected to size selection on the BluePippin System using a 15 kb cut-off. The DNA yield and % recovery of various steps, library preparation efficiency and size-selection distribution (based on Fig. 2C) of the three DNA purification methods were compared. (C) Size, quantity and quality of SMRTbell libraries before and after size-selection were assessed using the Agilent DNA 12000 kit on the Agilent 2100 Bioanalyzer System.

    Techniques Used: Purification, Molecular Weight, DNA Extraction, Nucleic Acid Electrophoresis, Selection, DNA Purification

    14) Product Images from "Analysis of the complementarity determining regions β-chain genomic rearrangement using high-throughput sequencing in periphery cytotoxic T lymphocytes of patients with chronic hepatitis B"

    Article Title: Analysis of the complementarity determining regions β-chain genomic rearrangement using high-throughput sequencing in periphery cytotoxic T lymphocytes of patients with chronic hepatitis B

    Journal: Molecular Medicine Reports

    doi: 10.3892/mmr.2016.5329

    Mimic diagram of size distribution of polymerase chain reaction products with Agilent 2100 Bioanalyzer system analysis.
    Figure Legend Snippet: Mimic diagram of size distribution of polymerase chain reaction products with Agilent 2100 Bioanalyzer system analysis.

    Techniques Used: Polymerase Chain Reaction

    Agilent 2100 Bioanalyzer system analyzed data from samples of one patient (prior and subsequent to treatment). (A) Blank control. Size distribution was measured and polymerase chain reaction product quality was tested with Agilent 2100 Bioanalyzer analysis (B) prior to and (C) following treatment.
    Figure Legend Snippet: Agilent 2100 Bioanalyzer system analyzed data from samples of one patient (prior and subsequent to treatment). (A) Blank control. Size distribution was measured and polymerase chain reaction product quality was tested with Agilent 2100 Bioanalyzer analysis (B) prior to and (C) following treatment.

    Techniques Used: Polymerase Chain Reaction

    15) Product Images from "Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing"

    Article Title: Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing

    Journal: Standards in Genomic Sciences

    doi: 10.1186/s40793-017-0239-1

    Appearance of DNA libraries from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of DNA libraries sizes prepared for sequencing with the PacBio SMRTbell 10 kb Template Preparation Kit on the Agilent NGS Workstation. A typical electropherogram using the Agilent bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The DNA libraries and the upper marker co-elutes with each other, the sharper peak is the upper marker, shown in red on the gel image. The average library sizes are: Campylobacter ( green , 9.1 kb), Listeria ( blue , 9.5 kb), Vibrio ( aqua , 10 kb), and Salmonella ( red , 15 kb)
    Figure Legend Snippet: Appearance of DNA libraries from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of DNA libraries sizes prepared for sequencing with the PacBio SMRTbell 10 kb Template Preparation Kit on the Agilent NGS Workstation. A typical electropherogram using the Agilent bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The DNA libraries and the upper marker co-elutes with each other, the sharper peak is the upper marker, shown in red on the gel image. The average library sizes are: Campylobacter ( green , 9.1 kb), Listeria ( blue , 9.5 kb), Vibrio ( aqua , 10 kb), and Salmonella ( red , 15 kb)

    Techniques Used: Generated, Sequencing, Next-Generation Sequencing, Marker

    Appearance of sheared DNA from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) are used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of sheared bacterial genomic DNA with average shearing size for Campylobacter ( green , 10 kb), Listeria ( blue , 13.5 kb), Vibrio ( aqua ,11.6 kb), and Salmonella ( red , 17 kb). Peaks near 35 are the lower marker internal standard for the DNA 12000 kit. A typical electropherogram using the Agilent Bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The sheared DNA and the red upper marker, seen in the gel image, co-elute together
    Figure Legend Snippet: Appearance of sheared DNA from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) are used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of sheared bacterial genomic DNA with average shearing size for Campylobacter ( green , 10 kb), Listeria ( blue , 13.5 kb), Vibrio ( aqua ,11.6 kb), and Salmonella ( red , 17 kb). Peaks near 35 are the lower marker internal standard for the DNA 12000 kit. A typical electropherogram using the Agilent Bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The sheared DNA and the red upper marker, seen in the gel image, co-elute together

    Techniques Used: Generated, Marker

    16) Product Images from "A de novo transcriptome assembly of the zebra bullhead shark, Heterodontus zebra"

    Article Title: A de novo transcriptome assembly of the zebra bullhead shark, Heterodontus zebra

    Journal: Scientific Data

    doi: 10.1038/sdata.2018.197

    The zebra bullhead shark and sample preparation. ( a ) Juvnile zebra bullhead sharks. ( b ) A schematic diagram of a zebra bullhead shark embryo. Dashed lines, dissected positions; pctr, pectoral fins; plv, pelvic fins. ( c-e ) RNA length distribution analysis of head ( c ), trunk ( d ), and tail ( e ) samples on the 2100 Bioanalyzer, respectively. ( f ) DNA length distribution analysis of prepared libraries on the 2100 Bioanalyzer.
    Figure Legend Snippet: The zebra bullhead shark and sample preparation. ( a ) Juvnile zebra bullhead sharks. ( b ) A schematic diagram of a zebra bullhead shark embryo. Dashed lines, dissected positions; pctr, pectoral fins; plv, pelvic fins. ( c-e ) RNA length distribution analysis of head ( c ), trunk ( d ), and tail ( e ) samples on the 2100 Bioanalyzer, respectively. ( f ) DNA length distribution analysis of prepared libraries on the 2100 Bioanalyzer.

    Techniques Used: Sample Prep

    17) Product Images from "A rapid standardized quantitative microfluidic system approach for evaluating human tear proteins"

    Article Title: A rapid standardized quantitative microfluidic system approach for evaluating human tear proteins

    Journal: Molecular Vision

    doi:

    Analysis of tear proteins obtained by running aliquots from the same samples in parallel. Tear samples (one to eight) were runned through the 2100 Bioanalyzer (upper part of the figure, Protein 230 kit, gel-like view), and the 1D SDS–PAGE (lower part of the figure). The corresponding molecular weight in kDa is reported on the left of the ladder L : and of the prestained protein standard S : The same profiles were obtained for each sample in the two analytical methods.
    Figure Legend Snippet: Analysis of tear proteins obtained by running aliquots from the same samples in parallel. Tear samples (one to eight) were runned through the 2100 Bioanalyzer (upper part of the figure, Protein 230 kit, gel-like view), and the 1D SDS–PAGE (lower part of the figure). The corresponding molecular weight in kDa is reported on the left of the ladder L : and of the prestained protein standard S : The same profiles were obtained for each sample in the two analytical methods.

    Techniques Used: SDS Page, Molecular Weight

    Inter-practitioner (Techn1 and Techn2) measurement variability (reproducibility) for the Agilent 2100 Bioanalyzer is shown. A : The tear lysozyme measurements (mg/ml) performed by Techn1 (y-axis) and by Techn 2 (x-axis) on the same tear samples are graphed. B : The Bland–Altman plot for various tear samples analyzed for lysozyme content, performed by two different laboratory technicians (Techn 1 and Techn 2), is shown. The x-axis indicates the mean of the lysozyme content in mg/ml obtained by Techn 1 and Techn 2. The y-axis indicates the difference in measurement between the two technicians. The mean difference of the technicians is 0.01, with an upper specification limit of 0.23 and a lower specification limit of 0.20. C : The concordance correlation coefficients calculated for the two technicians are shown; all values demonstrated the high reproducibility of the Bioanalyzer method.
    Figure Legend Snippet: Inter-practitioner (Techn1 and Techn2) measurement variability (reproducibility) for the Agilent 2100 Bioanalyzer is shown. A : The tear lysozyme measurements (mg/ml) performed by Techn1 (y-axis) and by Techn 2 (x-axis) on the same tear samples are graphed. B : The Bland–Altman plot for various tear samples analyzed for lysozyme content, performed by two different laboratory technicians (Techn 1 and Techn 2), is shown. The x-axis indicates the mean of the lysozyme content in mg/ml obtained by Techn 1 and Techn 2. The y-axis indicates the difference in measurement between the two technicians. The mean difference of the technicians is 0.01, with an upper specification limit of 0.23 and a lower specification limit of 0.20. C : The concordance correlation coefficients calculated for the two technicians are shown; all values demonstrated the high reproducibility of the Bioanalyzer method.

    Techniques Used:

    Degree of agreement between measurements conducted on replicate specimens. The same tear samples were runned with two methods: monodimensional sodium dodecyl sulfate-polyacrylamide lectrophoresis (1D SDS–PAGE) electrophoresis and the 2100 Agilent Bioanalyzer (Protein 230 kit). A : The measurements obtained with 1D-SDS–PAGE electrophoresis (y-axis) and the 2100 Agilent Bioanalyzer (x-axis) are graphed. B : The Bland–Altman plot for various samples of tears analyzed for lysozyme content, performed with the two methods, is shown. The x-axis indicates the mean of the lysozyme content in mg/ml obtained with 1D SDS–PAGE electrophoresis and the 2100 Agilent Bioanalyzer. The y-axis indicates the difference in measurement between the two methods. The mean difference is 0.08, with an upper specification limit of 0.28 and a lower specification limit of 0.43. C : The concordance correlation coefficients calculated for the two methods are shown; all values demonstrated high correlation between the two methods.
    Figure Legend Snippet: Degree of agreement between measurements conducted on replicate specimens. The same tear samples were runned with two methods: monodimensional sodium dodecyl sulfate-polyacrylamide lectrophoresis (1D SDS–PAGE) electrophoresis and the 2100 Agilent Bioanalyzer (Protein 230 kit). A : The measurements obtained with 1D-SDS–PAGE electrophoresis (y-axis) and the 2100 Agilent Bioanalyzer (x-axis) are graphed. B : The Bland–Altman plot for various samples of tears analyzed for lysozyme content, performed with the two methods, is shown. The x-axis indicates the mean of the lysozyme content in mg/ml obtained with 1D SDS–PAGE electrophoresis and the 2100 Agilent Bioanalyzer. The y-axis indicates the difference in measurement between the two methods. The mean difference is 0.08, with an upper specification limit of 0.28 and a lower specification limit of 0.43. C : The concordance correlation coefficients calculated for the two methods are shown; all values demonstrated high correlation between the two methods.

    Techniques Used: SDS Page, Electrophoresis

    Inter-session (session 1 and session 2) measurement variability (repeatability) for the Agilent 2100 Bioanalyzer is shown. A : The tear lysozyme measurements (mg/ml) performed during session 1 (y-axis) and session 2 (x-axis) on the same tear samples are graphed. B : The Bland–Altman plot for various tear samples analyzed for lysozyme content, performed in two sessions, is shown. The x-axis indicates the mean of the lysozyme content in mg/ml obtained in session 1 and session 2. The y-axis indicates the difference in measurement between the two sessions. The mean difference of both sessions is 0.04, with an upper specification limit of 0.24 and a lower specification limit of 0.16. C : The concordance correlation coefficients calculated for the two sessions are shown; all values demonstrated the high repeatability of the Bioanalyzer method.
    Figure Legend Snippet: Inter-session (session 1 and session 2) measurement variability (repeatability) for the Agilent 2100 Bioanalyzer is shown. A : The tear lysozyme measurements (mg/ml) performed during session 1 (y-axis) and session 2 (x-axis) on the same tear samples are graphed. B : The Bland–Altman plot for various tear samples analyzed for lysozyme content, performed in two sessions, is shown. The x-axis indicates the mean of the lysozyme content in mg/ml obtained in session 1 and session 2. The y-axis indicates the difference in measurement between the two sessions. The mean difference of both sessions is 0.04, with an upper specification limit of 0.24 and a lower specification limit of 0.16. C : The concordance correlation coefficients calculated for the two sessions are shown; all values demonstrated the high repeatability of the Bioanalyzer method.

    Techniques Used:

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    Article Snippet: Briefly, 1000 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented by heat and converted to double stranded cDNA; cDNA was end-repaired and adenylated at the 3′ end to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98° for 30 sec, followed by 15 cycles of 98° for 10 sec, 60° for 30 sec and 72° for 30 sec, and finally an extension step for 5 min at 72°; Each sample was prepared with different indexed adapters to allow for multiplex sequencing. .. One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).

    Article Title: The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes
    Article Snippet: Briefly, 100–500 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented into the 200-300-bases range for 4 minutes at 94°C and converted to double stranded cDNA, end-repaired and adenylated at the 3’ to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98°C for 10 seconds, followed by 10 cycles of 98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds, and finally an extension step for 5 minutes at 72°C; at the amplification step, each sample were amplified with a different barcoded adapters to allow for multiplex sequencing. .. 1 μl of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems, Wilmington, MA).

    Article Title: Vector transmission regulates immune control of Plasmodium virulence
    Article Snippet: Sequencing templates were prepared by mixing 15μl cDNA, 5μl 33μM adaptors (based on the published adaptor with the addition of barcode sequences; oligos supplied by Integrated DNA Technologies), 25μl Quick Ligation buffer and 5μl Quick DNA ligase (both from New England Biolabs) and incubating for 15 minutes at 25°C. .. Final libraries were eluted in 30μl water, visualised on an Agilent Bioanalyzer 2100 High Sensitivity DNA chip and quantified by qPCR.

    Article Title: Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
    Article Snippet: 3 μg of genomic DNA was fragmented to a size range of 150-200 bp followed by end repair, adaptor ligation, and low cycle (5) PCR. .. Libraries were purified and validated for appropriate size (225-275 bp) on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Inc.).

    Article Title: An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers
    Article Snippet: The RNA products from the controlled fragmentation step were used to prepare the strand-specific metatranscriptomic library, following the manufacturer’s instruction of Apollo 324 PrepX mRNA library protocol (IntegenX), which is based on directional RNA adaptor ligation. .. Library concentration was quantified on Agilent 2100 BioAnalyzer DNA HS chip using Qubit DNA HS assay (Life Technologies).

    Methylation:

    Article Title: QSEA—modelling of genome-wide DNA methylation from sequencing enrichment experiments
    Article Snippet: The methylated adapter was then ligated to the fragmented DNA. .. The indexed DNA pool was analyzed with the 2100 Bioanalyzer High Sensitivity DNA assay (Agilent Technologies).

    Cell Culture:

    Article Title: The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes
    Article Snippet: To evaluate transcripts generated by the region of the QPD duplication, including the QPD breakpoint, approximately 1 μg of total RNA/sample from 3 control and 3 QPD samples of day 14 cultured megakaryocytes and affinity purified granulocytes was prepared. .. 1 μl of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems, Wilmington, MA).

    Generated:

    Article Title: The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes
    Article Snippet: To evaluate transcripts generated by the region of the QPD duplication, including the QPD breakpoint, approximately 1 μg of total RNA/sample from 3 control and 3 QPD samples of day 14 cultured megakaryocytes and affinity purified granulocytes was prepared. .. 1 μl of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems, Wilmington, MA).

    Article Title: An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers
    Article Snippet: Library concentration was quantified on Agilent 2100 BioAnalyzer DNA HS chip using Qubit DNA HS assay (Life Technologies). .. Sequencing of 141-nt single-end reads was performed on one lane of Illumina 2500 HiSeq platform with Illumina’s Truseq Rapid SBS chemistry.

    DNA HS Assay:

    Article Title: An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers
    Article Snippet: The RNA products from the controlled fragmentation step were used to prepare the strand-specific metatranscriptomic library, following the manufacturer’s instruction of Apollo 324 PrepX mRNA library protocol (IntegenX), which is based on directional RNA adaptor ligation. .. Library concentration was quantified on Agilent 2100 BioAnalyzer DNA HS chip using Qubit DNA HS assay (Life Technologies). .. Absolute quantitative PCR assay using SYBR FAST ABI Prism QPCR Mast Mix (Kapa Bio Systems) was performed to confirm amplification efficiency and to determine the library loading concentration for sequencing.

    Sequencing:

    Article Title: SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells
    Article Snippet: The NEBNext Ultra™ DNA Library Prep Kit for Illumina (E7370) and NEBNext Mutiplex Oligos for Illumina dual index kit (E7600) were used for end repair and adaptor ligation and quantification (bar coding for multiplex sequencing) using the standard manufacturer protocols. .. Each of the adaptor ligated, bar-coded DNA samples was ran on an Agilent 2100 Bioanalyzer Instrument (expert High-Sensitivity DNA chip) to assess sample DNA concentration and the presence and distribution of correct fragment sizes [ ].

    Article Title: Adaptive Changes in the Vestibular System of Land Snail to a 30-Day Spaceflight and Readaptation on Return to Earth
    Article Snippet: The quality of each prepared cDNA library was evaluated using Qubit® 2.0 Fluorometer (with Qubit® dsDNA HS Assay Kit) and Agilent 2100 Bioanalyzer (with High Sensitivity DNA chip and Agilent High Sensitivity DNA Kit). .. During the next step, clonal amplification was performed using Ion PI™ Template OT2 200 Kit v3 and Ion OneTouch™ 2 system (Life Technologies) in accordance with manufacturer's recommendations.

    Article Title: Noninvasive monitoring of infection and rejection after lung transplantation
    Article Snippet: Paragraph title: Sequencing Library Preparation and Sequencing. ... Libraries were characterized using the Agilent 2100 Bioanalyzer (High Sensitivity DNA Kit) or the AATI fragment analyzer, quantified by quantitative PCR, and sequenced (Illumina HiSeq 2000, HiSeq 2500, or NextSeq 500; 1 × 50 bp or 2 × 100 bp).

    Article Title: Identification of Human Papillomavirus Infection in Cancer Tissue by Targeted Next Generation Sequencing
    Article Snippet: Paragraph title: DNA Isolation, Library Preparation, and Sequencing ... During DNA isolation and library preparation, DNA concentration was measured by fluorometry, DNA quality was assessed using the Agilent 2100 Bioanalyzer high sensitivity DNA assay, and DNA size was determined by Experion automated electrophoresis system (BioRad, Hercules CA) or by Agilent TapeStation.

    Article Title: Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance
    Article Snippet: A further amplification step was performed to add barcode sequences for sample pooling and sequencing analysis via the Illumina HiSeq2000 platform. .. The indexed DNA pool was analyzed with the 2100 Bioanalyzer High Sensitivity DNA assay (Agilent Technologies) prior to sequencing. .. Adapter sequences in paired-end Methyl-Seq reads were trimmed using trim_galore version 0.4.0 and then aligned using bismark v0.10.0 based on bowtie2 version 2.2.1 with default parameters [ , ].

    Article Title: Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci
    Article Snippet: Libraries were subjected to an additional electrophoresis step on an E-Gel EX 2% agarose gel (Invitrogen), and gel fragments correlating to 100–1,000 bp were excised and purified. .. The quality of the library preparation was determined by evaluation of the electropherogram traces from an Agilent 2100 Bioanalyzer DNA High Sensitivity, and libraries demonstrating appropriate nucleosomal enrichment were multiplexed and subjected to a lane of Illumina HiSeq 2500 sequencing. .. HCASMCs were cultured in normal media containing serum and fixed in 1% formaldehyde to crosslink chromatin, followed by quenching with glycine.

    Article Title: Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
    Article Snippet: Briefly, 1000 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented by heat and converted to double stranded cDNA; cDNA was end-repaired and adenylated at the 3′ end to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98° for 30 sec, followed by 15 cycles of 98° for 10 sec, 60° for 30 sec and 72° for 30 sec, and finally an extension step for 5 min at 72°; Each sample was prepared with different indexed adapters to allow for multiplex sequencing. .. One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).

    Article Title: The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes
    Article Snippet: Briefly, 100–500 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented into the 200-300-bases range for 4 minutes at 94°C and converted to double stranded cDNA, end-repaired and adenylated at the 3’ to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98°C for 10 seconds, followed by 10 cycles of 98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds, and finally an extension step for 5 minutes at 72°C; at the amplification step, each sample were amplified with a different barcoded adapters to allow for multiplex sequencing. .. 1 μl of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems, Wilmington, MA).

    Article Title: Vector transmission regulates immune control of Plasmodium virulence
    Article Snippet: Sequencing templates were prepared by mixing 15μl cDNA, 5μl 33μM adaptors (based on the published adaptor with the addition of barcode sequences; oligos supplied by Integrated DNA Technologies), 25μl Quick Ligation buffer and 5μl Quick DNA ligase (both from New England Biolabs) and incubating for 15 minutes at 25°C. .. Final libraries were eluted in 30μl water, visualised on an Agilent Bioanalyzer 2100 High Sensitivity DNA chip and quantified by qPCR.

    Article Title: Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
    Article Snippet: Paragraph title: Whole exome sequencing (WES) ... Libraries were purified and validated for appropriate size (225-275 bp) on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Inc.).

    Article Title: Whole-genome sequencing of a malignant granular cell tumor with metabolic response to pazopanib
    Article Snippet: Paragraph title: Whole-Genome Sequencing (WGS) ... Following purification, the fragmented DNA was PCR amplified for five cycles, purified, and validated for appropriate size on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies).

    Article Title: An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers
    Article Snippet: Before sequencing, the total RNA sample was analyzed on the Agilent 2100 BioAnalyzer system using RNA 6000 Nano kit. .. Library concentration was quantified on Agilent 2100 BioAnalyzer DNA HS chip using Qubit DNA HS assay (Life Technologies).

    Article Title: Chemostat culture systems support diverse bacteriophage communities from human feces
    Article Snippet: We amplified the bacterial 16S rRNA gene V1-V2 hypervariable region using the forward primer 8F fused with the Ion Torrent Adaptor A sequence and one of 23 unique 10 base pair barcodes and reverse primer 357R fused with the Ion Torrent Adaptor P1 from the each donor and sample type [ ]. .. Amplicons were further purified with Ampure XP beads (Beckman-Coulter, Brea, CA), and molar equivalents were determined for each sample using a Bioanalyzer 2100 HS DNA Kit (Agilent Technologies, Santa Clara, CA).

    Article Title: Whole-Transcriptome Profiling of Canine and Human in Vitro Models Exposed to a G-Quadruplex Binding Small Molecule
    Article Snippet: The PCR-amplified libraries were purified with the AMPure XP beads (Beckman Coulter, Brea, CA, USA) and, then, assessed for their quality and fragments distribution using the 2100 Bioanalyzer DNA 1000 assay (Agilent Technologies, Santa Clara, CA, USA). .. Libraries were quantified using both the Qubit® Fluorometer (Life Technologies, USA) and the qPCR-based NEBNext library quantification kit (New England BioLabs, UK).

    Article Title: MSTO1 is a cytoplasmic pro‐mitochondrial fusion protein, whose mutation induces myopathy and ataxia in humans
    Article Snippet: The total coding region of mtDNA was screened by Sanger sequencing using ABI Prism 3500 DNA Sequencer (Applied Biosystems, Foster City, USA); the obtained sequences were compared with the mitomap databases using NCBI's Blast® application, while mtDNA deletion was investigated with long PCRs using Phusion High‐Fidelity DNA Polymerase (Finnzyme, Vanta, Finland). .. Crude pre‐captured genomic library was analyzed by Agilent 2100 Bioanalyzer 1000 DNA chip to assess library quality.

    Sonication:

    Article Title: Identification of Human Papillomavirus Infection in Cancer Tissue by Targeted Next Generation Sequencing
    Article Snippet: DNA was extracted from fresh frozen tissue samples (16 cases) or from FFPE tissue sections (5 cases) using either the Gentra Puregene Tissue Kit (QIAGEN, Valencia CA) or the Maxwell 16 DNA purification platform (Promega Corp, Madison, WI), and then fragmented by sonication. .. During DNA isolation and library preparation, DNA concentration was measured by fluorometry, DNA quality was assessed using the Agilent 2100 Bioanalyzer high sensitivity DNA assay, and DNA size was determined by Experion automated electrophoresis system (BioRad, Hercules CA) or by Agilent TapeStation.

    Affinity Purification:

    Article Title: The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes
    Article Snippet: To evaluate transcripts generated by the region of the QPD duplication, including the QPD breakpoint, approximately 1 μg of total RNA/sample from 3 control and 3 QPD samples of day 14 cultured megakaryocytes and affinity purified granulocytes was prepared. .. 1 μl of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems, Wilmington, MA).

    Binding Assay:

    Article Title: Whole-Transcriptome Profiling of Canine and Human in Vitro Models Exposed to a G-Quadruplex Binding Small Molecule
    Article Snippet: In brief, poly(A) RNA was purified from 1 µg of total RNA using two serial rounds of binding to oligo(dT) magnetic particles; then, fragmented RNA was reverse transcribed to generate cDNA. .. The PCR-amplified libraries were purified with the AMPure XP beads (Beckman Coulter, Brea, CA, USA) and, then, assessed for their quality and fragments distribution using the 2100 Bioanalyzer DNA 1000 assay (Agilent Technologies, Santa Clara, CA, USA).

    Multiplexing:

    Article Title: Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
    Article Snippet: Libraries were purified and validated for appropriate size (225-275 bp) on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Inc.). .. The captured regions were then bound to Streptavidin T1 magnetic beads (Life Technologies, Inc.) and washed to remove any non-specific bound products.

    Article Title: Whole-Transcriptome Profiling of Canine and Human in Vitro Models Exposed to a G-Quadruplex Binding Small Molecule
    Article Snippet: An Illumina-specific adaptor was sequentially ligated to the 3′ end of cDNA fragments, purified using the AMPure XP beads (Beckman Coulter, Brea, CA, USA), and finally PCR-amplified (13 cycles) using an appropriate indexing primer to allow further samples multiplexing. .. The PCR-amplified libraries were purified with the AMPure XP beads (Beckman Coulter, Brea, CA, USA) and, then, assessed for their quality and fragments distribution using the 2100 Bioanalyzer DNA 1000 assay (Agilent Technologies, Santa Clara, CA, USA).

    RNA Sequencing Assay:

    Article Title: Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
    Article Snippet: Paragraph title: RNA-seq: data generation and bioinformatics ... One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).

    Article Title: Fingerprinting of Proteins that Mediate Quagga Mussel Adhesion using a De Novo Assembled Foot Transcriptome
    Article Snippet: Paragraph title: Illumina RNA-sequencing and transcriptome library construction ... Libraries were checked on a Bioanalyzer 2100 DNA High Sensitivity Chip (Agilent Technologies) to check for size and quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit (KAPA Biosystems) following the manufacturer’s recommended protocol.

    Article Title: The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes
    Article Snippet: Paragraph title: RNA-seq ... 1 μl of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems, Wilmington, MA).

    Article Title: Vector transmission regulates immune control of Plasmodium virulence
    Article Snippet: Paragraph title: Amplification-free RNA-seq libraries ... Final libraries were eluted in 30μl water, visualised on an Agilent Bioanalyzer 2100 High Sensitivity DNA chip and quantified by qPCR.

    Article Title: An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers
    Article Snippet: Paragraph title: Directional RNA-Sequencing. ... Library concentration was quantified on Agilent 2100 BioAnalyzer DNA HS chip using Qubit DNA HS assay (Life Technologies).

    Article Title: Whole-Transcriptome Profiling of Canine and Human in Vitro Models Exposed to a G-Quadruplex Binding Small Molecule
    Article Snippet: Paragraph title: Library preparation and RNA-Seq analysis ... The PCR-amplified libraries were purified with the AMPure XP beads (Beckman Coulter, Brea, CA, USA) and, then, assessed for their quality and fragments distribution using the 2100 Bioanalyzer DNA 1000 assay (Agilent Technologies, Santa Clara, CA, USA).

    Article Title: Progerin accelerates atherosclerosis by inducing endoplasmic reticulum stress in vascular smooth muscle cells
    Article Snippet: Paragraph title: Library preparation and RNA sequencing ... After PCR library amplification, its size was tested using the Agilent 2100 Bioanalyzer DNA 1000 chip and concentration was measured in a Qubit fluorometer (Life Technologies).

    RNA HS Assay:

    Article Title: Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
    Article Snippet: Concentration was measured by Qubit RNA HS Assay on a Qubit fluorometer (ThermoFisher). .. One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).

    Magnetic Beads:

    Article Title: QSEA—modelling of genome-wide DNA methylation from sequencing enrichment experiments
    Article Snippet: Following the capturing of the RNA-DNA hybrids using streptavidine-coated magnetic beads, the DNA was separated from the beads, eluted and bisulfite converted using the EpiTECT Kit (Qiagen). .. The indexed DNA pool was analyzed with the 2100 Bioanalyzer High Sensitivity DNA assay (Agilent Technologies).

    Article Title: Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance
    Article Snippet: Following the capturing of the RNA-DNA hybrids using streptavidine-coated magnetic beads, DNA was separated from the beads, eluted, and bisulfite-treated using the EpiTect Bisulfite Kit. .. The indexed DNA pool was analyzed with the 2100 Bioanalyzer High Sensitivity DNA assay (Agilent Technologies) prior to sequencing.

    Article Title: Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
    Article Snippet: Libraries were purified and validated for appropriate size (225-275 bp) on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Inc.). .. 750 ng of purified library was then hybridized to the SureSelectXT Human All Exon 50 Mb library for 18 hours at 65°C.

    Article Title: Progerin accelerates atherosclerosis by inducing endoplasmic reticulum stress in vascular smooth muscle cells
    Article Snippet: In brief, poly‐A+ RNA was isolated using poly‐T oligo‐attached magnetic beads followed by fragmentation and first and second cDNA strand synthesis. cDNA 3′ ends were adenylated and the adapters were ligated. .. After PCR library amplification, its size was tested using the Agilent 2100 Bioanalyzer DNA 1000 chip and concentration was measured in a Qubit fluorometer (Life Technologies).

    Isolation:

    Article Title: Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
    Article Snippet: Ribonucleic acid (RNA) was isolated from peripheral blood leukocytes using QIAsymphony PAXgene Blood RNA Kit (Qiagen) and sequenced using the Illumina Hi-Seq 2500. .. One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).

    Article Title: Progerin accelerates atherosclerosis by inducing endoplasmic reticulum stress in vascular smooth muscle cells
    Article Snippet: In brief, poly‐A+ RNA was isolated using poly‐T oligo‐attached magnetic beads followed by fragmentation and first and second cDNA strand synthesis. cDNA 3′ ends were adenylated and the adapters were ligated. .. After PCR library amplification, its size was tested using the Agilent 2100 Bioanalyzer DNA 1000 chip and concentration was measured in a Qubit fluorometer (Life Technologies).

    Size-exclusion Chromatography:

    Article Title: Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
    Article Snippet: Briefly, 1000 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented by heat and converted to double stranded cDNA; cDNA was end-repaired and adenylated at the 3′ end to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98° for 30 sec, followed by 15 cycles of 98° for 10 sec, 60° for 30 sec and 72° for 30 sec, and finally an extension step for 5 min at 72°; Each sample was prepared with different indexed adapters to allow for multiplex sequencing. .. One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).

    Purification:

    Article Title: SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells
    Article Snippet: Clean-up of adaptor-ligated DNA was performed using Agencourt AMPure XP - PCR Purification ( ) following the manufacturer’s standard protocol. .. Each of the adaptor ligated, bar-coded DNA samples was ran on an Agilent 2100 Bioanalyzer Instrument (expert High-Sensitivity DNA chip) to assess sample DNA concentration and the presence and distribution of correct fragment sizes [ ].

    Article Title: Adaptive Changes in the Vestibular System of Land Snail to a 30-Day Spaceflight and Readaptation on Return to Earth
    Article Snippet: Concentration of amplified cDNA was measured using NanoDrop 2000 spectrophotometer. cDNA libraries were then prepared using Ion Plus Fragment library Kit (Ion Torrent, Life Technologies) following manufacturer's protocols. cDNA libraries were purified using Magnetic Bead Cleanup Module (Ion Torrent, Life Technologies). .. The quality of each prepared cDNA library was evaluated using Qubit® 2.0 Fluorometer (with Qubit® dsDNA HS Assay Kit) and Agilent 2100 Bioanalyzer (with High Sensitivity DNA chip and Agilent High Sensitivity DNA Kit).

    Article Title: Noninvasive monitoring of infection and rejection after lung transplantation
    Article Snippet: Sequencing libraries were prepared from purified plasma DNA using the NEBNext DNA Library Prep Master Mix Set for Illumina with standard Illumina indexed adapters (IDT) or using a microfluidics-based automated library preparation platform (Mondrian ST; Ovation SP Ultralow Library Systems). .. Libraries were characterized using the Agilent 2100 Bioanalyzer (High Sensitivity DNA Kit) or the AATI fragment analyzer, quantified by quantitative PCR, and sequenced (Illumina HiSeq 2000, HiSeq 2500, or NextSeq 500; 1 × 50 bp or 2 × 100 bp).

    Article Title: The mammalian ribo-interactome reveals ribosome functional diversity and heterogeneity
    Article Snippet: PCR product was PAGE purified from 8% TBE polyacrylamide gels, extracted overnight using DNA extraction buffer, and isopropanol precipitated overnight at −80°C. .. DNA was measured and quality controlled on the Agilent 2100 Bioanalyzer (High-Sensitivity DNA) by the Stanford Protein and Nucleic Acid Facility.

    Article Title: QSEA—modelling of genome-wide DNA methylation from sequencing enrichment experiments
    Article Snippet: The bisulfite-treated libraries were PCR amplified and purified. .. The indexed DNA pool was analyzed with the 2100 Bioanalyzer High Sensitivity DNA assay (Agilent Technologies).

    Article Title: Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance
    Article Snippet: The bisulfite-converted DNA libraries were PCR-amplified and purified. .. The indexed DNA pool was analyzed with the 2100 Bioanalyzer High Sensitivity DNA assay (Agilent Technologies) prior to sequencing.

    Article Title: Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci
    Article Snippet: Libraries were subjected to an additional electrophoresis step on an E-Gel EX 2% agarose gel (Invitrogen), and gel fragments correlating to 100–1,000 bp were excised and purified. .. The quality of the library preparation was determined by evaluation of the electropherogram traces from an Agilent 2100 Bioanalyzer DNA High Sensitivity, and libraries demonstrating appropriate nucleosomal enrichment were multiplexed and subjected to a lane of Illumina HiSeq 2500 sequencing.

    Article Title: Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
    Article Snippet: 3 μg of genomic DNA was fragmented to a size range of 150-200 bp followed by end repair, adaptor ligation, and low cycle (5) PCR. .. Libraries were purified and validated for appropriate size (225-275 bp) on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Inc.). .. 750 ng of purified library was then hybridized to the SureSelectXT Human All Exon 50 Mb library for 18 hours at 65°C.

    Article Title: Whole-genome sequencing of a malignant granular cell tumor with metabolic response to pazopanib
    Article Snippet: Following end repair and 3′ adenylation, indexing adapters were ligated to the fragment ends. .. Following purification, the fragmented DNA was PCR amplified for five cycles, purified, and validated for appropriate size on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies). .. Each DNA library was quantitated using quantitative PCR (KAPA Biosystems) prior to normalization.

    Article Title: Chemostat culture systems support diverse bacteriophage communities from human feces
    Article Snippet: Resulting amplicons were purified on a 2 % agarose gel stained with SYBR Safe (Invitrogen, Carlsbad, CA) using the MinElute PCR Purification kit (Qiagen, Valencia, CA). .. Amplicons were further purified with Ampure XP beads (Beckman-Coulter, Brea, CA), and molar equivalents were determined for each sample using a Bioanalyzer 2100 HS DNA Kit (Agilent Technologies, Santa Clara, CA). .. Samples were pooled into equimolar proportions and sequenced on 314 chips using an Ion Torrent PGM according to manufacturer’s instructions (Life Technologies, Grand Island, NY) [ ].

    Article Title: Whole-Transcriptome Profiling of Canine and Human in Vitro Models Exposed to a G-Quadruplex Binding Small Molecule
    Article Snippet: An Illumina-specific adaptor was sequentially ligated to the 3′ end of cDNA fragments, purified using the AMPure XP beads (Beckman Coulter, Brea, CA, USA), and finally PCR-amplified (13 cycles) using an appropriate indexing primer to allow further samples multiplexing. .. The PCR-amplified libraries were purified with the AMPure XP beads (Beckman Coulter, Brea, CA, USA) and, then, assessed for their quality and fragments distribution using the 2100 Bioanalyzer DNA 1000 assay (Agilent Technologies, Santa Clara, CA, USA). .. In the presence of adaptor-dimers (Electropherogram’s peak at 100 to 150-bp), another round of magnetic beads purification was performed.

    Article Title: MSTO1 is a cytoplasmic pro‐mitochondrial fusion protein, whose mutation induces myopathy and ataxia in humans
    Article Snippet: First pre‐capture genomic library was prepared using 1 μg of highly purified genomic DNA. .. Crude pre‐captured genomic library was analyzed by Agilent 2100 Bioanalyzer 1000 DNA chip to assess library quality.

    Polymerase Chain Reaction:

    Article Title: SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells
    Article Snippet: Clean-up of adaptor-ligated DNA was performed using Agencourt AMPure XP - PCR Purification ( ) following the manufacturer’s standard protocol. .. Each of the adaptor ligated, bar-coded DNA samples was ran on an Agilent 2100 Bioanalyzer Instrument (expert High-Sensitivity DNA chip) to assess sample DNA concentration and the presence and distribution of correct fragment sizes [ ].

    Article Title: The mammalian ribo-interactome reveals ribosome functional diversity and heterogeneity
    Article Snippet: PCR product was PAGE purified from 8% TBE polyacrylamide gels, extracted overnight using DNA extraction buffer, and isopropanol precipitated overnight at −80°C. .. DNA was measured and quality controlled on the Agilent 2100 Bioanalyzer (High-Sensitivity DNA) by the Stanford Protein and Nucleic Acid Facility.

    Article Title: QSEA—modelling of genome-wide DNA methylation from sequencing enrichment experiments
    Article Snippet: The bisulfite-treated libraries were PCR amplified and purified. .. The indexed DNA pool was analyzed with the 2100 Bioanalyzer High Sensitivity DNA assay (Agilent Technologies).

    Article Title: Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance
    Article Snippet: The bisulfite-converted DNA libraries were PCR-amplified and purified. .. The indexed DNA pool was analyzed with the 2100 Bioanalyzer High Sensitivity DNA assay (Agilent Technologies) prior to sequencing.

    Article Title: Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
    Article Snippet: 3 μg of genomic DNA was fragmented to a size range of 150-200 bp followed by end repair, adaptor ligation, and low cycle (5) PCR. .. Libraries were purified and validated for appropriate size (225-275 bp) on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Inc.).

    Article Title: Whole-genome sequencing of a malignant granular cell tumor with metabolic response to pazopanib
    Article Snippet: Following end repair and 3′ adenylation, indexing adapters were ligated to the fragment ends. .. Following purification, the fragmented DNA was PCR amplified for five cycles, purified, and validated for appropriate size on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies). .. Each DNA library was quantitated using quantitative PCR (KAPA Biosystems) prior to normalization.

    Article Title: Chemostat culture systems support diverse bacteriophage communities from human feces
    Article Snippet: Resulting amplicons were purified on a 2 % agarose gel stained with SYBR Safe (Invitrogen, Carlsbad, CA) using the MinElute PCR Purification kit (Qiagen, Valencia, CA). .. Amplicons were further purified with Ampure XP beads (Beckman-Coulter, Brea, CA), and molar equivalents were determined for each sample using a Bioanalyzer 2100 HS DNA Kit (Agilent Technologies, Santa Clara, CA).

    Article Title: Whole-Transcriptome Profiling of Canine and Human in Vitro Models Exposed to a G-Quadruplex Binding Small Molecule
    Article Snippet: An Illumina-specific adaptor was sequentially ligated to the 3′ end of cDNA fragments, purified using the AMPure XP beads (Beckman Coulter, Brea, CA, USA), and finally PCR-amplified (13 cycles) using an appropriate indexing primer to allow further samples multiplexing. .. The PCR-amplified libraries were purified with the AMPure XP beads (Beckman Coulter, Brea, CA, USA) and, then, assessed for their quality and fragments distribution using the 2100 Bioanalyzer DNA 1000 assay (Agilent Technologies, Santa Clara, CA, USA). .. In the presence of adaptor-dimers (Electropherogram’s peak at 100 to 150-bp), another round of magnetic beads purification was performed.

    Article Title: MSTO1 is a cytoplasmic pro‐mitochondrial fusion protein, whose mutation induces myopathy and ataxia in humans
    Article Snippet: Crude pre‐captured genomic library was analyzed by Agilent 2100 Bioanalyzer 1000 DNA chip to assess library quality. .. Crude pre‐captured genomic library was analyzed by Agilent 2100 Bioanalyzer 1000 DNA chip to assess library quality.

    Article Title: Progerin accelerates atherosclerosis by inducing endoplasmic reticulum stress in vascular smooth muscle cells
    Article Snippet: In brief, poly‐A+ RNA was isolated using poly‐T oligo‐attached magnetic beads followed by fragmentation and first and second cDNA strand synthesis. cDNA 3′ ends were adenylated and the adapters were ligated. .. After PCR library amplification, its size was tested using the Agilent 2100 Bioanalyzer DNA 1000 chip and concentration was measured in a Qubit fluorometer (Life Technologies). .. Libraries were sequenced on a HiSeq2500 sequencer (Illumina), 60‐base single reads were generated.

    Polyacrylamide Gel Electrophoresis:

    Article Title: The mammalian ribo-interactome reveals ribosome functional diversity and heterogeneity
    Article Snippet: PCR product was PAGE purified from 8% TBE polyacrylamide gels, extracted overnight using DNA extraction buffer, and isopropanol precipitated overnight at −80°C. .. DNA was measured and quality controlled on the Agilent 2100 Bioanalyzer (High-Sensitivity DNA) by the Stanford Protein and Nucleic Acid Facility.

    cDNA Library Assay:

    Article Title: Adaptive Changes in the Vestibular System of Land Snail to a 30-Day Spaceflight and Readaptation on Return to Earth
    Article Snippet: Concentration of amplified cDNA was measured using NanoDrop 2000 spectrophotometer. cDNA libraries were then prepared using Ion Plus Fragment library Kit (Ion Torrent, Life Technologies) following manufacturer's protocols. cDNA libraries were purified using Magnetic Bead Cleanup Module (Ion Torrent, Life Technologies). .. The quality of each prepared cDNA library was evaluated using Qubit® 2.0 Fluorometer (with Qubit® dsDNA HS Assay Kit) and Agilent 2100 Bioanalyzer (with High Sensitivity DNA chip and Agilent High Sensitivity DNA Kit). .. In our samples, the amount of short cDNA fragments with length of 25–160 bp did not exceed 10%.

    Agarose Gel Electrophoresis:

    Article Title: Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci
    Article Snippet: Libraries were subjected to an additional electrophoresis step on an E-Gel EX 2% agarose gel (Invitrogen), and gel fragments correlating to 100–1,000 bp were excised and purified. .. The quality of the library preparation was determined by evaluation of the electropherogram traces from an Agilent 2100 Bioanalyzer DNA High Sensitivity, and libraries demonstrating appropriate nucleosomal enrichment were multiplexed and subjected to a lane of Illumina HiSeq 2500 sequencing.

    Article Title: Chemostat culture systems support diverse bacteriophage communities from human feces
    Article Snippet: Resulting amplicons were purified on a 2 % agarose gel stained with SYBR Safe (Invitrogen, Carlsbad, CA) using the MinElute PCR Purification kit (Qiagen, Valencia, CA). .. Amplicons were further purified with Ampure XP beads (Beckman-Coulter, Brea, CA), and molar equivalents were determined for each sample using a Bioanalyzer 2100 HS DNA Kit (Agilent Technologies, Santa Clara, CA).

    Chromatin Immunoprecipitation:

    Article Title: SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells
    Article Snippet: Clean-up of adaptor-ligated DNA was performed using Agencourt AMPure XP - PCR Purification ( ) following the manufacturer’s standard protocol. .. Each of the adaptor ligated, bar-coded DNA samples was ran on an Agilent 2100 Bioanalyzer Instrument (expert High-Sensitivity DNA chip) to assess sample DNA concentration and the presence and distribution of correct fragment sizes [ ]. .. Indexed libraries were pooled, and paired-end multiplexed sequencing (2 × 310 bp) was performed on an Illumina Miseq platform using MiSeq Reagent Kit v3.

    Article Title: Adaptive Changes in the Vestibular System of Land Snail to a 30-Day Spaceflight and Readaptation on Return to Earth
    Article Snippet: Concentration of amplified cDNA was measured using NanoDrop 2000 spectrophotometer. cDNA libraries were then prepared using Ion Plus Fragment library Kit (Ion Torrent, Life Technologies) following manufacturer's protocols. cDNA libraries were purified using Magnetic Bead Cleanup Module (Ion Torrent, Life Technologies). .. The quality of each prepared cDNA library was evaluated using Qubit® 2.0 Fluorometer (with Qubit® dsDNA HS Assay Kit) and Agilent 2100 Bioanalyzer (with High Sensitivity DNA chip and Agilent High Sensitivity DNA Kit). .. In our samples, the amount of short cDNA fragments with length of 25–160 bp did not exceed 10%.

    Article Title: Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
    Article Snippet: Briefly, 1000 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented by heat and converted to double stranded cDNA; cDNA was end-repaired and adenylated at the 3′ end to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98° for 30 sec, followed by 15 cycles of 98° for 10 sec, 60° for 30 sec and 72° for 30 sec, and finally an extension step for 5 min at 72°; Each sample was prepared with different indexed adapters to allow for multiplex sequencing. .. One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems). .. Libraries were pooled in equimolar quantities and paired-end sequenced on a Rapid Run Mode flowcell with the V3 sequencing chemistry on an Illumina HiSeq 2500 platform following Illumina’s recommended protocol to generate paired-end reads of 100-bases in length.

    Article Title: Fingerprinting of Proteins that Mediate Quagga Mussel Adhesion using a De Novo Assembled Foot Transcriptome
    Article Snippet: D, September 2012), following the recommended protocol. .. Libraries were checked on a Bioanalyzer 2100 DNA High Sensitivity Chip (Agilent Technologies) to check for size and quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit (KAPA Biosystems) following the manufacturer’s recommended protocol. .. Libraries were pooled in equimolar quantities and paired end sequenced on an Illumina 2500 platform using a Rapid Run Mode Flow Cell and the V3 sequencing chemistry following Illumina’s recommended protocol to generate paired-end reads of 150-bases in length (150 × 2).

    Article Title: The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes
    Article Snippet: Briefly, 100–500 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented into the 200-300-bases range for 4 minutes at 94°C and converted to double stranded cDNA, end-repaired and adenylated at the 3’ to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98°C for 10 seconds, followed by 10 cycles of 98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds, and finally an extension step for 5 minutes at 72°C; at the amplification step, each sample were amplified with a different barcoded adapters to allow for multiplex sequencing. .. 1 μl of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems, Wilmington, MA). .. Libraries were pooled in equimolar quantities and paired-end sequenced on a Rapid Run Mode flowcell with the V3 sequencing chemistry on an Illumina HiSeq 2500 platform (Illumina Inc., San Diego, CA) following Illumina’s recommended protocol to generate paired-end reads of 100-bases in length.

    Article Title: Vector transmission regulates immune control of Plasmodium virulence
    Article Snippet: Excess adaptors were removed with 2 rounds of clean up with 50μl of Agencourt AMPure XP Beads (Beckman Coulter). .. Final libraries were eluted in 30μl water, visualised on an Agilent Bioanalyzer 2100 High Sensitivity DNA chip and quantified by qPCR. .. A pool of the 5 indexed libraries was sequenced on an Illumina HiSeq2000, with 100bp paired-end reads.

    Article Title: Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
    Article Snippet: 3 μg of genomic DNA was fragmented to a size range of 150-200 bp followed by end repair, adaptor ligation, and low cycle (5) PCR. .. Libraries were purified and validated for appropriate size (225-275 bp) on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Inc.). .. 750 ng of purified library was then hybridized to the SureSelectXT Human All Exon 50 Mb library for 18 hours at 65°C.

    Article Title: Whole-genome sequencing of a malignant granular cell tumor with metabolic response to pazopanib
    Article Snippet: Following end repair and 3′ adenylation, indexing adapters were ligated to the fragment ends. .. Following purification, the fragmented DNA was PCR amplified for five cycles, purified, and validated for appropriate size on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies). .. Each DNA library was quantitated using quantitative PCR (KAPA Biosystems) prior to normalization.

    Article Title: An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers
    Article Snippet: The RNA products from the controlled fragmentation step were used to prepare the strand-specific metatranscriptomic library, following the manufacturer’s instruction of Apollo 324 PrepX mRNA library protocol (IntegenX), which is based on directional RNA adaptor ligation. .. Library concentration was quantified on Agilent 2100 BioAnalyzer DNA HS chip using Qubit DNA HS assay (Life Technologies). .. Absolute quantitative PCR assay using SYBR FAST ABI Prism QPCR Mast Mix (Kapa Bio Systems) was performed to confirm amplification efficiency and to determine the library loading concentration for sequencing.

    Article Title: MSTO1 is a cytoplasmic pro‐mitochondrial fusion protein, whose mutation induces myopathy and ataxia in humans
    Article Snippet: First pre‐capture genomic library was prepared using 1 μg of highly purified genomic DNA. .. Crude pre‐captured genomic library was analyzed by Agilent 2100 Bioanalyzer 1000 DNA chip to assess library quality. .. Next, during exome enrichment step, individual pre‐captured libraries were hybridized to biotinylated NimbleGen SeqCap EZ Human Exome Library for 68–70 h at 47°C.

    Article Title: Progerin accelerates atherosclerosis by inducing endoplasmic reticulum stress in vascular smooth muscle cells
    Article Snippet: In brief, poly‐A+ RNA was isolated using poly‐T oligo‐attached magnetic beads followed by fragmentation and first and second cDNA strand synthesis. cDNA 3′ ends were adenylated and the adapters were ligated. .. After PCR library amplification, its size was tested using the Agilent 2100 Bioanalyzer DNA 1000 chip and concentration was measured in a Qubit fluorometer (Life Technologies). .. Libraries were sequenced on a HiSeq2500 sequencer (Illumina), 60‐base single reads were generated.

    Software:

    Article Title: Whole-genome sequencing of a malignant granular cell tumor with metabolic response to pazopanib
    Article Snippet: Following purification, the fragmented DNA was PCR amplified for five cycles, purified, and validated for appropriate size on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies). .. Libraries were loaded and clustered to individual lanes of a HiSeq Flow Cell using an Illumina cBot (TruSeq PE Cluster Kit v3), followed by 2 × 100 cycle paired-end WGS on a HiSeq2000 sequencer according to the manufacturer's recommended protocol (Illumina).

    Real-time Polymerase Chain Reaction:

    Article Title: Noninvasive monitoring of infection and rejection after lung transplantation
    Article Snippet: Sequencing libraries were prepared from purified plasma DNA using the NEBNext DNA Library Prep Master Mix Set for Illumina with standard Illumina indexed adapters (IDT) or using a microfluidics-based automated library preparation platform (Mondrian ST; Ovation SP Ultralow Library Systems). .. Libraries were characterized using the Agilent 2100 Bioanalyzer (High Sensitivity DNA Kit) or the AATI fragment analyzer, quantified by quantitative PCR, and sequenced (Illumina HiSeq 2000, HiSeq 2500, or NextSeq 500; 1 × 50 bp or 2 × 100 bp). .. Whole-blood samples were collected from the donor and recipient.

    Article Title: Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
    Article Snippet: Briefly, 1000 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented by heat and converted to double stranded cDNA; cDNA was end-repaired and adenylated at the 3′ end to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98° for 30 sec, followed by 15 cycles of 98° for 10 sec, 60° for 30 sec and 72° for 30 sec, and finally an extension step for 5 min at 72°; Each sample was prepared with different indexed adapters to allow for multiplex sequencing. .. One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems). .. Libraries were pooled in equimolar quantities and paired-end sequenced on a Rapid Run Mode flowcell with the V3 sequencing chemistry on an Illumina HiSeq 2500 platform following Illumina’s recommended protocol to generate paired-end reads of 100-bases in length.

    Article Title: Fingerprinting of Proteins that Mediate Quagga Mussel Adhesion using a De Novo Assembled Foot Transcriptome
    Article Snippet: D, September 2012), following the recommended protocol. .. Libraries were checked on a Bioanalyzer 2100 DNA High Sensitivity Chip (Agilent Technologies) to check for size and quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit (KAPA Biosystems) following the manufacturer’s recommended protocol. .. Libraries were pooled in equimolar quantities and paired end sequenced on an Illumina 2500 platform using a Rapid Run Mode Flow Cell and the V3 sequencing chemistry following Illumina’s recommended protocol to generate paired-end reads of 150-bases in length (150 × 2).

    Article Title: The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes
    Article Snippet: Briefly, 100–500 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented into the 200-300-bases range for 4 minutes at 94°C and converted to double stranded cDNA, end-repaired and adenylated at the 3’ to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98°C for 10 seconds, followed by 10 cycles of 98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds, and finally an extension step for 5 minutes at 72°C; at the amplification step, each sample were amplified with a different barcoded adapters to allow for multiplex sequencing. .. 1 μl of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems, Wilmington, MA). .. Libraries were pooled in equimolar quantities and paired-end sequenced on a Rapid Run Mode flowcell with the V3 sequencing chemistry on an Illumina HiSeq 2500 platform (Illumina Inc., San Diego, CA) following Illumina’s recommended protocol to generate paired-end reads of 100-bases in length.

    Article Title: Vector transmission regulates immune control of Plasmodium virulence
    Article Snippet: Excess adaptors were removed with 2 rounds of clean up with 50μl of Agencourt AMPure XP Beads (Beckman Coulter). .. Final libraries were eluted in 30μl water, visualised on an Agilent Bioanalyzer 2100 High Sensitivity DNA chip and quantified by qPCR. .. A pool of the 5 indexed libraries was sequenced on an Illumina HiSeq2000, with 100bp paired-end reads.

    Article Title: Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
    Article Snippet: Libraries were purified and validated for appropriate size (225-275 bp) on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Inc.). .. Eluted library underwent a second 11 cycle PCR amplification using Herculase II Fusion Polymerase (Agilent Technologies, Inc.) to add sample specific barcodes necessary for multiplexing.

    Article Title: Whole-Transcriptome Profiling of Canine and Human in Vitro Models Exposed to a G-Quadruplex Binding Small Molecule
    Article Snippet: The PCR-amplified libraries were purified with the AMPure XP beads (Beckman Coulter, Brea, CA, USA) and, then, assessed for their quality and fragments distribution using the 2100 Bioanalyzer DNA 1000 assay (Agilent Technologies, Santa Clara, CA, USA). .. In the presence of adaptor-dimers (Electropherogram’s peak at 100 to 150-bp), another round of magnetic beads purification was performed.

    Multiplex Assay:

    Article Title: SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells
    Article Snippet: The NEBNext Ultra™ DNA Library Prep Kit for Illumina (E7370) and NEBNext Mutiplex Oligos for Illumina dual index kit (E7600) were used for end repair and adaptor ligation and quantification (bar coding for multiplex sequencing) using the standard manufacturer protocols. .. Each of the adaptor ligated, bar-coded DNA samples was ran on an Agilent 2100 Bioanalyzer Instrument (expert High-Sensitivity DNA chip) to assess sample DNA concentration and the presence and distribution of correct fragment sizes [ ].

    Article Title: Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
    Article Snippet: Briefly, 1000 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented by heat and converted to double stranded cDNA; cDNA was end-repaired and adenylated at the 3′ end to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98° for 30 sec, followed by 15 cycles of 98° for 10 sec, 60° for 30 sec and 72° for 30 sec, and finally an extension step for 5 min at 72°; Each sample was prepared with different indexed adapters to allow for multiplex sequencing. .. One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).

    Article Title: The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes
    Article Snippet: Briefly, 100–500 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented into the 200-300-bases range for 4 minutes at 94°C and converted to double stranded cDNA, end-repaired and adenylated at the 3’ to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98°C for 10 seconds, followed by 10 cycles of 98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds, and finally an extension step for 5 minutes at 72°C; at the amplification step, each sample were amplified with a different barcoded adapters to allow for multiplex sequencing. .. 1 μl of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems, Wilmington, MA).

    Selection:

    Article Title: Fingerprinting of Proteins that Mediate Quagga Mussel Adhesion using a De Novo Assembled Foot Transcriptome
    Article Snippet: Libraries were checked on a Bioanalyzer 2100 DNA High Sensitivity Chip (Agilent Technologies) to check for size and quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit (KAPA Biosystems) following the manufacturer’s recommended protocol. .. Libraries were checked on a Bioanalyzer 2100 DNA High Sensitivity Chip (Agilent Technologies) to check for size and quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit (KAPA Biosystems) following the manufacturer’s recommended protocol.

    Sample Prep:

    Article Title: Fingerprinting of Proteins that Mediate Quagga Mussel Adhesion using a De Novo Assembled Foot Transcriptome
    Article Snippet: Library preparation was performed with the Illumina TruSeq RNA Sample Preparation V2 Guide (Rev. .. Libraries were checked on a Bioanalyzer 2100 DNA High Sensitivity Chip (Agilent Technologies) to check for size and quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit (KAPA Biosystems) following the manufacturer’s recommended protocol.

    Article Title: MSTO1 is a cytoplasmic pro‐mitochondrial fusion protein, whose mutation induces myopathy and ataxia in humans
    Article Snippet: Genomic DNA library preparation was performed by using TruSeq® DNA Sample Prep Kit v2‐Set A (Illumina), followed by NimbleGen SeqCap EZ Human Exome Library v3.0 Kit exome enrichment (Roche). .. Crude pre‐captured genomic library was analyzed by Agilent 2100 Bioanalyzer 1000 DNA chip to assess library quality.

    Article Title: Progerin accelerates atherosclerosis by inducing endoplasmic reticulum stress in vascular smooth muscle cells
    Article Snippet: Total RNA (500 ng) was used to prepare barcoded RNA sequencing libraries using the TruSeq RNA sample preparation kit v2 (Illumina) as described before (Villa‐Bellosta et al , ). .. After PCR library amplification, its size was tested using the Agilent 2100 Bioanalyzer DNA 1000 chip and concentration was measured in a Qubit fluorometer (Life Technologies).

    Next-Generation Sequencing:

    Article Title: SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells
    Article Snippet: Paragraph title: Bisulphite conversion of DNA and targeted Illumina NGS ... Each of the adaptor ligated, bar-coded DNA samples was ran on an Agilent 2100 Bioanalyzer Instrument (expert High-Sensitivity DNA chip) to assess sample DNA concentration and the presence and distribution of correct fragment sizes [ ].

    Article Title: Adaptive Changes in the Vestibular System of Land Snail to a 30-Day Spaceflight and Readaptation on Return to Earth
    Article Snippet: Paragraph title: Total RNA preparation and cDNA library construction for NGS ... The quality of each prepared cDNA library was evaluated using Qubit® 2.0 Fluorometer (with Qubit® dsDNA HS Assay Kit) and Agilent 2100 Bioanalyzer (with High Sensitivity DNA chip and Agilent High Sensitivity DNA Kit).

    Article Title: Fingerprinting of Proteins that Mediate Quagga Mussel Adhesion using a De Novo Assembled Foot Transcriptome
    Article Snippet: Next-generation sequencing was completed at The Centre for Applied Genomics (TCAG) at the Hospital for Sick Children in Toronto, Ontario. .. Libraries were checked on a Bioanalyzer 2100 DNA High Sensitivity Chip (Agilent Technologies) to check for size and quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit (KAPA Biosystems) following the manufacturer’s recommended protocol.

    Article Title: Progerin accelerates atherosclerosis by inducing endoplasmic reticulum stress in vascular smooth muscle cells
    Article Snippet: After PCR library amplification, its size was tested using the Agilent 2100 Bioanalyzer DNA 1000 chip and concentration was measured in a Qubit fluorometer (Life Technologies). .. After PCR library amplification, its size was tested using the Agilent 2100 Bioanalyzer DNA 1000 chip and concentration was measured in a Qubit fluorometer (Life Technologies).

    Random Hexamer Labeling:

    Article Title: Vector transmission regulates immune control of Plasmodium virulence
    Article Snippet: First strand cDNA was synthesised with Random Hexamer primers and SuperScript II Reverse Transcriptase (Life Technologies), following the manufacturer’s instructions. .. Final libraries were eluted in 30μl water, visualised on an Agilent Bioanalyzer 2100 High Sensitivity DNA chip and quantified by qPCR.

    Spectrophotometry:

    Article Title: Adaptive Changes in the Vestibular System of Land Snail to a 30-Day Spaceflight and Readaptation on Return to Earth
    Article Snippet: Concentration of amplified cDNA was measured using NanoDrop 2000 spectrophotometer. cDNA libraries were then prepared using Ion Plus Fragment library Kit (Ion Torrent, Life Technologies) following manufacturer's protocols. cDNA libraries were purified using Magnetic Bead Cleanup Module (Ion Torrent, Life Technologies). .. The quality of each prepared cDNA library was evaluated using Qubit® 2.0 Fluorometer (with Qubit® dsDNA HS Assay Kit) and Agilent 2100 Bioanalyzer (with High Sensitivity DNA chip and Agilent High Sensitivity DNA Kit).

    Concentration Assay:

    Article Title: SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells
    Article Snippet: Clean-up of adaptor-ligated DNA was performed using Agencourt AMPure XP - PCR Purification ( ) following the manufacturer’s standard protocol. .. Each of the adaptor ligated, bar-coded DNA samples was ran on an Agilent 2100 Bioanalyzer Instrument (expert High-Sensitivity DNA chip) to assess sample DNA concentration and the presence and distribution of correct fragment sizes [ ]. .. Indexed libraries were pooled, and paired-end multiplexed sequencing (2 × 310 bp) was performed on an Illumina Miseq platform using MiSeq Reagent Kit v3.

    Article Title: Adaptive Changes in the Vestibular System of Land Snail to a 30-Day Spaceflight and Readaptation on Return to Earth
    Article Snippet: Concentration of amplified cDNA was measured using NanoDrop 2000 spectrophotometer. cDNA libraries were then prepared using Ion Plus Fragment library Kit (Ion Torrent, Life Technologies) following manufacturer's protocols. cDNA libraries were purified using Magnetic Bead Cleanup Module (Ion Torrent, Life Technologies). .. The quality of each prepared cDNA library was evaluated using Qubit® 2.0 Fluorometer (with Qubit® dsDNA HS Assay Kit) and Agilent 2100 Bioanalyzer (with High Sensitivity DNA chip and Agilent High Sensitivity DNA Kit).

    Article Title: Identification of Human Papillomavirus Infection in Cancer Tissue by Targeted Next Generation Sequencing
    Article Snippet: Relevant to the current work, capture probes incorporate viral genome sequence for HPV strains 16 and 18 (GenBank IDs and , respectively). .. During DNA isolation and library preparation, DNA concentration was measured by fluorometry, DNA quality was assessed using the Agilent 2100 Bioanalyzer high sensitivity DNA assay, and DNA size was determined by Experion automated electrophoresis system (BioRad, Hercules CA) or by Agilent TapeStation. .. Sequencing was then performed using a HiSeq2000 sequencer (Illumina Inc, San Diego CA).

    Article Title: Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
    Article Snippet: Concentration was measured by Qubit RNA HS Assay on a Qubit fluorometer (ThermoFisher). .. One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).

    Article Title: An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers
    Article Snippet: The RNA products from the controlled fragmentation step were used to prepare the strand-specific metatranscriptomic library, following the manufacturer’s instruction of Apollo 324 PrepX mRNA library protocol (IntegenX), which is based on directional RNA adaptor ligation. .. Library concentration was quantified on Agilent 2100 BioAnalyzer DNA HS chip using Qubit DNA HS assay (Life Technologies). .. Absolute quantitative PCR assay using SYBR FAST ABI Prism QPCR Mast Mix (Kapa Bio Systems) was performed to confirm amplification efficiency and to determine the library loading concentration for sequencing.

    Article Title: Progerin accelerates atherosclerosis by inducing endoplasmic reticulum stress in vascular smooth muscle cells
    Article Snippet: In brief, poly‐A+ RNA was isolated using poly‐T oligo‐attached magnetic beads followed by fragmentation and first and second cDNA strand synthesis. cDNA 3′ ends were adenylated and the adapters were ligated. .. After PCR library amplification, its size was tested using the Agilent 2100 Bioanalyzer DNA 1000 chip and concentration was measured in a Qubit fluorometer (Life Technologies). .. Libraries were sequenced on a HiSeq2500 sequencer (Illumina), 60‐base single reads were generated.

    DNA Purification:

    Article Title: Identification of Human Papillomavirus Infection in Cancer Tissue by Targeted Next Generation Sequencing
    Article Snippet: DNA was extracted from fresh frozen tissue samples (16 cases) or from FFPE tissue sections (5 cases) using either the Gentra Puregene Tissue Kit (QIAGEN, Valencia CA) or the Maxwell 16 DNA purification platform (Promega Corp, Madison, WI), and then fragmented by sonication. .. During DNA isolation and library preparation, DNA concentration was measured by fluorometry, DNA quality was assessed using the Agilent 2100 Bioanalyzer high sensitivity DNA assay, and DNA size was determined by Experion automated electrophoresis system (BioRad, Hercules CA) or by Agilent TapeStation.

    Standard Deviation:

    Article Title: Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
    Article Snippet: One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems). .. One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).

    Staining:

    Article Title: Chemostat culture systems support diverse bacteriophage communities from human feces
    Article Snippet: Resulting amplicons were purified on a 2 % agarose gel stained with SYBR Safe (Invitrogen, Carlsbad, CA) using the MinElute PCR Purification kit (Qiagen, Valencia, CA). .. Amplicons were further purified with Ampure XP beads (Beckman-Coulter, Brea, CA), and molar equivalents were determined for each sample using a Bioanalyzer 2100 HS DNA Kit (Agilent Technologies, Santa Clara, CA).

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    Agilent technologies 2100 bioanalyzer
    Postfixation processing of an RNA 50mer with excess formaldehyde removed. Gel-simulated image (Agilent <t>2100</t> <t>Bioanalyzer)</t> of the RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. A: Lane L: RNA ladder. Lane 1: Non–formaldehyde-treated
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    Postfixation processing of an RNA 50mer with excess formaldehyde removed. Gel-simulated image (Agilent 2100 Bioanalyzer) of the RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. A: Lane L: RNA ladder. Lane 1: Non–formaldehyde-treated

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

    Figure Lengend Snippet: Postfixation processing of an RNA 50mer with excess formaldehyde removed. Gel-simulated image (Agilent 2100 Bioanalyzer) of the RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. A: Lane L: RNA ladder. Lane 1: Non–formaldehyde-treated

    Article Snippet: The compositions of the total HeLa RNA and RNA 50mer preparations were characterized by capillary electrophoresis using a 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

    Techniques:

    Effects of fixation and postfixation processing on total cellular RNA: gel-simulated image (Agilent 2100 Bioanalyzer) of total cellular RNA fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. Lane L: RNA ladder. Lane 1: Native non–formaldehyde-treated

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

    Figure Lengend Snippet: Effects of fixation and postfixation processing on total cellular RNA: gel-simulated image (Agilent 2100 Bioanalyzer) of total cellular RNA fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. Lane L: RNA ladder. Lane 1: Native non–formaldehyde-treated

    Article Snippet: The compositions of the total HeLa RNA and RNA 50mer preparations were characterized by capillary electrophoresis using a 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

    Techniques:

    Effects of buffer composition on postfixation processing of an RNA 50mer: gel-simulated image (Agilent 2100 Bioanalyzer). Lane L: RNA ladder. Lane 1: Native RNA 50mer. Lane 2: RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. Excess formaldehyde

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

    Figure Lengend Snippet: Effects of buffer composition on postfixation processing of an RNA 50mer: gel-simulated image (Agilent 2100 Bioanalyzer). Lane L: RNA ladder. Lane 1: Native RNA 50mer. Lane 2: RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. Excess formaldehyde

    Article Snippet: The compositions of the total HeLa RNA and RNA 50mer preparations were characterized by capillary electrophoresis using a 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

    Techniques:

    Postformaldehyde fixation processing of an RNA 50mer. Gel-simulated image (Agilent 2100 Bioanalyzer) of the RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours and then heated at 70°C for 30 minutes, where indicated, in the following

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

    Figure Lengend Snippet: Postformaldehyde fixation processing of an RNA 50mer. Gel-simulated image (Agilent 2100 Bioanalyzer) of the RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours and then heated at 70°C for 30 minutes, where indicated, in the following

    Article Snippet: The compositions of the total HeLa RNA and RNA 50mer preparations were characterized by capillary electrophoresis using a 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

    Techniques:

    Effects of fixation and postfixation processing on total HeLa RNA. Electropherograms (Agilent 2100 Bioanalyzer) of total cellular RNA fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. FU denotes fluorescence units. A: Non–formaldehyde-treated

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

    Figure Lengend Snippet: Effects of fixation and postfixation processing on total HeLa RNA. Electropherograms (Agilent 2100 Bioanalyzer) of total cellular RNA fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. FU denotes fluorescence units. A: Non–formaldehyde-treated

    Article Snippet: The compositions of the total HeLa RNA and RNA 50mer preparations were characterized by capillary electrophoresis using a 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

    Techniques: Fluorescence

    Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 22°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in K 3 EDTA tubes at days 0, 3, 7, 14 and 28. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in ProTeck tubes at days 0, 3, 7, 14 and 28. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Journal: PLoS ONE

    Article Title: A novel approach to stabilize fetal cell-free DNA fraction in maternal blood samples for extended period of time

    doi: 10.1371/journal.pone.0208508

    Figure Lengend Snippet: Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 22°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in K 3 EDTA tubes at days 0, 3, 7, 14 and 28. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in ProTeck tubes at days 0, 3, 7, 14 and 28. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Article Snippet: The Agilent 2100 Expert software analyze DNA profile of each sample automatically and displays electropherogram for each sample.

    Techniques:

    Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 30°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored in K 3 EDTA tubes at days 0, 2, 3, 7 and 14. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored in ProTeck tubes at days 0, 2, 3, 7 and 14. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Journal: PLoS ONE

    Article Title: A novel approach to stabilize fetal cell-free DNA fraction in maternal blood samples for extended period of time

    doi: 10.1371/journal.pone.0208508

    Figure Lengend Snippet: Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 30°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored in K 3 EDTA tubes at days 0, 2, 3, 7 and 14. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored in ProTeck tubes at days 0, 2, 3, 7 and 14. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Article Snippet: The Agilent 2100 Expert software analyze DNA profile of each sample automatically and displays electropherogram for each sample.

    Techniques:

    Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 4°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored in K 3 EDTA tubes at days 0, 3, 7, 14 and 21. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored in ProTeck tubes at days 0, 3, 7, 14 and 21. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Journal: PLoS ONE

    Article Title: A novel approach to stabilize fetal cell-free DNA fraction in maternal blood samples for extended period of time

    doi: 10.1371/journal.pone.0208508

    Figure Lengend Snippet: Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 4°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored in K 3 EDTA tubes at days 0, 3, 7, 14 and 21. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored in ProTeck tubes at days 0, 3, 7, 14 and 21. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Article Snippet: The Agilent 2100 Expert software analyze DNA profile of each sample automatically and displays electropherogram for each sample.

    Techniques:

    Application of Nextera DNA Flex to bacterial amplicons. a Libraries prepared using Nextera DNA Flex showed more consistent, even coverage compared with libraries prepared using Nextera XT; data depicts the sequence coverage of libraries prepared from the 3 kb E. coli amplicon. b PCR products ranging in size from 50 bp to 3 kb amplified from E. coli gDNA visualized on a 1% agarose gel. c Libraries prepared from a 1 ng input of these E. coli amplicons resulted in Bioanalyzer traces that depicted a slight increase in fragment size with increasing amplicon size. d Libraries were sequenced on a MiSeq and coverage of the E. coli genome determined for the different amplicon fragment size inputs. Sequenceable libraries were generated from amplicons ranging in size from 50 bp to 3 kb. e When sequencing data was downsampled to 25,000 reads, the larger fragment inputs were reaching a coverage maximum

    Journal: BMC Genomics

    Article Title: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation

    doi: 10.1186/s12864-018-5096-9

    Figure Lengend Snippet: Application of Nextera DNA Flex to bacterial amplicons. a Libraries prepared using Nextera DNA Flex showed more consistent, even coverage compared with libraries prepared using Nextera XT; data depicts the sequence coverage of libraries prepared from the 3 kb E. coli amplicon. b PCR products ranging in size from 50 bp to 3 kb amplified from E. coli gDNA visualized on a 1% agarose gel. c Libraries prepared from a 1 ng input of these E. coli amplicons resulted in Bioanalyzer traces that depicted a slight increase in fragment size with increasing amplicon size. d Libraries were sequenced on a MiSeq and coverage of the E. coli genome determined for the different amplicon fragment size inputs. Sequenceable libraries were generated from amplicons ranging in size from 50 bp to 3 kb. e When sequencing data was downsampled to 25,000 reads, the larger fragment inputs were reaching a coverage maximum

    Article Snippet: Where described, library quality was determined by running 1 μl of the pooled library or an individual library on a Bioanalyzer (Agilent 2100 Bioanalyzer) using a High Sensitivity DNA kit (Agilent, cat. no. 5067–4626) or on a Fragment Analyzer (Advanced Analytical Fragment Analyzer) with the High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical, cat. no. DNF-474).

    Techniques: Sequencing, Amplification, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Generated

    Bioanalyzer traces of libraries prepared from various sample types and species. a Libraries prepared from samples with a varied degree of formalin fixation; a higher ΔCq indicates more FFPE-induced DNA degradation compared with a positive control. b Increasing FFPE-induced DNA degradation has a small effect on average fragment size but a marked effect on the total library yield. Increasing the DNA input from 100 ng to 150 ng did not increase library yield, indicating bead saturation at a DNA input of around 100 ng regardless of the degree of DNA degradation. c Libraries prepared from gDNA from a range of animal (human, Angus, and mouse), plant (Arabidopsis and alfalfa), and bacterial ( E. coli and B. cereus ) species

    Journal: BMC Genomics

    Article Title: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation

    doi: 10.1186/s12864-018-5096-9

    Figure Lengend Snippet: Bioanalyzer traces of libraries prepared from various sample types and species. a Libraries prepared from samples with a varied degree of formalin fixation; a higher ΔCq indicates more FFPE-induced DNA degradation compared with a positive control. b Increasing FFPE-induced DNA degradation has a small effect on average fragment size but a marked effect on the total library yield. Increasing the DNA input from 100 ng to 150 ng did not increase library yield, indicating bead saturation at a DNA input of around 100 ng regardless of the degree of DNA degradation. c Libraries prepared from gDNA from a range of animal (human, Angus, and mouse), plant (Arabidopsis and alfalfa), and bacterial ( E. coli and B. cereus ) species

    Article Snippet: Where described, library quality was determined by running 1 μl of the pooled library or an individual library on a Bioanalyzer (Agilent 2100 Bioanalyzer) using a High Sensitivity DNA kit (Agilent, cat. no. 5067–4626) or on a Fragment Analyzer (Advanced Analytical Fragment Analyzer) with the High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical, cat. no. DNF-474).

    Techniques: Formalin-fixed Paraffin-Embedded, Positive Control

    Application of Nextera DNA Flex to human amplicons. a Human leukocyte antigen (HLA) gene amplicons used as inputs for library preparation visualized on a 1% agarose gel. Lanes and expected amplicon sizes are as follows: 1, KBL Ladder; 2, HLA-A (4.1 kb); 3, HLA-B (2.8 kb); 4, HLA-C (4.2 kb); 5, HLA-DPA1 (10.3 kb); 6, HLA-DPB1 (9.7 kb); 7, HLA-DQA1 (7.3 kb); 8, HLA-DRB2 (4.6 kb); 9, HLA-DQB1 (7.1 kb). b Nextera DNA Flex library yields of all HLA amplicons were within the acceptable values of > 4 ng/μl and 9–13 ng/μl for 1 ng and 100–300 ng inputs, respectively. The yields for Nextera DNA Flex libraries were higher than for those prepared using TruSight HLA; for TruSight HLA, libraries were prepared from 1 ng of each amplicon and then pooled. c The Bioanalyzer profiles depict library fragment size distributions within the acceptable range; the distribution is narrower for the Nextera DNA Flex libraries (1 ng DNA inputs) than the TruSight HLA libraries. d Sequencing coverage depth and uniformity were higher for libraries prepared using Nextera DNA Flex (Flex) compared with TruSight HLA (TS HLA). e Libraries were sequenced on a NextSeq 550, with downsampling to 25,000 reads per amplicon. Library preparation using Nextera DNA Flex (orange) resulted in more uniform coverage of the entire human mitochondrial chromosome when compared with Nextera XT (grey). The location of the PCR primers used to create the two mtDNA amplicons are depicted by blue and red arrows. Dotted-line rectangle indicates the D-Loop region. f Zoomed in view shows more uniform coverage with Nextera DNA Flex within the D-Loop region

    Journal: BMC Genomics

    Article Title: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation

    doi: 10.1186/s12864-018-5096-9

    Figure Lengend Snippet: Application of Nextera DNA Flex to human amplicons. a Human leukocyte antigen (HLA) gene amplicons used as inputs for library preparation visualized on a 1% agarose gel. Lanes and expected amplicon sizes are as follows: 1, KBL Ladder; 2, HLA-A (4.1 kb); 3, HLA-B (2.8 kb); 4, HLA-C (4.2 kb); 5, HLA-DPA1 (10.3 kb); 6, HLA-DPB1 (9.7 kb); 7, HLA-DQA1 (7.3 kb); 8, HLA-DRB2 (4.6 kb); 9, HLA-DQB1 (7.1 kb). b Nextera DNA Flex library yields of all HLA amplicons were within the acceptable values of > 4 ng/μl and 9–13 ng/μl for 1 ng and 100–300 ng inputs, respectively. The yields for Nextera DNA Flex libraries were higher than for those prepared using TruSight HLA; for TruSight HLA, libraries were prepared from 1 ng of each amplicon and then pooled. c The Bioanalyzer profiles depict library fragment size distributions within the acceptable range; the distribution is narrower for the Nextera DNA Flex libraries (1 ng DNA inputs) than the TruSight HLA libraries. d Sequencing coverage depth and uniformity were higher for libraries prepared using Nextera DNA Flex (Flex) compared with TruSight HLA (TS HLA). e Libraries were sequenced on a NextSeq 550, with downsampling to 25,000 reads per amplicon. Library preparation using Nextera DNA Flex (orange) resulted in more uniform coverage of the entire human mitochondrial chromosome when compared with Nextera XT (grey). The location of the PCR primers used to create the two mtDNA amplicons are depicted by blue and red arrows. Dotted-line rectangle indicates the D-Loop region. f Zoomed in view shows more uniform coverage with Nextera DNA Flex within the D-Loop region

    Article Snippet: Where described, library quality was determined by running 1 μl of the pooled library or an individual library on a Bioanalyzer (Agilent 2100 Bioanalyzer) using a High Sensitivity DNA kit (Agilent, cat. no. 5067–4626) or on a Fragment Analyzer (Advanced Analytical Fragment Analyzer) with the High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical, cat. no. DNF-474).

    Techniques: Agarose Gel Electrophoresis, Amplification, Sequencing, Polymerase Chain Reaction