high sensitivity dna kit  (Agilent technologies)

 
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    Name:
    High Sensitivity DNA BioAnalyzer Kit
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    Catalog Number:
    1806
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    Score:
    85
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    Structured Review

    Agilent technologies high sensitivity dna kit
    Comparison of sample fragmentation by nebulization with Covaris AFA. 4.5 μg human genomic <t>DNA</t> was fragmented by nebulization (red line) and AFA (blue line). Both were purified using a spin column and eluted in 30 μl EB buffer (Qiagen). 1 μl of each eluate was run on an <t>Agilent</t> Bioanalyzer DNA 2100 chip. Image adapted with permission from Macmillan Publishers Ltd. .

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    Images

    1) Product Images from "Improved Protocols for Illumina Sequencing"

    Article Title: Improved Protocols for Illumina Sequencing

    Journal:

    doi: 10.1002/0471142905.hg1802s62

    Comparison of sample fragmentation by nebulization with Covaris AFA. 4.5 μg human genomic DNA was fragmented by nebulization (red line) and AFA (blue line). Both were purified using a spin column and eluted in 30 μl EB buffer (Qiagen). 1 μl of each eluate was run on an Agilent Bioanalyzer DNA 2100 chip. Image adapted with permission from Macmillan Publishers Ltd. .
    Figure Legend Snippet: Comparison of sample fragmentation by nebulization with Covaris AFA. 4.5 μg human genomic DNA was fragmented by nebulization (red line) and AFA (blue line). Both were purified using a spin column and eluted in 30 μl EB buffer (Qiagen). 1 μl of each eluate was run on an Agilent Bioanalyzer DNA 2100 chip. Image adapted with permission from Macmillan Publishers Ltd. .

    Techniques Used: Purification, Chromatin Immunoprecipitation

    2) Product Images from "Expanded subgenomic mRNA transcriptome and coding capacity of a nidovirus"

    Article Title: Expanded subgenomic mRNA transcriptome and coding capacity of a nidovirus

    Journal:

    doi: 10.1073/pnas.1706696114

    Northern blot analysis of sg mRNAs produced in SHFVic-infected MA104 cells. ( A ) MA104 cells were mock infected or infected with SHFVic at an MOI of 1. At different times post infection, total intracellular RNA was extracted, and 1 µg of RNA was separated on a 1% denaturing agarose gel followed by transfer to an Hybond-N+ membrane. After UV cross-linking, the membrane was hybridized to a DIG-labeled RNA probe specific for sg mRNA7. ( B ) Total intracellular RNA collected at 12 hpi from three biological repeats was hybridized separately to DIG-labeled RNA probes specific for sg mRNA5 or sg mRNA6. The RNA bands detected were labeled based on the estimated sizes of the predicted structural protein sg mRNAs and on the probe used. The additional sg mRNA band detected is indicated. The RNA ladder was cut from the membrane, stained with methylene blue, and imaged. L, DNA ladder; M, mock-infected; 1, 2, and 3 indicate the different biological repeat samples tested.
    Figure Legend Snippet: Northern blot analysis of sg mRNAs produced in SHFVic-infected MA104 cells. ( A ) MA104 cells were mock infected or infected with SHFVic at an MOI of 1. At different times post infection, total intracellular RNA was extracted, and 1 µg of RNA was separated on a 1% denaturing agarose gel followed by transfer to an Hybond-N+ membrane. After UV cross-linking, the membrane was hybridized to a DIG-labeled RNA probe specific for sg mRNA7. ( B ) Total intracellular RNA collected at 12 hpi from three biological repeats was hybridized separately to DIG-labeled RNA probes specific for sg mRNA5 or sg mRNA6. The RNA bands detected were labeled based on the estimated sizes of the predicted structural protein sg mRNAs and on the probe used. The additional sg mRNA band detected is indicated. The RNA ladder was cut from the membrane, stained with methylene blue, and imaged. L, DNA ladder; M, mock-infected; 1, 2, and 3 indicate the different biological repeat samples tested.

    Techniques Used: Northern Blot, Produced, Infection, Agarose Gel Electrophoresis, Labeling, Staining

    3) Product Images from "A quantitative analysis of the potential biomarkers of non-small cell lung cancer by circulating cell-free DNA"

    Article Title: A quantitative analysis of the potential biomarkers of non-small cell lung cancer by circulating cell-free DNA

    Journal: Oncology Letters

    doi: 10.3892/ol.2018.9198

    Line charts of serum cfDNA, CEA and CYFRA21-1 concentrations at serial time-points in patients with NSCLC. SD, stable disease; PR, partial response; PD, progressive disease; cfDNA, cell-free DNA; NSCLC, non-small cell lung cancer. Disease was detected by medical imaging.
    Figure Legend Snippet: Line charts of serum cfDNA, CEA and CYFRA21-1 concentrations at serial time-points in patients with NSCLC. SD, stable disease; PR, partial response; PD, progressive disease; cfDNA, cell-free DNA; NSCLC, non-small cell lung cancer. Disease was detected by medical imaging.

    Techniques Used: Imaging

    Diagnostic utility of serum cfDNA, CEA and CYFRA21-1 in NSCLC patients. (A) ROC curves of serum cfDNA, CEA, CYFRA21-1 and the combination of the three markers for distinguishing NSCLC patients from normal controls. (B) ROC curves of pairwise combinations of cfDNA, CEA, and CYFRA21-1 for distinguishing NSCLC patients from normal controls. cfDNA, cell-free DNA; NSCLC, non-small cell lung cancer; ROC, receiver operating characteristic.
    Figure Legend Snippet: Diagnostic utility of serum cfDNA, CEA and CYFRA21-1 in NSCLC patients. (A) ROC curves of serum cfDNA, CEA, CYFRA21-1 and the combination of the three markers for distinguishing NSCLC patients from normal controls. (B) ROC curves of pairwise combinations of cfDNA, CEA, and CYFRA21-1 for distinguishing NSCLC patients from normal controls. cfDNA, cell-free DNA; NSCLC, non-small cell lung cancer; ROC, receiver operating characteristic.

    Techniques Used: Diagnostic Assay

    4) Product Images from "New evidence that a large proportion of human blood plasma cell-free DNA is localized in exosomes"

    Article Title: New evidence that a large proportion of human blood plasma cell-free DNA is localized in exosomes

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0183915

    Analysis of exosome DNA by agarose gel separation and Agilent Bioanalyzer. A, Exosome DNA without RNase treatment. B, Exosome DNA with RNase treatment. High molecular weight band is removed by RNase treatment indicating that band represents RNA. Low molecular weight band is resistant to RNase treatment indicating that it is DNA. Majority of exosome DNA are in 200 bp size range. C, Overlaid Agilent 2100 Bioanalyzer electropherograms. Exosome DNA was extracted from two individual donors. Exosome DNA from both donors were either treated with RNase or not treated. RNase treated and not treated DNA were analyzed by Agilent Bioanalyzer and RNase treated and not treated electropherograms were overlaid.
    Figure Legend Snippet: Analysis of exosome DNA by agarose gel separation and Agilent Bioanalyzer. A, Exosome DNA without RNase treatment. B, Exosome DNA with RNase treatment. High molecular weight band is removed by RNase treatment indicating that band represents RNA. Low molecular weight band is resistant to RNase treatment indicating that it is DNA. Majority of exosome DNA are in 200 bp size range. C, Overlaid Agilent 2100 Bioanalyzer electropherograms. Exosome DNA was extracted from two individual donors. Exosome DNA from both donors were either treated with RNase or not treated. RNase treated and not treated DNA were analyzed by Agilent Bioanalyzer and RNase treated and not treated electropherograms were overlaid.

    Techniques Used: Agarose Gel Electrophoresis, Molecular Weight

    5) Product Images from "New evidence that a large proportion of human blood plasma cell-free DNA is localized in exosomes"

    Article Title: New evidence that a large proportion of human blood plasma cell-free DNA is localized in exosomes

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0183915

    Effect of blood sample storage (at 22°C) on exosome and exosome DNA concentration in plasma. A, Effect of blood storage on exosome concentration analyzed by NanoSight instrument under light scatter mode. Blood from each donor was divided into 4 aliquots and stored at 22°C. Plasma separated from each aliquot at indicated days, exosomes isolated and enumerated. B, Effect of blood storage on proteins CD9, CD63 and CD235a in plasma exosome pellet (isolated by Invitrogen method). C, Effect of storage on proteins CD41 and CD45 in plasma exosome pellet. D, Effect of blood storage on exosome DNA concentration as detected by β-actin ddPCR assay. Blood from each donor was divided into 4 aliquots and stored at 22°C. Plasma separated from each aliquot at indicated days, exosomes isolated. DNA extracted from exosomes and β-actin copy number detected by ddPCR assay. Error bars indicate SD. Panel B is in logarithmic scale.
    Figure Legend Snippet: Effect of blood sample storage (at 22°C) on exosome and exosome DNA concentration in plasma. A, Effect of blood storage on exosome concentration analyzed by NanoSight instrument under light scatter mode. Blood from each donor was divided into 4 aliquots and stored at 22°C. Plasma separated from each aliquot at indicated days, exosomes isolated and enumerated. B, Effect of blood storage on proteins CD9, CD63 and CD235a in plasma exosome pellet (isolated by Invitrogen method). C, Effect of storage on proteins CD41 and CD45 in plasma exosome pellet. D, Effect of blood storage on exosome DNA concentration as detected by β-actin ddPCR assay. Blood from each donor was divided into 4 aliquots and stored at 22°C. Plasma separated from each aliquot at indicated days, exosomes isolated. DNA extracted from exosomes and β-actin copy number detected by ddPCR assay. Error bars indicate SD. Panel B is in logarithmic scale.

    Techniques Used: Concentration Assay, Isolation

    Analysis of exosome DNA by agarose gel separation and Agilent Bioanalyzer. A, Exosome DNA without RNase treatment. B, Exosome DNA with RNase treatment. High molecular weight band is removed by RNase treatment indicating that band represents RNA. Low molecular weight band is resistant to RNase treatment indicating that it is DNA. Majority of exosome DNA are in 200 bp size range. C, Overlaid Agilent 2100 Bioanalyzer electropherograms. Exosome DNA was extracted from two individual donors. Exosome DNA from both donors were either treated with RNase or not treated. RNase treated and not treated DNA were analyzed by Agilent Bioanalyzer and RNase treated and not treated electropherograms were overlaid.
    Figure Legend Snippet: Analysis of exosome DNA by agarose gel separation and Agilent Bioanalyzer. A, Exosome DNA without RNase treatment. B, Exosome DNA with RNase treatment. High molecular weight band is removed by RNase treatment indicating that band represents RNA. Low molecular weight band is resistant to RNase treatment indicating that it is DNA. Majority of exosome DNA are in 200 bp size range. C, Overlaid Agilent 2100 Bioanalyzer electropherograms. Exosome DNA was extracted from two individual donors. Exosome DNA from both donors were either treated with RNase or not treated. RNase treated and not treated DNA were analyzed by Agilent Bioanalyzer and RNase treated and not treated electropherograms were overlaid.

    Techniques Used: Agarose Gel Electrophoresis, Molecular Weight

    Total and amplifiable DNA concentrations in plasma and plasma exosomes. A, Comparison of total DNA concentrations in plasma (median 6.86 ng/mL) and plasma exosomes (median 4.9 ng/mL). B, Comparison of total DNA concentrations in exosome pellet (median 5.6 ng/mL) and plasma supernatant (median 0.0 ng/mL). C, Comparison of β-actin DNA concentrations in plasma and plasma exosomes detected by a ddPCR assay. There was no statistically significant difference between β-actin DNA concentrations in plasma (median 1600 β-actin copies/mL plasma) and plasma exosomes (median 1560 β-actin copies/mL plasma). D, Comparison of β-actin DNA concentrations in plasma exosome pellet (median 888 β-actin copies/mL plasma) and plasma supernatant (median 52 β-actin copies/mL plasma) detected by ddPCR assay. The line inside of the box indicates median value. The limits of the box represent the 75th and 25th percentiles. The whiskers indicate the 10th and 90th percentiles. Panels A and C; n = 23. Panels B and D; n = 16. * p
    Figure Legend Snippet: Total and amplifiable DNA concentrations in plasma and plasma exosomes. A, Comparison of total DNA concentrations in plasma (median 6.86 ng/mL) and plasma exosomes (median 4.9 ng/mL). B, Comparison of total DNA concentrations in exosome pellet (median 5.6 ng/mL) and plasma supernatant (median 0.0 ng/mL). C, Comparison of β-actin DNA concentrations in plasma and plasma exosomes detected by a ddPCR assay. There was no statistically significant difference between β-actin DNA concentrations in plasma (median 1600 β-actin copies/mL plasma) and plasma exosomes (median 1560 β-actin copies/mL plasma). D, Comparison of β-actin DNA concentrations in plasma exosome pellet (median 888 β-actin copies/mL plasma) and plasma supernatant (median 52 β-actin copies/mL plasma) detected by ddPCR assay. The line inside of the box indicates median value. The limits of the box represent the 75th and 25th percentiles. The whiskers indicate the 10th and 90th percentiles. Panels A and C; n = 23. Panels B and D; n = 16. * p

    Techniques Used:

    6) Product Images from "Investigation of appropriate pre-analytical procedure for circulating free DNA from liquid biopsy"

    Article Title: Investigation of appropriate pre-analytical procedure for circulating free DNA from liquid biopsy

    Journal: Oncotarget

    doi: 10.18632/oncotarget.25881

    Influence of anticoagulant and blood preservation conditions on quality of cfDNA from healthy volunteers cfDNA concentrations were examined at the indicated time after blood collection using sodium citrate tubes ( A ) or EDTA 2K tubes ( B ) from ten healthy volunteers. Blood storage temperature until plasma separation was 4° C (white box) or room temperature (gray box). Size distribution of plasma DNA was analyzed with an Agilent bioanalyzer ® ; representative examples are shown in panels C-F. Sodium citrate tubes ( C , E ) or EDTA 2K tubes ( D , F ) were used for blood collection, and blood storage until plasma separation was at RT (C, D) or 4° C (E, F). DNA concentration of 1000 bp to 9000 bp fragments ( G ) and of 100 bp to 250 bp fragments ( H ) in all samples stored at 4° C was measured with an Agilent bioanalyzer ® as described in “Materials and methods”. Blood was collected into sodium citrate tubes (white box) or EDTA 2K tubes (gray box). Statistical analyses were performed with Friedman’s rank test.
    Figure Legend Snippet: Influence of anticoagulant and blood preservation conditions on quality of cfDNA from healthy volunteers cfDNA concentrations were examined at the indicated time after blood collection using sodium citrate tubes ( A ) or EDTA 2K tubes ( B ) from ten healthy volunteers. Blood storage temperature until plasma separation was 4° C (white box) or room temperature (gray box). Size distribution of plasma DNA was analyzed with an Agilent bioanalyzer ® ; representative examples are shown in panels C-F. Sodium citrate tubes ( C , E ) or EDTA 2K tubes ( D , F ) were used for blood collection, and blood storage until plasma separation was at RT (C, D) or 4° C (E, F). DNA concentration of 1000 bp to 9000 bp fragments ( G ) and of 100 bp to 250 bp fragments ( H ) in all samples stored at 4° C was measured with an Agilent bioanalyzer ® as described in “Materials and methods”. Blood was collected into sodium citrate tubes (white box) or EDTA 2K tubes (gray box). Statistical analyses were performed with Friedman’s rank test.

    Techniques Used: Preserving, Concentration Assay

    7) Product Images from "Expanding Duplication of Free Fatty Acid Receptor-2 (GPR43) Genes in the Chicken Genome"

    Article Title: Expanding Duplication of Free Fatty Acid Receptor-2 (GPR43) Genes in the Chicken Genome

    Journal: Genome Biology and Evolution

    doi: 10.1093/gbe/evv072

    FFAR2 has numerous copies in European broiler and in ancestral chicken genome. qPCR on genomic DNA shows clear difference in ΔCq between FFAR2 genes and the genes carrying only one copy per genome (four genes in European lines and three genes in Ancestral lines). qPCR was performed using “universal” primers able to amplify the 26 sequences of FFAR2 (see supplementary data S1 , Supplementary Material online). FFAR2 error bars indicate standard deviation between two individual chickens. For the single copy genes, error bars represent standard deviation between the Cq measures for the three or four genes from two individual chickens.
    Figure Legend Snippet: FFAR2 has numerous copies in European broiler and in ancestral chicken genome. qPCR on genomic DNA shows clear difference in ΔCq between FFAR2 genes and the genes carrying only one copy per genome (four genes in European lines and three genes in Ancestral lines). qPCR was performed using “universal” primers able to amplify the 26 sequences of FFAR2 (see supplementary data S1 , Supplementary Material online). FFAR2 error bars indicate standard deviation between two individual chickens. For the single copy genes, error bars represent standard deviation between the Cq measures for the three or four genes from two individual chickens.

    Techniques Used: Real-time Polymerase Chain Reaction, Standard Deviation

    8) Product Images from "Forensic SNP Genotyping using Nanopore MinION Sequencing"

    Article Title: Forensic SNP Genotyping using Nanopore MinION Sequencing

    Journal: Scientific Reports

    doi: 10.1038/srep41759

    ( A ) Length profile (bp) of concatenated amplicons as measured with an Agilent High-Sensitivity DNA chip; internal marker at 35 bp and 10380 bp. ( B ) Read length (bp) histogram of the high quality two-directional (2D) nanopore reads.
    Figure Legend Snippet: ( A ) Length profile (bp) of concatenated amplicons as measured with an Agilent High-Sensitivity DNA chip; internal marker at 35 bp and 10380 bp. ( B ) Read length (bp) histogram of the high quality two-directional (2D) nanopore reads.

    Techniques Used: Chromatin Immunoprecipitation, Marker

    9) Product Images from "Investigation of Gene Expressions of Myeloma Cells in the Bone Marrow of Multiple Myeloma Patients by Transcriptome Analysis"

    Article Title: Investigation of Gene Expressions of Myeloma Cells in the Bone Marrow of Multiple Myeloma Patients by Transcriptome Analysis

    Journal: Balkan Medical Journal

    doi: 10.4274/balkanmedj.2018.0356

    In Agilent Bioanalyzer gel-like image of cDNA. This image shows produced cDNA samples quality controls. After library construction for the quality of the libraries was validated using the Agilent High Sensitivity DNA kit on the Agilent 2100 Bioanalyzer. DNA ladder (L), Lanes 1-3-5 (control cDNA library), the lanes 3-5 are ten-fold diluted sample 1. Lanels 2-4-6 (Multiple myeloma cDNA library). The lanes 4-6 are ten- fold diluted sample 2. Lane 7 (negative). Green lines indicate the low weight (35 base pairs) DNA ladder, Purple lines the high weight (10380 base pairs) DNA ladder.
    Figure Legend Snippet: In Agilent Bioanalyzer gel-like image of cDNA. This image shows produced cDNA samples quality controls. After library construction for the quality of the libraries was validated using the Agilent High Sensitivity DNA kit on the Agilent 2100 Bioanalyzer. DNA ladder (L), Lanes 1-3-5 (control cDNA library), the lanes 3-5 are ten-fold diluted sample 1. Lanels 2-4-6 (Multiple myeloma cDNA library). The lanes 4-6 are ten- fold diluted sample 2. Lane 7 (negative). Green lines indicate the low weight (35 base pairs) DNA ladder, Purple lines the high weight (10380 base pairs) DNA ladder.

    Techniques Used: Produced, cDNA Library Assay

    10) Product Images from "Bead-linked transposomes enable a normalization-free workflow for NGS library preparation"

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

    Journal: BMC Genomics

    doi: 10.1186/s12864-018-5096-9

    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
    Figure Legend 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

    Techniques Used: 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
    Figure Legend 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

    Techniques Used: 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
    Figure Legend 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

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

    11) Product Images from "Exosomes maintain cellular homeostasis by excreting harmful DNA from cells"

    Article Title: Exosomes maintain cellular homeostasis by excreting harmful DNA from cells

    Journal: Nature Communications

    doi: 10.1038/ncomms15287

    Exosomes contain chromosome fragments. ( a ) transmission electron microscopy micrograph of MVE in pre-senescent TIG-3 cells following immuno-gold labelling for dsDNA. Gold particles are depicted as black dots. Right image shows a digitally zoomed area of exosome. ( b , c ) Exosomal DNA isolated from pre-senescent TIG-3 cells were subjected to size distribution analysis using Electrophoresis Bioanalyzer system ( b ) or to deep sequencing analysis ( c ). Genomic DNA of TIG-3 cells are also subjected to deep sequencing analysis, as control ( c ). The read count of each 500-kb bin was normalized to RPKM and corrected by the mappability ( c ). ( d ) Purified exosomes from pre-senescent TIG-3 cells were subjected to sucrose density-gradient separation followed by western blotting using antibodies shown right, NanoSight analysis (NTA) for quantitative measurement of isolated exosome particles and quantitative PCR analysis for detection of genomic DNA fragments (GRM7 and GPC6).
    Figure Legend Snippet: Exosomes contain chromosome fragments. ( a ) transmission electron microscopy micrograph of MVE in pre-senescent TIG-3 cells following immuno-gold labelling for dsDNA. Gold particles are depicted as black dots. Right image shows a digitally zoomed area of exosome. ( b , c ) Exosomal DNA isolated from pre-senescent TIG-3 cells were subjected to size distribution analysis using Electrophoresis Bioanalyzer system ( b ) or to deep sequencing analysis ( c ). Genomic DNA of TIG-3 cells are also subjected to deep sequencing analysis, as control ( c ). The read count of each 500-kb bin was normalized to RPKM and corrected by the mappability ( c ). ( d ) Purified exosomes from pre-senescent TIG-3 cells were subjected to sucrose density-gradient separation followed by western blotting using antibodies shown right, NanoSight analysis (NTA) for quantitative measurement of isolated exosome particles and quantitative PCR analysis for detection of genomic DNA fragments (GRM7 and GPC6).

    Techniques Used: Transmission Assay, Electron Microscopy, Isolation, Electrophoresis, Sequencing, Purification, Western Blot, Real-time Polymerase Chain Reaction

    12) Product Images from "Methodology for Y Chromosome Capture: A complete genome sequence of  Y chromosome using flow cytometry, laser microdissection and magnetic streptavidin-beads"

    Article Title: Methodology for Y Chromosome Capture: A complete genome sequence of  Y chromosome using flow cytometry, laser microdissection and magnetic streptavidin-beads

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-27819-x

    ( A ) Microfluidic electrophoretic separation of the different methods of Y chromosome capture using a DNA high sensitivity (HS) Bioanalyzer assay. Sample 1: flow cytometry capture, Sample 2: laser capture microdissection, Sample 3: magnetic streptavidin-bead capture. The HS ladder (on left) ranges from 35 base pair (bp) to 7000 bp. All sample peaks appear between the lower and upper marker peaks (35–10380 bp). ( B ) Bioanalyzer high sensitivity profiles of each capture technique. The protocol for this assay is as follows: The captured DNA (putative Y chromosome) was sonicated to a size between 150 and 500 bp and after the sonication DNA was loaded on the Bioanalyzer assay. The sonication program (see 4.5.1. DNA Shearing) was tested previously to obtain the specific fragment size, which has been verified to be proper for preparing a DNA library.
    Figure Legend Snippet: ( A ) Microfluidic electrophoretic separation of the different methods of Y chromosome capture using a DNA high sensitivity (HS) Bioanalyzer assay. Sample 1: flow cytometry capture, Sample 2: laser capture microdissection, Sample 3: magnetic streptavidin-bead capture. The HS ladder (on left) ranges from 35 base pair (bp) to 7000 bp. All sample peaks appear between the lower and upper marker peaks (35–10380 bp). ( B ) Bioanalyzer high sensitivity profiles of each capture technique. The protocol for this assay is as follows: The captured DNA (putative Y chromosome) was sonicated to a size between 150 and 500 bp and after the sonication DNA was loaded on the Bioanalyzer assay. The sonication program (see 4.5.1. DNA Shearing) was tested previously to obtain the specific fragment size, which has been verified to be proper for preparing a DNA library.

    Techniques Used: Flow Cytometry, Cytometry, Laser Capture Microdissection, Marker, Sonication

    13) Product Images from "Clinical significance of the mutational landscape and fragmentation of circulating tumor DNA in renal cell carcinoma, et al. Clinical significance of the mutational landscape and fragmentation of circulating tumor DNA in renal cell carcinoma"

    Article Title: Clinical significance of the mutational landscape and fragmentation of circulating tumor DNA in renal cell carcinoma, et al. Clinical significance of the mutational landscape and fragmentation of circulating tumor DNA in renal cell carcinoma

    Journal: Cancer Science

    doi: 10.1111/cas.13906

    Positive circulating tumor DNA (ctDNA) and short fragment size of plasma cell‐free DNA (cfDNA) were associated with poor prognosis. (Kaplan‐Meier method and log‐rank test). A,B, Prognosis was analyzed in 27 renal cell carcinoma (RCC) patients whose cfDNA samples were sequenced at pretreatment state. Association of ctDNA status (positive vs negative) for progression‐free survival (PFS) (A) and cancer‐specific survival (CSS) (B). C,D, Association of cfDNA fragment size using a microfluidics‐based platform between ≤166 bp (the prominent peak of the distribution of cfDNA fragments according to size) (short) and > 166 bp (long) for PFS (C) and CSS (D). E,F, Prognosis was analyzed in 13 RCC patients with metastasis whose cfDNA samples were sequenced at pretreatment state as in A‐D. Association of ctDNA status (positive vs negative) (E) and cfDNA fragment size (short vs long) (F) for CSS
    Figure Legend Snippet: Positive circulating tumor DNA (ctDNA) and short fragment size of plasma cell‐free DNA (cfDNA) were associated with poor prognosis. (Kaplan‐Meier method and log‐rank test). A,B, Prognosis was analyzed in 27 renal cell carcinoma (RCC) patients whose cfDNA samples were sequenced at pretreatment state. Association of ctDNA status (positive vs negative) for progression‐free survival (PFS) (A) and cancer‐specific survival (CSS) (B). C,D, Association of cfDNA fragment size using a microfluidics‐based platform between ≤166 bp (the prominent peak of the distribution of cfDNA fragments according to size) (short) and > 166 bp (long) for PFS (C) and CSS (D). E,F, Prognosis was analyzed in 13 RCC patients with metastasis whose cfDNA samples were sequenced at pretreatment state as in A‐D. Association of ctDNA status (positive vs negative) (E) and cfDNA fragment size (short vs long) (F) for CSS

    Techniques Used:

    Renal cell carcinoma (RCC) patients with circulating tumor DNA (ctDNA) had shorter cell‐free DNA (cfDNA) fragments than those without ctDNA. A, Distributions of cfDNA fragments according to size were determined by targeted sequencing in 53 RCC patients. X‐axis shows cfDNA fragment size, and the Y‐axis shows the abundance of fragments of those specific sizes relative to the number of 166‐bp fragments. Red lines (n = 16) indicate the distributions of cfDNA fragments for patients with ctDNA, and blue lines (n = 37) for patients without ctDNA. B, Proportion of cfDNA fragments (PCF) was defined as the ratio of short cfDNA fragments (50‐166 bp; green) to long fragments (167‐250 bp; blue) as determined by next‐generation sequencing (NGS). Using a microfluidics‐based platform, average cfDNA fragment size in case 50 was classified as short (154 bp), whereas that in case 52 was classified as long (174 bp). C, PCF in patients with short cfDNA fragment size (≤166 bp, n = 24) as measured by a microfluidics‐based platform tended to be higher than in those with long cfDNA fragments ( > 166 bp, n = 29; P = .085). (Wilcoxon test). D, PCF was weakly correlated with cfDNA fragment size as determined by a microfluidics‐based platform (n = 53). (correlation analysis). E, Association between ctDNA status and cfDNA fragment size as determined by a microfluidics‐based platform (n = 53; P = .245). (Wilcoxon test). F, Association between ctDNA status and PCF (n = 53). * P
    Figure Legend Snippet: Renal cell carcinoma (RCC) patients with circulating tumor DNA (ctDNA) had shorter cell‐free DNA (cfDNA) fragments than those without ctDNA. A, Distributions of cfDNA fragments according to size were determined by targeted sequencing in 53 RCC patients. X‐axis shows cfDNA fragment size, and the Y‐axis shows the abundance of fragments of those specific sizes relative to the number of 166‐bp fragments. Red lines (n = 16) indicate the distributions of cfDNA fragments for patients with ctDNA, and blue lines (n = 37) for patients without ctDNA. B, Proportion of cfDNA fragments (PCF) was defined as the ratio of short cfDNA fragments (50‐166 bp; green) to long fragments (167‐250 bp; blue) as determined by next‐generation sequencing (NGS). Using a microfluidics‐based platform, average cfDNA fragment size in case 50 was classified as short (154 bp), whereas that in case 52 was classified as long (174 bp). C, PCF in patients with short cfDNA fragment size (≤166 bp, n = 24) as measured by a microfluidics‐based platform tended to be higher than in those with long cfDNA fragments ( > 166 bp, n = 29; P = .085). (Wilcoxon test). D, PCF was weakly correlated with cfDNA fragment size as determined by a microfluidics‐based platform (n = 53). (correlation analysis). E, Association between ctDNA status and cfDNA fragment size as determined by a microfluidics‐based platform (n = 53; P = .245). (Wilcoxon test). F, Association between ctDNA status and PCF (n = 53). * P

    Techniques Used: Sequencing, Next-Generation Sequencing

    Clinical course monitoring in renal cell carcinoma (RCC) patients with circulating tumor DNA (ctDNA). Clinical course was analyzed using mutant allele frequency (MAF) of ctDNA by droplet digital PCR (ddPCR), and cell‐free DNA (cfDNA) fragment size by a microfluidics‐based platform in RCC patients with ctDNA. PD, progressive disease. A, In case 45, MAF of ctDNA was evaluated in TP53 and VHL . B, In case 53, MAF of ctDNA was evaluated in MTOR and TSC1
    Figure Legend Snippet: Clinical course monitoring in renal cell carcinoma (RCC) patients with circulating tumor DNA (ctDNA). Clinical course was analyzed using mutant allele frequency (MAF) of ctDNA by droplet digital PCR (ddPCR), and cell‐free DNA (cfDNA) fragment size by a microfluidics‐based platform in RCC patients with ctDNA. PD, progressive disease. A, In case 45, MAF of ctDNA was evaluated in TP53 and VHL . B, In case 53, MAF of ctDNA was evaluated in MTOR and TSC1

    Techniques Used: Mutagenesis, Digital PCR

    14) Product Images from "Quantification of circulating cell-free DNA to predict patient survival in non-small-cell lung cancer"

    Article Title: Quantification of circulating cell-free DNA to predict patient survival in non-small-cell lung cancer

    Journal: Oncotarget

    doi: 10.18632/oncotarget.21769

    Changes in the cfDNA concentration during systemic therapy (A) Change in the cfDNA concentration from baseline to first response assessment, according to the radiological response category. (B) Waterfall plot for the percentage change in the cfDNA concentration at first response assessment. (C) Change in the cfDNA concentration from baseline to the radiological best response, according to the radiological best response category. (D) Waterfall plot for the percentage change in the cfDNA concentration at assessment of radiological best response. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PR, partial response; SD, stable disease; PD, progression of disease * Kruskal-Wallis test among PR, SD and PD groups ** Data are expressed as the median, followed by the interquartile range in parentheses *** Wilcoxon signed rank test between the cfDNA concentration at baseline and at first follow-up assessment or best response.
    Figure Legend Snippet: Changes in the cfDNA concentration during systemic therapy (A) Change in the cfDNA concentration from baseline to first response assessment, according to the radiological response category. (B) Waterfall plot for the percentage change in the cfDNA concentration at first response assessment. (C) Change in the cfDNA concentration from baseline to the radiological best response, according to the radiological best response category. (D) Waterfall plot for the percentage change in the cfDNA concentration at assessment of radiological best response. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PR, partial response; SD, stable disease; PD, progression of disease * Kruskal-Wallis test among PR, SD and PD groups ** Data are expressed as the median, followed by the interquartile range in parentheses *** Wilcoxon signed rank test between the cfDNA concentration at baseline and at first follow-up assessment or best response.

    Techniques Used: Concentration Assay

    Study flow diagram cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer, ADC, adenocarcinoma.
    Figure Legend Snippet: Study flow diagram cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer, ADC, adenocarcinoma.

    Techniques Used: Flow Cytometry

    Kaplan-Meier estimates of PFS and OS according to the cfDNA concentration in patients with NSCLC (A) PFS and (B) OS according to the baseline cfDNA concentration (≤ 70 ng/mL vs. > 70 ng/mL) in all patients with NSCLC. (C) PFS and (D) OS according to the baseline cfDNA concentration (≤ 70 ng/mL vs. > 70 ng/mL) in chemo-naive patients with stage IV adenocarcinoma. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PFS, progression-free survival; OS, overall survival.
    Figure Legend Snippet: Kaplan-Meier estimates of PFS and OS according to the cfDNA concentration in patients with NSCLC (A) PFS and (B) OS according to the baseline cfDNA concentration (≤ 70 ng/mL vs. > 70 ng/mL) in all patients with NSCLC. (C) PFS and (D) OS according to the baseline cfDNA concentration (≤ 70 ng/mL vs. > 70 ng/mL) in chemo-naive patients with stage IV adenocarcinoma. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PFS, progression-free survival; OS, overall survival.

    Techniques Used: Concentration Assay

    Circulating cfDNA time points coded by NSCLC patient identification number Graphical presentation of the association between the cfDNA level and the assessment of radiological response in patients with disease progression (A) and without progression (B) Change in the cfDNA concentration from baseline to best response, according to the radiological best response category; x-axis displays the time to clinical tumor progression. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PR, partial response; SD, stable disease; PD, progression of disease * Kruskal-Wallis test among PR, SD and PD groups ** Data are expressed as the median, followed by the interquartile range in parentheses *** Wilcoxon signed rank test between the cfDNA concentration at baseline and at best response.
    Figure Legend Snippet: Circulating cfDNA time points coded by NSCLC patient identification number Graphical presentation of the association between the cfDNA level and the assessment of radiological response in patients with disease progression (A) and without progression (B) Change in the cfDNA concentration from baseline to best response, according to the radiological best response category; x-axis displays the time to clinical tumor progression. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PR, partial response; SD, stable disease; PD, progression of disease * Kruskal-Wallis test among PR, SD and PD groups ** Data are expressed as the median, followed by the interquartile range in parentheses *** Wilcoxon signed rank test between the cfDNA concentration at baseline and at best response.

    Techniques Used: Concentration Assay

    Circulating cfDNA kinetics in patients with NSCLCQuantitative cfDNA dynamics during treatment for NSCLC (A) Change in the cfDNA concentration from baseline to disease progression, according to the radiological best response category. (B) Change in the cfDNA concentration from the previous level to disease progression, according to the radiological best response category. Colors and symbols in the panel represent individual patient cfDNA kinetics; x-axis displays the time to clinical tumor progression. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PR, partial response; SD, stable disease; PD, progression of disease * Kruskal-Wallis test among PR, SD and PD groups ** Data are expressed as the median, followed by the interquartile range in parentheses. *** Wilcoxon signed rank test between the cfDNA level at disease progression and the baseline or previous cfDNA level.
    Figure Legend Snippet: Circulating cfDNA kinetics in patients with NSCLCQuantitative cfDNA dynamics during treatment for NSCLC (A) Change in the cfDNA concentration from baseline to disease progression, according to the radiological best response category. (B) Change in the cfDNA concentration from the previous level to disease progression, according to the radiological best response category. Colors and symbols in the panel represent individual patient cfDNA kinetics; x-axis displays the time to clinical tumor progression. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PR, partial response; SD, stable disease; PD, progression of disease * Kruskal-Wallis test among PR, SD and PD groups ** Data are expressed as the median, followed by the interquartile range in parentheses. *** Wilcoxon signed rank test between the cfDNA level at disease progression and the baseline or previous cfDNA level.

    Techniques Used: Concentration Assay

    15) Product Images from "Quantification of circulating cell-free DNA to predict patient survival in non-small-cell lung cancer"

    Article Title: Quantification of circulating cell-free DNA to predict patient survival in non-small-cell lung cancer

    Journal: Oncotarget

    doi: 10.18632/oncotarget.21769

    Changes in the cfDNA concentration during systemic therapy (A) Change in the cfDNA concentration from baseline to first response assessment, according to the radiological response category. (B) Waterfall plot for the percentage change in the cfDNA concentration at first response assessment. (C) Change in the cfDNA concentration from baseline to the radiological best response, according to the radiological best response category. (D) Waterfall plot for the percentage change in the cfDNA concentration at assessment of radiological best response. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PR, partial response; SD, stable disease; PD, progression of disease * Kruskal-Wallis test among PR, SD and PD groups ** Data are expressed as the median, followed by the interquartile range in parentheses *** Wilcoxon signed rank test between the cfDNA concentration at baseline and at first follow-up assessment or best response.
    Figure Legend Snippet: Changes in the cfDNA concentration during systemic therapy (A) Change in the cfDNA concentration from baseline to first response assessment, according to the radiological response category. (B) Waterfall plot for the percentage change in the cfDNA concentration at first response assessment. (C) Change in the cfDNA concentration from baseline to the radiological best response, according to the radiological best response category. (D) Waterfall plot for the percentage change in the cfDNA concentration at assessment of radiological best response. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PR, partial response; SD, stable disease; PD, progression of disease * Kruskal-Wallis test among PR, SD and PD groups ** Data are expressed as the median, followed by the interquartile range in parentheses *** Wilcoxon signed rank test between the cfDNA concentration at baseline and at first follow-up assessment or best response.

    Techniques Used: Concentration Assay

    Study flow diagram cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer, ADC, adenocarcinoma.
    Figure Legend Snippet: Study flow diagram cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer, ADC, adenocarcinoma.

    Techniques Used: Flow Cytometry

    Kaplan-Meier estimates of PFS and OS according to the cfDNA concentration in patients with NSCLC (A) PFS and (B) OS according to the baseline cfDNA concentration (≤ 70 ng/mL vs. > 70 ng/mL) in all patients with NSCLC. (C) PFS and (D) OS according to the baseline cfDNA concentration (≤ 70 ng/mL vs. > 70 ng/mL) in chemo-naive patients with stage IV adenocarcinoma. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PFS, progression-free survival; OS, overall survival.
    Figure Legend Snippet: Kaplan-Meier estimates of PFS and OS according to the cfDNA concentration in patients with NSCLC (A) PFS and (B) OS according to the baseline cfDNA concentration (≤ 70 ng/mL vs. > 70 ng/mL) in all patients with NSCLC. (C) PFS and (D) OS according to the baseline cfDNA concentration (≤ 70 ng/mL vs. > 70 ng/mL) in chemo-naive patients with stage IV adenocarcinoma. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PFS, progression-free survival; OS, overall survival.

    Techniques Used: Concentration Assay

    Circulating cfDNA time points coded by NSCLC patient identification number Graphical presentation of the association between the cfDNA level and the assessment of radiological response in patients with disease progression (A) and without progression (B) Change in the cfDNA concentration from baseline to best response, according to the radiological best response category; x-axis displays the time to clinical tumor progression. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PR, partial response; SD, stable disease; PD, progression of disease * Kruskal-Wallis test among PR, SD and PD groups ** Data are expressed as the median, followed by the interquartile range in parentheses *** Wilcoxon signed rank test between the cfDNA concentration at baseline and at best response.
    Figure Legend Snippet: Circulating cfDNA time points coded by NSCLC patient identification number Graphical presentation of the association between the cfDNA level and the assessment of radiological response in patients with disease progression (A) and without progression (B) Change in the cfDNA concentration from baseline to best response, according to the radiological best response category; x-axis displays the time to clinical tumor progression. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PR, partial response; SD, stable disease; PD, progression of disease * Kruskal-Wallis test among PR, SD and PD groups ** Data are expressed as the median, followed by the interquartile range in parentheses *** Wilcoxon signed rank test between the cfDNA concentration at baseline and at best response.

    Techniques Used: Concentration Assay

    Circulating cfDNA kinetics in patients with NSCLCQuantitative cfDNA dynamics during treatment for NSCLC (A) Change in the cfDNA concentration from baseline to disease progression, according to the radiological best response category. (B) Change in the cfDNA concentration from the previous level to disease progression, according to the radiological best response category. Colors and symbols in the panel represent individual patient cfDNA kinetics; x-axis displays the time to clinical tumor progression. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PR, partial response; SD, stable disease; PD, progression of disease * Kruskal-Wallis test among PR, SD and PD groups ** Data are expressed as the median, followed by the interquartile range in parentheses. *** Wilcoxon signed rank test between the cfDNA level at disease progression and the baseline or previous cfDNA level.
    Figure Legend Snippet: Circulating cfDNA kinetics in patients with NSCLCQuantitative cfDNA dynamics during treatment for NSCLC (A) Change in the cfDNA concentration from baseline to disease progression, according to the radiological best response category. (B) Change in the cfDNA concentration from the previous level to disease progression, according to the radiological best response category. Colors and symbols in the panel represent individual patient cfDNA kinetics; x-axis displays the time to clinical tumor progression. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PR, partial response; SD, stable disease; PD, progression of disease * Kruskal-Wallis test among PR, SD and PD groups ** Data are expressed as the median, followed by the interquartile range in parentheses. *** Wilcoxon signed rank test between the cfDNA level at disease progression and the baseline or previous cfDNA level.

    Techniques Used: Concentration Assay

    16) Product Images from "Genome-wide co-localization of active EGFR and downstream ERK pathway kinases mirrors mitogen-inducible RNA polymerase 2 genomic occupancy"

    Article Title: Genome-wide co-localization of active EGFR and downstream ERK pathway kinases mirrors mitogen-inducible RNA polymerase 2 genomic occupancy

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkw763

    EGF and FBS-induced EGR1 expression and co-recruitment of Pol2 with active kinases to EGR1, FOS, HBB and GAPDH loci . ( A ) HeLa S3 cells were treated with EGF (100 ng/ml) or 10% FBS and harvested at indicated time point then RNA extracted with Trizol followed by RT-qPCR measurements. EGR1 expression was normalized to RPLP0 mRNA ( n = 3;±SD). ( B ) Cells were treated as in A and collected at indicated time point. A total of 5 μg of whole cell extract was resolved by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and electrotransferred to PVDF membranes. Western blot analysis was performed using anti-pMEK1/2, anti-pERK1/2 and anti-β-Actin antibodies. ( C ) HeLa S3 cells were challenged with either EGF (100 ng/ml) or 10% FBS and fixed with 1% formaldehyde at indicated time point. Chromatin was isolated and used in ChIP assays with unspecific IgG, anti-Pol2, anti-pEGFR, anti-pMEK1/2 and anti-pERK1/2 antibody. Isolated DNA was used as the template in qPCR analyses with primers designed to amplify exon1 of EGR1 , exon1-intron1 junction of FOS gene and promoters of the β-globin ( HBB ), and glyceraldehyde-3-phosphate dehydrogenase ( GAPDH ). Data are expressed as a percentage of input chromatin ( n = 3;±SD).
    Figure Legend Snippet: EGF and FBS-induced EGR1 expression and co-recruitment of Pol2 with active kinases to EGR1, FOS, HBB and GAPDH loci . ( A ) HeLa S3 cells were treated with EGF (100 ng/ml) or 10% FBS and harvested at indicated time point then RNA extracted with Trizol followed by RT-qPCR measurements. EGR1 expression was normalized to RPLP0 mRNA ( n = 3;±SD). ( B ) Cells were treated as in A and collected at indicated time point. A total of 5 μg of whole cell extract was resolved by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and electrotransferred to PVDF membranes. Western blot analysis was performed using anti-pMEK1/2, anti-pERK1/2 and anti-β-Actin antibodies. ( C ) HeLa S3 cells were challenged with either EGF (100 ng/ml) or 10% FBS and fixed with 1% formaldehyde at indicated time point. Chromatin was isolated and used in ChIP assays with unspecific IgG, anti-Pol2, anti-pEGFR, anti-pMEK1/2 and anti-pERK1/2 antibody. Isolated DNA was used as the template in qPCR analyses with primers designed to amplify exon1 of EGR1 , exon1-intron1 junction of FOS gene and promoters of the β-globin ( HBB ), and glyceraldehyde-3-phosphate dehydrogenase ( GAPDH ). Data are expressed as a percentage of input chromatin ( n = 3;±SD).

    Techniques Used: Expressing, Quantitative RT-PCR, Polyacrylamide Gel Electrophoresis, Western Blot, Isolation, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction

    EGF-inducible EGFR and ERK pathway components binding at ACTB and ACTG1 loci. ( A ) ChIP-seq overview of active kinases and Pol2 binding to ACTB and ACTG1 genes depicted in IGV genome browser. Pol2 ENCODE ChIP-Seq data for HeLa-S3 growing cells (ID: wgEncodeBroadHistoneHelas3Pol2bStdSig) were included to show similarities in transcriptional complex binding between datasets. A vertical dotted line marks TSS. ( B ) Time-course ChIP-qPCR measurements confirm EGFR and ERK pathway components binding to ACTB and ACTG1 following EGF treatment. ChIP analysis of sheared chromatin from a time course of EGF-treated (100 ng/ml EGF for 0, 10, 20, 45 and 60 min) HeLa-S3 cells was done using Matrix-ChIP method in 96-well polypropylene plates as described ( 8 ). qPCR was performed using primers (Supplementary Table S1) spanning an area depicted in a cartoon above each gene. ChIP data are expressed as DNA recovered as the percentage (%) of input DNA ( n = 3; mean ±SD). Statistical analysis of differences between mean DNA recovery for a given factor in quiescent cells and EGF time points was performed using t -tests. A P -value of ≤ 0.05 (*) was considered significant, **; P -value ≤ 0.01. ( C ) Time-course RT-qPCR analyses of ACTB and ACTG1 mRNA and pre-mRNA during EGF time course. Cells were harvested at indicated time point, RNA extracted with Trizol, DNAze treated and submitted to RT-qPCR measurements. RNA expression was normalized to RPLP0 mRNA and presented as fold change of expression measured in quiescent cells ( n = 3; mean ±SD). Statistical analysis of differences between mean cDNA levels for quiescent cells and given EGF time point was performed using t -tests. A P -value of ≤ 0.05 (*) was considered significant, **; P -value ≤ 0.01. Gene cartoon depicts localization of primers amplifying either mature (RT, spanning exon-exon) or unspliced (pre-mRNA, spanning exon-intron) form of transcript.
    Figure Legend Snippet: EGF-inducible EGFR and ERK pathway components binding at ACTB and ACTG1 loci. ( A ) ChIP-seq overview of active kinases and Pol2 binding to ACTB and ACTG1 genes depicted in IGV genome browser. Pol2 ENCODE ChIP-Seq data for HeLa-S3 growing cells (ID: wgEncodeBroadHistoneHelas3Pol2bStdSig) were included to show similarities in transcriptional complex binding between datasets. A vertical dotted line marks TSS. ( B ) Time-course ChIP-qPCR measurements confirm EGFR and ERK pathway components binding to ACTB and ACTG1 following EGF treatment. ChIP analysis of sheared chromatin from a time course of EGF-treated (100 ng/ml EGF for 0, 10, 20, 45 and 60 min) HeLa-S3 cells was done using Matrix-ChIP method in 96-well polypropylene plates as described ( 8 ). qPCR was performed using primers (Supplementary Table S1) spanning an area depicted in a cartoon above each gene. ChIP data are expressed as DNA recovered as the percentage (%) of input DNA ( n = 3; mean ±SD). Statistical analysis of differences between mean DNA recovery for a given factor in quiescent cells and EGF time points was performed using t -tests. A P -value of ≤ 0.05 (*) was considered significant, **; P -value ≤ 0.01. ( C ) Time-course RT-qPCR analyses of ACTB and ACTG1 mRNA and pre-mRNA during EGF time course. Cells were harvested at indicated time point, RNA extracted with Trizol, DNAze treated and submitted to RT-qPCR measurements. RNA expression was normalized to RPLP0 mRNA and presented as fold change of expression measured in quiescent cells ( n = 3; mean ±SD). Statistical analysis of differences between mean cDNA levels for quiescent cells and given EGF time point was performed using t -tests. A P -value of ≤ 0.05 (*) was considered significant, **; P -value ≤ 0.01. Gene cartoon depicts localization of primers amplifying either mature (RT, spanning exon-exon) or unspliced (pre-mRNA, spanning exon-intron) form of transcript.

    Techniques Used: Binding Assay, Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Quantitative RT-PCR, RNA Expression, Expressing

    AP2M1 depletion reduces EGF-inducible Pol2, EGFR, MEK1/2 and ERK1/2 binding to EGR1 locus. ( A ) HeLa-S3 cells line were transfected with either one of two AP2M1 siRNAs or non-specific siRNA in a presence of Lipofectamine 3000. Twenty-four hours after transfection, cells were switched to serum free medium, and 48 h after quiescence, cells were treated with EGF (100 ng/ml) for 0, 45 and 180 min. Cells were harvested at indicated time point then RNA extracted with Trizol followed by RT-qPCR measurements. EGR1 and AP2M1 expression was normalized to RPLP0 mRNA ( n = 3; ±SD). (B ) Cells were prepared as in A and challenged with EGF (100 ng/ml) for 0, 5, 20 and 60 min then fixed, chromatin isolated and sheared. Matrix ChIP assay was done using antibodies to Pol2, pEGFR, pMEK1/2 and pERK1/2. ChIP data are expressed as DNA recovery in percentage (%) of input (means ± S.D., n = 3). Statistical analysis of differences between mean DNA recovery for control and AP2M1-depleted chromatin at given time point was performed using t -tests. ChIP results are shown for PCR product depicted on gene cartoon. A P -value of
    Figure Legend Snippet: AP2M1 depletion reduces EGF-inducible Pol2, EGFR, MEK1/2 and ERK1/2 binding to EGR1 locus. ( A ) HeLa-S3 cells line were transfected with either one of two AP2M1 siRNAs or non-specific siRNA in a presence of Lipofectamine 3000. Twenty-four hours after transfection, cells were switched to serum free medium, and 48 h after quiescence, cells were treated with EGF (100 ng/ml) for 0, 45 and 180 min. Cells were harvested at indicated time point then RNA extracted with Trizol followed by RT-qPCR measurements. EGR1 and AP2M1 expression was normalized to RPLP0 mRNA ( n = 3; ±SD). (B ) Cells were prepared as in A and challenged with EGF (100 ng/ml) for 0, 5, 20 and 60 min then fixed, chromatin isolated and sheared. Matrix ChIP assay was done using antibodies to Pol2, pEGFR, pMEK1/2 and pERK1/2. ChIP data are expressed as DNA recovery in percentage (%) of input (means ± S.D., n = 3). Statistical analysis of differences between mean DNA recovery for control and AP2M1-depleted chromatin at given time point was performed using t -tests. ChIP results are shown for PCR product depicted on gene cartoon. A P -value of

    Techniques Used: Binding Assay, Transfection, Quantitative RT-PCR, Expressing, Isolation, Chromatin Immunoprecipitation, Polymerase Chain Reaction

    17) Product Images from "Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing"

    Article Title: Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing

    Journal: Nature methods

    doi: 10.1038/nmeth.2408

    ASRs validation. ( a ) Fraction of input DNA captured by ChIP in regions with significant (grey highlight) vs. non-significant aphidicolin effect in HeLa cells treated (orange) or not (green) with aphidicolin. Mean ± s.d. are shown for n = 3 biological replicates. Genomic coordinates of amplicons analyzed by qPCR are reported. Chr: chromosome. Coord: genomic coordinate. ( b ) Comparison of aphidicolin effect measured by BLESS vs. ChIP in regions described in ( a ). Captured DNA ratio: ratio of captured DNA in aphidicolin-treated (A) vs. control (C) HeLa. R: Pearson’s correlation coefficient.
    Figure Legend Snippet: ASRs validation. ( a ) Fraction of input DNA captured by ChIP in regions with significant (grey highlight) vs. non-significant aphidicolin effect in HeLa cells treated (orange) or not (green) with aphidicolin. Mean ± s.d. are shown for n = 3 biological replicates. Genomic coordinates of amplicons analyzed by qPCR are reported. Chr: chromosome. Coord: genomic coordinate. ( b ) Comparison of aphidicolin effect measured by BLESS vs. ChIP in regions described in ( a ). Captured DNA ratio: ratio of captured DNA in aphidicolin-treated (A) vs. control (C) HeLa. R: Pearson’s correlation coefficient.

    Techniques Used: Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction

    18) Product Images from "Phase-defined complete sequencing of the HLA genes by next-generation sequencing"

    Article Title: Phase-defined complete sequencing of the HLA genes by next-generation sequencing

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-14-355

    Size selection of the Nextera DNA libraries by agarose gel size selection. ( A ) Electropherogram of DNA library analyzed by 2100 Bioanalyzer. The library size of the Nextera DNA Sample Prep Kits was 150 bp to more than 10 kb (mean size: 902 bp). ( B ) Bioanalyzer electropherogram of a selected DNA library by cutting from the agarose gel. We selected large fragments with sizes ranging from 500 to 2,000 bp to remove short DNA fragments for effective HLA gene haplotype phasing. The size selection also determines an actual molar concentration for bridge PCR to generate clusters in flowcell, because DNA fragments with over 1.5 kb size are not efficiently amplified. The mean size of the selected fragments was 1,561 bp.
    Figure Legend Snippet: Size selection of the Nextera DNA libraries by agarose gel size selection. ( A ) Electropherogram of DNA library analyzed by 2100 Bioanalyzer. The library size of the Nextera DNA Sample Prep Kits was 150 bp to more than 10 kb (mean size: 902 bp). ( B ) Bioanalyzer electropherogram of a selected DNA library by cutting from the agarose gel. We selected large fragments with sizes ranging from 500 to 2,000 bp to remove short DNA fragments for effective HLA gene haplotype phasing. The size selection also determines an actual molar concentration for bridge PCR to generate clusters in flowcell, because DNA fragments with over 1.5 kb size are not efficiently amplified. The mean size of the selected fragments was 1,561 bp.

    Techniques Used: Selection, Agarose Gel Electrophoresis, Sample Prep, Concentration Assay, Bridge PCR, Amplification

    19) Product Images from "Proliferation Cycle Causes Age Dependent Mitochondrial Deficiencies and Contributes to the Aging of Stem Cells"

    Article Title: Proliferation Cycle Causes Age Dependent Mitochondrial Deficiencies and Contributes to the Aging of Stem Cells

    Journal: Genes

    doi: 10.3390/genes8120397

    Mitochondrial DNA (mtDNA) rearrangements and impaired mtDNA replication in ovaries of aged flies. ( A ) Schematic drawing of Drosophila melanogaster (Dm.) mtDNA. Enzyme sites of HindIII (H) and XhoI (X) are indicated. Sizes of digested fragments are also labelled. ( B ) Representative gel image of rolling cycle amplification of mtDNA (arrowhead) and DNA marker (M, kb). ( C ) Pattern of rolling cycle amplification (RCA) amplified mtDNA digested by XhoI and HindIII. The 5.8 kb fragment spanning the AT-rich region was recovered for restriction fragment length polymorphism (RFLP) analysis. ( D ) Schematic map of SspI site on 5.8 kb AT-rich region. ( E ) densitometry plot of SspI digestion pattern of 5.8 fragments spanning the AT-rich region from young (2-day-old) and old (60-day-old) ovaries, analyzed by Agilent Bioanalyzer 2100. Note the difference of bands (open arrowheads) demonstrating the rearrangements of AT-rich regions in aged ovaries. DNA dye standard (closed arrowheads) and DNA ladder are marked (M, bp). ( F ) Representative images showing 5-ethynyl-2’-deoxyuridine (EdU) incorporation into mtDNA (green puncta, arrowheads) in ovaries (dashed line, anterior toward left) from young (2-day-old) and old (40-day-old) female flies. Note that the number of EdU puncta was dramatically reduced in germarium from old fly. Arrowhead: mtDNA; arrow: nuclear DNA; scale bar: 10 µm.
    Figure Legend Snippet: Mitochondrial DNA (mtDNA) rearrangements and impaired mtDNA replication in ovaries of aged flies. ( A ) Schematic drawing of Drosophila melanogaster (Dm.) mtDNA. Enzyme sites of HindIII (H) and XhoI (X) are indicated. Sizes of digested fragments are also labelled. ( B ) Representative gel image of rolling cycle amplification of mtDNA (arrowhead) and DNA marker (M, kb). ( C ) Pattern of rolling cycle amplification (RCA) amplified mtDNA digested by XhoI and HindIII. The 5.8 kb fragment spanning the AT-rich region was recovered for restriction fragment length polymorphism (RFLP) analysis. ( D ) Schematic map of SspI site on 5.8 kb AT-rich region. ( E ) densitometry plot of SspI digestion pattern of 5.8 fragments spanning the AT-rich region from young (2-day-old) and old (60-day-old) ovaries, analyzed by Agilent Bioanalyzer 2100. Note the difference of bands (open arrowheads) demonstrating the rearrangements of AT-rich regions in aged ovaries. DNA dye standard (closed arrowheads) and DNA ladder are marked (M, bp). ( F ) Representative images showing 5-ethynyl-2’-deoxyuridine (EdU) incorporation into mtDNA (green puncta, arrowheads) in ovaries (dashed line, anterior toward left) from young (2-day-old) and old (40-day-old) female flies. Note that the number of EdU puncta was dramatically reduced in germarium from old fly. Arrowhead: mtDNA; arrow: nuclear DNA; scale bar: 10 µm.

    Techniques Used: Amplification, Marker

    20) Product Images from "Integrative microRNA and mRNA deep-sequencing expression profiling in endemic Burkitt lymphoma"

    Article Title: Integrative microRNA and mRNA deep-sequencing expression profiling in endemic Burkitt lymphoma

    Journal: BMC Cancer

    doi: 10.1186/s12885-017-3711-9

    Aberrant transcriptome expression pivotal to eBL lymphomagenesis. a Schematic illustration of the aberrant gene expression and miRNA mediated regulatory changes that would initiate lymphomagenesis as a result of DNA damage. Combined loss of p53 function due to small interfering RNA-mediated regulation of ATM and NLK together with upregulation of TFAP4, would facilitate survival of cells with the c-myc-Igh chromosomal translocation and MYC induced cell cycle progression initiating eBL tumor development. ATM checkpoint kinase, transduces genomic stress signals to halt cell cycle progression in response to DNA damage. It is critical in the regulation of apoptosis and lymphomagenesis in c-myc induced lymphomas. ATM is downregulated in eBL and it is targeted by 4 miRs that are Upregulated in eBL. NLK is required for the upregulation of P53 expression in response to DNA damage. It interacts with P53 to enhance its stability and activity by abrogating MDM2 mediated degradation. NLK is downregulated in eBL tumor cells and also targeted by 2 miRs that are upregulated in eBL tumor cells. TFAP4/AP4 is a central mediator of cell cycle progression in response to c-MYC activation. b RNA seq. Expression counts of MYC , TFAP4 , ATM and NLK in eBL tumor cells and GC B cells. c Hierarchical clustering of eBL and GC B cells based on the expression profiles of MYC , TFAP4 , ATM and NLK also revealed a clear separation of the two groups. d . miRNA seq. Expression counts of hsa-miR-26a-5p, hsa-miR-27b-3p, hsa-miR-30b-5p, miR-17~92-cluster members (hsa-miR-19b-3p, and hsa-miR-92a-3p), and let-7-family miRs (hsa-let-7a-5p, hsa-let-7b-5p, hsa-let-7d-5p, hsa-let-7e-5p, and hsa-let-7 g-5p) in eBL tumor cells and GC B cells
    Figure Legend Snippet: Aberrant transcriptome expression pivotal to eBL lymphomagenesis. a Schematic illustration of the aberrant gene expression and miRNA mediated regulatory changes that would initiate lymphomagenesis as a result of DNA damage. Combined loss of p53 function due to small interfering RNA-mediated regulation of ATM and NLK together with upregulation of TFAP4, would facilitate survival of cells with the c-myc-Igh chromosomal translocation and MYC induced cell cycle progression initiating eBL tumor development. ATM checkpoint kinase, transduces genomic stress signals to halt cell cycle progression in response to DNA damage. It is critical in the regulation of apoptosis and lymphomagenesis in c-myc induced lymphomas. ATM is downregulated in eBL and it is targeted by 4 miRs that are Upregulated in eBL. NLK is required for the upregulation of P53 expression in response to DNA damage. It interacts with P53 to enhance its stability and activity by abrogating MDM2 mediated degradation. NLK is downregulated in eBL tumor cells and also targeted by 2 miRs that are upregulated in eBL tumor cells. TFAP4/AP4 is a central mediator of cell cycle progression in response to c-MYC activation. b RNA seq. Expression counts of MYC , TFAP4 , ATM and NLK in eBL tumor cells and GC B cells. c Hierarchical clustering of eBL and GC B cells based on the expression profiles of MYC , TFAP4 , ATM and NLK also revealed a clear separation of the two groups. d . miRNA seq. Expression counts of hsa-miR-26a-5p, hsa-miR-27b-3p, hsa-miR-30b-5p, miR-17~92-cluster members (hsa-miR-19b-3p, and hsa-miR-92a-3p), and let-7-family miRs (hsa-let-7a-5p, hsa-let-7b-5p, hsa-let-7d-5p, hsa-let-7e-5p, and hsa-let-7 g-5p) in eBL tumor cells and GC B cells

    Techniques Used: Expressing, Small Interfering RNA, Translocation Assay, Activity Assay, Activation Assay, RNA Sequencing Assay, Gas Chromatography

    Related Articles

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    Whole Genome Amplification:

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    Polymerase Chain Reaction:

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    Article Title: Phase-defined complete sequencing of the HLA genes by next-generation sequencing
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    Article Title: Current Protocols in Molecular Biology Unit 4.23
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    Article Title: Haplotyping germline and cancer genomes using high-throughput linked-read sequencing
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    Article Title: First Genome Sequence of Newcastle Disease Virus of Genotype VIIi from Jordan
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    Article Title: Construction and Characterization of Synthetic Bacterial Community for Experimental Ecology and Evolution
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    Construct:

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    Real-time Polymerase Chain Reaction:

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    Article Title: Current Protocols in Molecular Biology Unit 4.23
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    Article Title: Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA
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    Multiplex Assay:

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    Article Title: Phase-defined complete sequencing of the HLA genes by next-generation sequencing
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    Incubation:

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    Article Snippet: When working with lower RNA input, the protocol offers modifications at several steps, for example a longer incubation time and reduced temperatures in the adaptor ligation step. .. A concluding Bioanalyzer 2100 run with the High Sensitivity DNA Kit (Agilent Technologies, Germany) that allows the analysis of DNA libraries regarding size, purity and concentration completed the workflow of library preparation.

    Expressing:

    Article Title: Exosomes impact survival to radiation exposure in cell line models of nervous system cancer
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    Modification:

    Article Title: Exosomes impact survival to radiation exposure in cell line models of nervous system cancer
    Article Snippet: Briefly, 1-2 ng of total RNA was ligated with chemically modified 3′- and 5′- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification. .. Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).

    Hybridization:

    Article Title: Physiological Expression of Ion Channel Receptors in Human Periodontal Ligament Stem Cells
    Article Snippet: The Bioanalyzer instrument (Agilent High Sensitivity DNA Kit, Richardson, TX, USA) was used to validate the quality of the library. .. The Bioanalyzer instrument (Agilent High Sensitivity DNA Kit, Richardson, TX, USA) was used to validate the quality of the library.

    Article Title: Optimization of Extraction of Circulating RNAs from Plasma – Enabling Small RNA Sequencing
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    Flow Cytometry:

    Article Title: Exosomes impact survival to radiation exposure in cell line models of nervous system cancer
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    Article Title: Next-generation sequencing using a pre-designed gene panel for the molecular diagnosis of congenital disorders in pediatric patients
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    Ligation:

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    Methylation:

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    Generated:

    Article Title: Genome Sequencing of Museum Specimens Reveals Rapid Changes in the Genetic Composition of Honey Bees in California
    Article Snippet: Library success was confirmed by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies). .. DNA sequencing of 100 bp single-end reads on Illumina HiSeq2000 was performed at Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley.

    Article Title: Genetic analysis of Ikaros target genes and tumor suppressor function in BCR-ABL1+ pre–B ALL
    Article Snippet: Libraries were generated using custom Nextera barcoded primers ( ) and were amplified for a total of 10 cycles. .. Libraries were purified with AMPure beads (Agencourt) and library quality was assessed using the Agilent Bioanalyzer High-Sensitivity DNA kit.

    Article Title: Exosomes impact survival to radiation exposure in cell line models of nervous system cancer
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    Article Title: First Genome Sequence of Newcastle Disease Virus of Genotype VIIi from Jordan
    Article Snippet: The size distribution and concentration of DNA in the prepared libraries were checked on a Bioanalyzer 2100 and a Qubit instrument using a high-sensitivity (HS) DNA kit (Agilent Technologies, Germany) and a Qubit double-stranded DNA (dsDNA) HS assay kit (Life Technologies, USA), respectively ( ). .. Raw sequence data were analyzed and assembled with MIRA version 3.4.1 within a customized workflow on the Galaxy platform as described previously ( ).

    DNA Sequencing:

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    Article Title: Enterobacter asburiae Strain L1: Complete Genome and Whole Genome Optical Mapping Analysis of a Quorum Sensing Bacterium
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    Sequencing:

    Article Title: Physiological Expression of Ion Channel Receptors in Human Periodontal Ligament Stem Cells
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    Article Title: Phase-defined complete sequencing of the HLA genes by next-generation sequencing
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    Article Title: Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs
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    Article Title: Current Protocols in Molecular Biology Unit 4.23
    Article Snippet: After purification by an 8% polyacrylamide gel, a DNA library can be quantified by Agilent Bioanalyzer analysis (High-sensitivity DNA Kit) as well as by Quantitative-PCR (Q-PCR) analysis by comparison to previously calibrated/sequenced DNA libraries using Q-PCR checking primers F and R ( ). .. After purification by an 8% polyacrylamide gel, a DNA library can be quantified by Agilent Bioanalyzer analysis (High-sensitivity DNA Kit) as well as by Quantitative-PCR (Q-PCR) analysis by comparison to previously calibrated/sequenced DNA libraries using Q-PCR checking primers F and R ( ).

    Article Title: Genome Sequencing of Museum Specimens Reveals Rapid Changes in the Genetic Composition of Honey Bees in California
    Article Snippet: Library success was confirmed by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies). .. Library success was confirmed by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies).

    Article Title: Exosomes impact survival to radiation exposure in cell line models of nervous system cancer
    Article Snippet: Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies). .. Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).

    Article Title: Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA
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    Article Title: Next-generation sequencing using a pre-designed gene panel for the molecular diagnosis of congenital disorders in pediatric patients
    Article Snippet: Paragraph title: Library construction, sequencing, and data analysis ... Amplicons ranging from 150 to 550 bp were then quantified using an Agilent BioAnalyzer High Sensitivity DNA Assay kit on the 2100 Bioanalyzer to validate the enrichment of the libraries.

    Article Title: First Genome Sequence of Newcastle Disease Virus of Genotype VIIi from Jordan
    Article Snippet: The size distribution and concentration of DNA in the prepared libraries were checked on a Bioanalyzer 2100 and a Qubit instrument using a high-sensitivity (HS) DNA kit (Agilent Technologies, Germany) and a Qubit double-stranded DNA (dsDNA) HS assay kit (Life Technologies, USA), respectively ( ). .. Paired-end sequencing (2 × 250 bp) of the generated libraries was performed on a MiSeq instrument with the 500-cycle MiSeq reagent kit version 2 (Illumina, USA).

    Article Title: Construction and Characterization of Synthetic Bacterial Community for Experimental Ecology and Evolution
    Article Snippet: Paragraph title: DNA Extraction and Sequencing for 16S rRNA Amplicon Analysis ... The ready amplicon library was diluted to 1:10 and 1:20 and quantified with the Agilent 2100 Bioanalyzer High Sensitivity DNA Analysis Kit (Agilent Genomics, Santa Clara, CA, United States).

    Article Title: Draft Genome of the Multidrug-Resistant Acinetobacter baumannii Strain A155 Clinical Isolate
    Article Snippet: A. baumannii A155 whole-genome sequencing and annotation were performed as described previously ( ). .. The Bioanalyzer 2100 High Sensitivity DNA analysis kit (Agilent Technologies, Santa Clara, CA, USA) with version B.02.08.SI648 software was used to determine the fragmentation of the resultant libraries.

    Article Title: A Multicenter Study To Evaluate the Performance of High-Throughput Sequencing for Virus Detection
    Article Snippet: The resulting cDNA was converted into an appropriately sized, sequencing-compatible DNA library using Roche’s Rapid Library Preparation method. .. The quality (average DNA fragment length) of the DNA library was assessed twice, after fragmentation and upon completion of DNA library construction using an Agilent 2100 Bioanalyzer high-sensitivity DNA kit and compared against defined acceptance criteria.

    Article Title: Enterobacter asburiae Strain L1: Complete Genome and Whole Genome Optical Mapping Analysis of a Quorum Sensing Bacterium
    Article Snippet: DNA sequencing template was obtained from sheared genomic DNA using the Pacific Bioscience 10 kb SMRTbell library template preparation kit per the manufacturer's instructions (Pacific Biosciences, Menlo Park, CA, USA). .. The quality sizing analysis of DNA library was validated by Bioanalyzer 2100 high sensitivity DNA kit (Agilent Technologies, Inc., Santa Clara, CA, USA) prior to sequencing. .. PacBio RS II sequencing technology (Pacific Biosciences) was used as the sequencing platform.

    Binding Assay:

    Article Title: Methodology for Y Chromosome Capture: A complete genome sequence of  Y chromosome using flow cytometry, laser microdissection and magnetic streptavidin-beads
    Article Snippet: We removed the sheared DNA into a low binding plastic tube and kept it on ice. .. We checked the quality using the 2100 Bioanalyzer System with the Agilent Technologies High Sensitivity DNA Kit.

    DNA Extraction:

    Article Title: Construction and Characterization of Synthetic Bacterial Community for Experimental Ecology and Evolution
    Article Snippet: Paragraph title: DNA Extraction and Sequencing for 16S rRNA Amplicon Analysis ... The ready amplicon library was diluted to 1:10 and 1:20 and quantified with the Agilent 2100 Bioanalyzer High Sensitivity DNA Analysis Kit (Agilent Genomics, Santa Clara, CA, United States).

    RNA Sequencing Assay:

    Article Title: Physiological Expression of Ion Channel Receptors in Human Periodontal Ligament Stem Cells
    Article Snippet: Paragraph title: 2.10. RNA-Seq Preparation ... The Bioanalyzer instrument (Agilent High Sensitivity DNA Kit, Richardson, TX, USA) was used to validate the quality of the library.

    Article Title: Optimization of Extraction of Circulating RNAs from Plasma – Enabling Small RNA Sequencing
    Article Snippet: Paragraph title: Library Preparation and small RNA Sequencing ... A concluding Bioanalyzer 2100 run with the High Sensitivity DNA Kit (Agilent Technologies, Germany) that allows the analysis of DNA libraries regarding size, purity and concentration completed the workflow of library preparation.

    Article Title: Exosomes impact survival to radiation exposure in cell line models of nervous system cancer
    Article Snippet: Small RNA-seq libraries was generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer's instructions. .. Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).

    Article Title: First Genome Sequence of Newcastle Disease Virus of Genotype VIIi from Jordan
    Article Snippet: RNA was reverse transcribed, and DNA libraries for next-generation sequencing (NGS) were prepared using the KAPA stranded RNA-Seq library preparation kit (Kapa Biosystems, USA) according to the manufacturer’s instructions. .. The size distribution and concentration of DNA in the prepared libraries were checked on a Bioanalyzer 2100 and a Qubit instrument using a high-sensitivity (HS) DNA kit (Agilent Technologies, Germany) and a Qubit double-stranded DNA (dsDNA) HS assay kit (Life Technologies, USA), respectively ( ).

    Fluorescence:

    Article Title: Draft Genome of the Multidrug-Resistant Acinetobacter baumannii Strain A155 Clinical Isolate
    Article Snippet: The SYBR Green (Life Technologies, Grand Island, NY, USA) standard curve method was used to estimate DNA concentration for library preparation in a black 96-well plate (Corning, Tewksbury, MA, USA), and fluorescence values were obtained using a FilterMax F5 spectrophotometer with Multi-Mode Analysis software version 3.4.0.25 (Molecular Devices, Sunnyvale, CA, USA). .. The Bioanalyzer 2100 High Sensitivity DNA analysis kit (Agilent Technologies, Santa Clara, CA, USA) with version B.02.08.SI648 software was used to determine the fragmentation of the resultant libraries.

    Magnetic Beads:

    Article Title: Physiological Expression of Ion Channel Receptors in Human Periodontal Ligament Stem Cells
    Article Snippet: The Bioanalyzer instrument (Agilent High Sensitivity DNA Kit, Richardson, TX, USA) was used to validate the quality of the library. .. The Bioanalyzer instrument (Agilent High Sensitivity DNA Kit, Richardson, TX, USA) was used to validate the quality of the library.

    Article Title: Current Protocols in Molecular Biology Unit 4.23
    Article Snippet: Based on our experience, it normally takes additional two rounds of purification by SPRI magnetic beads to completely remove DNA fragments smaller than 200 bp. .. After purification by an 8% polyacrylamide gel, a DNA library can be quantified by Agilent Bioanalyzer analysis (High-sensitivity DNA Kit) as well as by Quantitative-PCR (Q-PCR) analysis by comparison to previously calibrated/sequenced DNA libraries using Q-PCR checking primers F and R ( ).

    Article Title: Next-generation sequencing using a pre-designed gene panel for the molecular diagnosis of congenital disorders in pediatric patients
    Article Snippet: Circularized target DNA-HaloPlex probe hybrids containing biotin were then captured by HaloPlex Magnetic Beads on the Agencourt SPRIPlate Super magnet magnetic plate. .. Amplicons ranging from 150 to 550 bp were then quantified using an Agilent BioAnalyzer High Sensitivity DNA Assay kit on the 2100 Bioanalyzer to validate the enrichment of the libraries.

    Isolation:

    Article Title: Draft Genome of the Multidrug-Resistant Acinetobacter baumannii Strain A155 Clinical Isolate
    Article Snippet: Briefly, the A155 isolate was routinely stored at −80°C in 10% glycerol, passaged to overnight LB cultures grown with agitation at 37°C, and total DNA was isolated using the DNeasy blood and tissue kit (Qiagen, Valencia, CA, USA). .. The Bioanalyzer 2100 High Sensitivity DNA analysis kit (Agilent Technologies, Santa Clara, CA, USA) with version B.02.08.SI648 software was used to determine the fragmentation of the resultant libraries.

    Size-exclusion Chromatography:

    Article Title: Phase-defined complete sequencing of the HLA genes by next-generation sequencing
    Article Snippet: Cycling parameters were as follows: initial denaturation of 94°C/2 min followed by 30 cycles of 98°C/10 sec, 60°C/15 sec and 68°C/10 min. DNA libraries of these PCR products were prepared by a transposase-mediated library preparation method with the Nextera DNA Sample Preparation Kit (Illumina, San Diego, CA, USA) allowing reduced amount of DNA (50 ng) and time for the library construction (90 min). .. Each sample was dual indexed and equally pooled by evaluating the molar concentration by Agilent High Sensitivity DNA Kit and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

    Article Title: Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA
    Article Snippet: Following a 2 min denaturation step at 98 °C, we cycled libraries using an ABI 7900 Real-Time PCR machine and the following 2-step program: (1) denaturation at 98 °C for 20 sec, (2) annealing and extension at 55 °C for 190 sec. .. Finally, we quantified libraries using a KAPA Library Quantification Kit (Kapa Biosystems) and an Agilent Bioanalyzer High Sensitivity DNA Kit.

    Purification:

    Article Title: Physiological Expression of Ion Channel Receptors in Human Periodontal Ligament Stem Cells
    Article Snippet: The Bioanalyzer instrument (Agilent High Sensitivity DNA Kit, Richardson, TX, USA) was used to validate the quality of the library. .. The Bioanalyzer instrument (Agilent High Sensitivity DNA Kit, Richardson, TX, USA) was used to validate the quality of the library.

    Article Title: Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing
    Article Snippet: We purified PCR products of size comprised between 300 and 800 nt in gel, and analyzed them on the 2100 Bioanalyzer (Agilent) prior to sequencing. .. We assessed library quality and quantity on the 2100 Bioanalyzer (Agilent) using the High Sensitivity DNA Kit (Agilent), and by qPCR with the Kapa Library quantification Kit (KapaBiosystems).

    Article Title: Optimization of Extraction of Circulating RNAs from Plasma – Enabling Small RNA Sequencing
    Article Snippet: After PCR pre-amplification, the cDNA constructs were purified with the MinElute PCR Purification Kit (Qiagen, Germany) and loaded on the Bioanalyzer 2100 (Agilent, Germany) using the DNA 1000 Kit (Agilent, Germany) according to the manufacturer's protocol. .. A concluding Bioanalyzer 2100 run with the High Sensitivity DNA Kit (Agilent Technologies, Germany) that allows the analysis of DNA libraries regarding size, purity and concentration completed the workflow of library preparation.

    Article Title: Phf8 loss confers resistance to depression-like and anxiety-like behaviors in mice
    Article Snippet: RNA from ESCs, NPCs, the prefrontal cortex or the ventral striatum was purified using an RNeasy kit (Qiagen) and including the optional DNase digest step. .. Library quality was again assessed with the BioAnalyzer Agilent High Sensitivity DNA kit.

    Article Title: Current Protocols in Molecular Biology Unit 4.23
    Article Snippet: One potential drawback is that it can be time consuming to gel purify each library individually if multiple libraries are planned to be combined for a single sequencing run. .. After purification by an 8% polyacrylamide gel, a DNA library can be quantified by Agilent Bioanalyzer analysis (High-sensitivity DNA Kit) as well as by Quantitative-PCR (Q-PCR) analysis by comparison to previously calibrated/sequenced DNA libraries using Q-PCR checking primers F and R ( ). .. In theory, quantification by Q-PCR leads to a more accurate estimation of the amount of DNA that can be effectively clustered on the surface of flow cell.

    Article Title: Genetic analysis of Ikaros target genes and tumor suppressor function in BCR-ABL1+ pre–B ALL
    Article Snippet: Libraries were generated using custom Nextera barcoded primers ( ) and were amplified for a total of 10 cycles. .. Libraries were purified with AMPure beads (Agencourt) and library quality was assessed using the Agilent Bioanalyzer High-Sensitivity DNA kit. .. Libraries were quantitated using Qubit (Life Technologies).

    Article Title: Aneuploidy of chromosome 8 and mutation of circulating tumor cells predict pathologic complete response in the treatment of locally advanced rectal cancer
    Article Snippet: MALBAC products were purified with 1.4× Ampure XP beads (Beckman Coulter, Inc., Brea, CA, USA) and assessed by 2100 BioAnalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA). .. A BioAnalyzer High Sensitivity DNA kit (Agilent Technologies, Inc.) was used to visualize the size range of MALBAC products.

    Article Title: Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA
    Article Snippet: We added adapters in approximately 15-fold excess of library targets, and removed un-ligated adapters and adapter-dimers using 1.0X AmpureXP SPRI bead purification (Agencourt). .. Finally, we quantified libraries using a KAPA Library Quantification Kit (Kapa Biosystems) and an Agilent Bioanalyzer High Sensitivity DNA Kit.

    Article Title: Next-generation sequencing using a pre-designed gene panel for the molecular diagnosis of congenital disorders in pediatric patients
    Article Snippet: The target libraries were then amplified with 18 PCR cycles and purified using AMPure XP beads. .. Amplicons ranging from 150 to 550 bp were then quantified using an Agilent BioAnalyzer High Sensitivity DNA Assay kit on the 2100 Bioanalyzer to validate the enrichment of the libraries.

    Article Title: First Genome Sequence of Newcastle Disease Virus of Genotype VIIi from Jordan
    Article Snippet: RNA extraction from fresh spleen tissue was performed with TRIzol (Ambion-Thermo Fisher Scientific) followed by purification with a Direct-zol kit (Zymo Research). .. The size distribution and concentration of DNA in the prepared libraries were checked on a Bioanalyzer 2100 and a Qubit instrument using a high-sensitivity (HS) DNA kit (Agilent Technologies, Germany) and a Qubit double-stranded DNA (dsDNA) HS assay kit (Life Technologies, USA), respectively ( ).

    Article Title: Construction and Characterization of Synthetic Bacterial Community for Experimental Ecology and Evolution
    Article Snippet: Samples were pooled together in equal volumes and purified with Agencourt® AMPure® XP beads (Beckman Coulter, Brea, CA, United States) twice using 0.8 × volume of beads compared to the sample pool volume (40 μl). .. The ready amplicon library was diluted to 1:10 and 1:20 and quantified with the Agilent 2100 Bioanalyzer High Sensitivity DNA Analysis Kit (Agilent Genomics, Santa Clara, CA, United States).

    Article Title: A Multicenter Study To Evaluate the Performance of High-Throughput Sequencing for Virus Detection
    Article Snippet: This was followed by a purification step and quality assessment using the Agilent 2100 Bioanalyzer high-sensitivity DNA kit. .. The quality (average DNA fragment length) of the DNA library was assessed twice, after fragmentation and upon completion of DNA library construction using an Agilent 2100 Bioanalyzer high-sensitivity DNA kit and compared against defined acceptance criteria.

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Phf8 loss confers resistance to depression-like and anxiety-like behaviors in mice
    Article Snippet: Library quality was again assessed with the BioAnalyzer Agilent High Sensitivity DNA kit. .. Bar-coded libraries were then pooled at equimolar concentration and sequenced on an Illumina HiSeq 2000.

    Article Title: Haplotyping germline and cancer genomes using high-throughput linked-read sequencing
    Article Snippet: Paragraph title: RT-PCR validation of EML4-ALK fusion ... The PCR products were visualized using the BioAnalyzer High Sensitivity DNA Kit (Agilent), with respectively the amplicons ACTB diluted 1:50, EML4/ALK 1:20, and ALK/PTPN3 diluted 1:3.

    Article Title: First Genome Sequence of Newcastle Disease Virus of Genotype VIIi from Jordan
    Article Snippet: Proventriculus, spleen, intestine, liver, heart, and lung samples were collected for laboratory testing and determined to be NDV positive with reverse transcriptase PCR (RT-PCR). .. The size distribution and concentration of DNA in the prepared libraries were checked on a Bioanalyzer 2100 and a Qubit instrument using a high-sensitivity (HS) DNA kit (Agilent Technologies, Germany) and a Qubit double-stranded DNA (dsDNA) HS assay kit (Life Technologies, USA), respectively ( ).

    Quantitative RT-PCR:

    Article Title: Phf8 loss confers resistance to depression-like and anxiety-like behaviors in mice
    Article Snippet: Paragraph title: RNA preparation for sequencing and RT-qPCR ... Library quality was again assessed with the BioAnalyzer Agilent High Sensitivity DNA kit.

    Gel Extraction:

    Article Title: Optimization of Extraction of Circulating RNAs from Plasma – Enabling Small RNA Sequencing
    Article Snippet: For the size selection of amplified cDNA libraries, PCR products were loaded on an agarose gel (4%), appropriate bands of approximately 135 bp to 160 bp in size were cut out and passed on to gel extraction with the MinElute Gel Extraction Kit (Qiagen, Germany). .. A concluding Bioanalyzer 2100 run with the High Sensitivity DNA Kit (Agilent Technologies, Germany) that allows the analysis of DNA libraries regarding size, purity and concentration completed the workflow of library preparation.

    cDNA Library Assay:

    Article Title: Physiological Expression of Ion Channel Receptors in Human Periodontal Ligament Stem Cells
    Article Snippet: The procedure allowed us to mix the exome capture probes with the cDNA library. .. The Bioanalyzer instrument (Agilent High Sensitivity DNA Kit, Richardson, TX, USA) was used to validate the quality of the library.

    Agarose Gel Electrophoresis:

    Article Title: Optimization of Extraction of Circulating RNAs from Plasma – Enabling Small RNA Sequencing
    Article Snippet: For the size selection of amplified cDNA libraries, PCR products were loaded on an agarose gel (4%), appropriate bands of approximately 135 bp to 160 bp in size were cut out and passed on to gel extraction with the MinElute Gel Extraction Kit (Qiagen, Germany). .. A concluding Bioanalyzer 2100 run with the High Sensitivity DNA Kit (Agilent Technologies, Germany) that allows the analysis of DNA libraries regarding size, purity and concentration completed the workflow of library preparation.

    Chromatin Immunoprecipitation:

    Article Title: Next-generation sequencing using a pre-designed gene panel for the molecular diagnosis of congenital disorders in pediatric patients
    Article Snippet: Amplicons ranging from 150 to 550 bp were then quantified using an Agilent BioAnalyzer High Sensitivity DNA Assay kit on the 2100 Bioanalyzer to validate the enrichment of the libraries. .. Equimolar amounts of four multiplexed bar-coded libraries were pooled and clonally amplified by emulsion PCR, using the Ion PGM Template OT2 200 Kit 9 (Life Technologies, Carlsbad, CA, USA).

    RNA Extraction:

    Article Title: First Genome Sequence of Newcastle Disease Virus of Genotype VIIi from Jordan
    Article Snippet: RNA extraction from fresh spleen tissue was performed with TRIzol (Ambion-Thermo Fisher Scientific) followed by purification with a Direct-zol kit (Zymo Research). .. The size distribution and concentration of DNA in the prepared libraries were checked on a Bioanalyzer 2100 and a Qubit instrument using a high-sensitivity (HS) DNA kit (Agilent Technologies, Germany) and a Qubit double-stranded DNA (dsDNA) HS assay kit (Life Technologies, USA), respectively ( ).

    Software:

    Article Title: Draft Genome of the Multidrug-Resistant Acinetobacter baumannii Strain A155 Clinical Isolate
    Article Snippet: The Nextera XT kit (Illumina, Inc., San Diego, CA, USA) was used to simultaneously fragment and construct adapter-tagged libraries per the manufacturer’s instructions. .. The Bioanalyzer 2100 High Sensitivity DNA analysis kit (Agilent Technologies, Santa Clara, CA, USA) with version B.02.08.SI648 software was used to determine the fragmentation of the resultant libraries. .. Individual libraries were normalized by bead-based affinity, pooled, and then sequenced using the MiSeq version 3 600-cycle kit (Illumina) to perform 300-bp paired-end sequencing on a MiSeq instrument (Illumina) per the manufacturer’s instructions.

    SYBR Green Assay:

    Article Title: Phf8 loss confers resistance to depression-like and anxiety-like behaviors in mice
    Article Snippet: Library quality was again assessed with the BioAnalyzer Agilent High Sensitivity DNA kit. .. Bar-coded libraries were then pooled at equimolar concentration and sequenced on an Illumina HiSeq 2000.

    Article Title: Haplotyping germline and cancer genomes using high-throughput linked-read sequencing
    Article Snippet: The gene ACTB was assayed using SYBR Green Kit Control Kit (Life Technologies). .. The PCR products were visualized using the BioAnalyzer High Sensitivity DNA Kit (Agilent), with respectively the amplicons ACTB diluted 1:50, EML4/ALK 1:20, and ALK/PTPN3 diluted 1:3.

    Article Title: Draft Genome of the Multidrug-Resistant Acinetobacter baumannii Strain A155 Clinical Isolate
    Article Snippet: The SYBR Green (Life Technologies, Grand Island, NY, USA) standard curve method was used to estimate DNA concentration for library preparation in a black 96-well plate (Corning, Tewksbury, MA, USA), and fluorescence values were obtained using a FilterMax F5 spectrophotometer with Multi-Mode Analysis software version 3.4.0.25 (Molecular Devices, Sunnyvale, CA, USA). .. The Bioanalyzer 2100 High Sensitivity DNA analysis kit (Agilent Technologies, Santa Clara, CA, USA) with version B.02.08.SI648 software was used to determine the fragmentation of the resultant libraries.

    Negative Control:

    Article Title: Haplotyping germline and cancer genomes using high-throughput linked-read sequencing
    Article Snippet: As a negative control, NA12878 cells were assayed in parallel. .. The PCR products were visualized using the BioAnalyzer High Sensitivity DNA Kit (Agilent), with respectively the amplicons ACTB diluted 1:50, EML4/ALK 1:20, and ALK/PTPN3 diluted 1:3.

    Selection:

    Article Title: Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing
    Article Snippet: For BLESS Illumina library preparation, we used the TruSeq DNA sample preparation kit v2 (Illumina) without DNA fragmentation and library size selection. .. We assessed library quality and quantity on the 2100 Bioanalyzer (Agilent) using the High Sensitivity DNA Kit (Agilent), and by qPCR with the Kapa Library quantification Kit (KapaBiosystems).

    Article Title: Optimization of Extraction of Circulating RNAs from Plasma – Enabling Small RNA Sequencing
    Article Snippet: For the size selection of amplified cDNA libraries, PCR products were loaded on an agarose gel (4%), appropriate bands of approximately 135 bp to 160 bp in size were cut out and passed on to gel extraction with the MinElute Gel Extraction Kit (Qiagen, Germany). .. A concluding Bioanalyzer 2100 run with the High Sensitivity DNA Kit (Agilent Technologies, Germany) that allows the analysis of DNA libraries regarding size, purity and concentration completed the workflow of library preparation.

    Article Title: Current Protocols in Molecular Biology Unit 4.23
    Article Snippet: While much faster than the gel purification, the drawback of performing two additional rounds of SPRI size selection is that a several-fold greater amount of initial material is required to offset the loss of material during the purification, in order to obtain a comparable amount of quality DNA libraries suitable for sequencing. .. After purification by an 8% polyacrylamide gel, a DNA library can be quantified by Agilent Bioanalyzer analysis (High-sensitivity DNA Kit) as well as by Quantitative-PCR (Q-PCR) analysis by comparison to previously calibrated/sequenced DNA libraries using Q-PCR checking primers F and R ( ).

    Sample Prep:

    Article Title: Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing
    Article Snippet: For BLESS Illumina library preparation, we used the TruSeq DNA sample preparation kit v2 (Illumina) without DNA fragmentation and library size selection. .. We assessed library quality and quantity on the 2100 Bioanalyzer (Agilent) using the High Sensitivity DNA Kit (Agilent), and by qPCR with the Kapa Library quantification Kit (KapaBiosystems).

    Article Title: Phase-defined complete sequencing of the HLA genes by next-generation sequencing
    Article Snippet: Cycling parameters were as follows: initial denaturation of 94°C/2 min followed by 30 cycles of 98°C/10 sec, 60°C/15 sec and 68°C/10 min. DNA libraries of these PCR products were prepared by a transposase-mediated library preparation method with the Nextera DNA Sample Preparation Kit (Illumina, San Diego, CA, USA) allowing reduced amount of DNA (50 ng) and time for the library construction (90 min). .. Each sample was dual indexed and equally pooled by evaluating the molar concentration by Agilent High Sensitivity DNA Kit and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

    Article Title: Phf8 loss confers resistance to depression-like and anxiety-like behaviors in mice
    Article Snippet: For library preparation, Illumina TruSeq RNA Sample Prep Kit was used with 1 μg of sample RNA. .. Library quality was again assessed with the BioAnalyzer Agilent High Sensitivity DNA kit.

    Electrophoresis:

    Article Title: Current Protocols in Molecular Biology Unit 4.23
    Article Snippet: Alternatively, the PCR-amplified DNA sequencing library can be directly purified by electrophoresis on an 8% TBE polyacrylamide gel in order to extract DNA fragments in the range of 175 – 500 bp. .. After purification by an 8% polyacrylamide gel, a DNA library can be quantified by Agilent Bioanalyzer analysis (High-sensitivity DNA Kit) as well as by Quantitative-PCR (Q-PCR) analysis by comparison to previously calibrated/sequenced DNA libraries using Q-PCR checking primers F and R ( ).

    Next-Generation Sequencing:

    Article Title: Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing
    Article Snippet: Paragraph title: Next-generation sequencing ... We assessed library quality and quantity on the 2100 Bioanalyzer (Agilent) using the High Sensitivity DNA Kit (Agilent), and by qPCR with the Kapa Library quantification Kit (KapaBiosystems).

    Article Title: First Genome Sequence of Newcastle Disease Virus of Genotype VIIi from Jordan
    Article Snippet: RNA was reverse transcribed, and DNA libraries for next-generation sequencing (NGS) were prepared using the KAPA stranded RNA-Seq library preparation kit (Kapa Biosystems, USA) according to the manufacturer’s instructions. .. The size distribution and concentration of DNA in the prepared libraries were checked on a Bioanalyzer 2100 and a Qubit instrument using a high-sensitivity (HS) DNA kit (Agilent Technologies, Germany) and a Qubit double-stranded DNA (dsDNA) HS assay kit (Life Technologies, USA), respectively ( ).

    Multiple Annealing and Looping–Based Amplification Cycles:

    Article Title: Aneuploidy of chromosome 8 and mutation of circulating tumor cells predict pathologic complete response in the treatment of locally advanced rectal cancer
    Article Snippet: Each MALBAC product was diluted to 1 ng/µl. .. A BioAnalyzer High Sensitivity DNA kit (Agilent Technologies, Inc.) was used to visualize the size range of MALBAC products. .. Samples were injected into the separation channel and their components were electrophoretically separated.

    Spectrophotometry:

    Article Title: First Genome Sequence of Newcastle Disease Virus of Genotype VIIi from Jordan
    Article Snippet: RNA was quantified with spectrophotometry and Qubit (Invitrogen) fluorimetry. .. The size distribution and concentration of DNA in the prepared libraries were checked on a Bioanalyzer 2100 and a Qubit instrument using a high-sensitivity (HS) DNA kit (Agilent Technologies, Germany) and a Qubit double-stranded DNA (dsDNA) HS assay kit (Life Technologies, USA), respectively ( ).

    Article Title: Draft Genome of the Multidrug-Resistant Acinetobacter baumannii Strain A155 Clinical Isolate
    Article Snippet: The SYBR Green (Life Technologies, Grand Island, NY, USA) standard curve method was used to estimate DNA concentration for library preparation in a black 96-well plate (Corning, Tewksbury, MA, USA), and fluorescence values were obtained using a FilterMax F5 spectrophotometer with Multi-Mode Analysis software version 3.4.0.25 (Molecular Devices, Sunnyvale, CA, USA). .. The Bioanalyzer 2100 High Sensitivity DNA analysis kit (Agilent Technologies, Santa Clara, CA, USA) with version B.02.08.SI648 software was used to determine the fragmentation of the resultant libraries.

    Concentration Assay:

    Article Title: Physiological Expression of Ion Channel Receptors in Human Periodontal Ligament Stem Cells
    Article Snippet: The Bioanalyzer instrument (Agilent High Sensitivity DNA Kit, Richardson, TX, USA) was used to validate the quality of the library. .. The Bioanalyzer instrument (Agilent High Sensitivity DNA Kit, Richardson, TX, USA) was used to validate the quality of the library.

    Article Title: Optimization of Extraction of Circulating RNAs from Plasma – Enabling Small RNA Sequencing
    Article Snippet: For the size selection of amplified cDNA libraries, PCR products were loaded on an agarose gel (4%), appropriate bands of approximately 135 bp to 160 bp in size were cut out and passed on to gel extraction with the MinElute Gel Extraction Kit (Qiagen, Germany). .. A concluding Bioanalyzer 2100 run with the High Sensitivity DNA Kit (Agilent Technologies, Germany) that allows the analysis of DNA libraries regarding size, purity and concentration completed the workflow of library preparation. .. The obtained sequence libraries were subjected to the Illumina sequencing pipeline, passing through clonal cluster generation on a single-read flow cell (Illumina Inc., USA) by bridge amplification on the cBot (TruSeq SR Cluster Kit v3-cBOT-HS, Illumina Inc., USA) and 50 cycles sequencing-by-synthesis on the HiSeq2000 (Illumina Inc., USA).

    Article Title: Phase-defined complete sequencing of the HLA genes by next-generation sequencing
    Article Snippet: Briefly, PCR product was treated with the Tn5 transposase artificially loaded with synthetic oligonucleotides, enabling simultaneous fragmentation and addition of an adaptor. .. Each sample was dual indexed and equally pooled by evaluating the molar concentration by Agilent High Sensitivity DNA Kit and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). .. Fragments ranging from 500 to 2,000 bp (mean size: 1,561 bp), were selected from the pooled library by adding size fractionation step from agarose gel (Figure ).

    Article Title: Genome Sequencing of Museum Specimens Reveals Rapid Changes in the Genetic Composition of Honey Bees in California
    Article Snippet: A vacuum centrifuge concentrator was used to increase DNA concentration for samples with a Qubit reading less than 2.5 ng/µl. .. Library success was confirmed by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies).

    Article Title: First Genome Sequence of Newcastle Disease Virus of Genotype VIIi from Jordan
    Article Snippet: RNA was reverse transcribed, and DNA libraries for next-generation sequencing (NGS) were prepared using the KAPA stranded RNA-Seq library preparation kit (Kapa Biosystems, USA) according to the manufacturer’s instructions. .. The size distribution and concentration of DNA in the prepared libraries were checked on a Bioanalyzer 2100 and a Qubit instrument using a high-sensitivity (HS) DNA kit (Agilent Technologies, Germany) and a Qubit double-stranded DNA (dsDNA) HS assay kit (Life Technologies, USA), respectively ( ). .. Paired-end sequencing (2 × 250 bp) of the generated libraries was performed on a MiSeq instrument with the 500-cycle MiSeq reagent kit version 2 (Illumina, USA).

    Article Title: Construction and Characterization of Synthetic Bacterial Community for Experimental Ecology and Evolution
    Article Snippet: Sample indexing was performed in a volume of 20 μl containing 1.5 μl (5 μM) of each index primer (final concentration 0.375 μM), 10 μl of 2 × Phusion High-Fidelity PCR Master Mix (Thermo Fisher Scientific, Waltham, MA, United States) and 1 μl of pooled PCR product. .. The ready amplicon library was diluted to 1:10 and 1:20 and quantified with the Agilent 2100 Bioanalyzer High Sensitivity DNA Analysis Kit (Agilent Genomics, Santa Clara, CA, United States).

    Article Title: Draft Genome of the Multidrug-Resistant Acinetobacter baumannii Strain A155 Clinical Isolate
    Article Snippet: The SYBR Green (Life Technologies, Grand Island, NY, USA) standard curve method was used to estimate DNA concentration for library preparation in a black 96-well plate (Corning, Tewksbury, MA, USA), and fluorescence values were obtained using a FilterMax F5 spectrophotometer with Multi-Mode Analysis software version 3.4.0.25 (Molecular Devices, Sunnyvale, CA, USA). .. The Bioanalyzer 2100 High Sensitivity DNA analysis kit (Agilent Technologies, Santa Clara, CA, USA) with version B.02.08.SI648 software was used to determine the fragmentation of the resultant libraries.

    Gel Purification:

    Article Title: Current Protocols in Molecular Biology Unit 4.23
    Article Snippet: While much faster than the gel purification, the drawback of performing two additional rounds of SPRI size selection is that a several-fold greater amount of initial material is required to offset the loss of material during the purification, in order to obtain a comparable amount of quality DNA libraries suitable for sequencing. .. After purification by an 8% polyacrylamide gel, a DNA library can be quantified by Agilent Bioanalyzer analysis (High-sensitivity DNA Kit) as well as by Quantitative-PCR (Q-PCR) analysis by comparison to previously calibrated/sequenced DNA libraries using Q-PCR checking primers F and R ( ).

    FACS:

    Article Title: Genetic analysis of Ikaros target genes and tumor suppressor function in BCR-ABL1+ pre–B ALL
    Article Snippet: ATAC-Seq was performed as previously described ( ) on 50,000 WT Ikaros or GFP control FACS sorted cells. .. Libraries were purified with AMPure beads (Agencourt) and library quality was assessed using the Agilent Bioanalyzer High-Sensitivity DNA kit.

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    Agilent technologies high sensitivity dna kit
    Changes in the <t>cfDNA</t> concentration during systemic therapy (A) Change in the cfDNA concentration from baseline to first response assessment, according to the radiological response category. (B) Waterfall plot for the percentage change in the cfDNA concentration at first response assessment. (C) Change in the cfDNA concentration from baseline to the radiological best response, according to the radiological best response category. (D) Waterfall plot for the percentage change in the cfDNA concentration at assessment of radiological best response. cfDNA, cell-free <t>DNA;</t> NSCLC, non-small-cell lung cancer; PR, partial response; SD, stable disease; PD, progression of disease * Kruskal-Wallis test among PR, SD and PD groups ** Data are expressed as the median, followed by the interquartile range in parentheses *** Wilcoxon signed rank test between the cfDNA concentration at baseline and at first follow-up assessment or best response.
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    Changes in the cfDNA concentration during systemic therapy (A) Change in the cfDNA concentration from baseline to first response assessment, according to the radiological response category. (B) Waterfall plot for the percentage change in the cfDNA concentration at first response assessment. (C) Change in the cfDNA concentration from baseline to the radiological best response, according to the radiological best response category. (D) Waterfall plot for the percentage change in the cfDNA concentration at assessment of radiological best response. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PR, partial response; SD, stable disease; PD, progression of disease * Kruskal-Wallis test among PR, SD and PD groups ** Data are expressed as the median, followed by the interquartile range in parentheses *** Wilcoxon signed rank test between the cfDNA concentration at baseline and at first follow-up assessment or best response.

    Journal: Oncotarget

    Article Title: Quantification of circulating cell-free DNA to predict patient survival in non-small-cell lung cancer

    doi: 10.18632/oncotarget.21769

    Figure Lengend Snippet: Changes in the cfDNA concentration during systemic therapy (A) Change in the cfDNA concentration from baseline to first response assessment, according to the radiological response category. (B) Waterfall plot for the percentage change in the cfDNA concentration at first response assessment. (C) Change in the cfDNA concentration from baseline to the radiological best response, according to the radiological best response category. (D) Waterfall plot for the percentage change in the cfDNA concentration at assessment of radiological best response. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PR, partial response; SD, stable disease; PD, progression of disease * Kruskal-Wallis test among PR, SD and PD groups ** Data are expressed as the median, followed by the interquartile range in parentheses *** Wilcoxon signed rank test between the cfDNA concentration at baseline and at first follow-up assessment or best response.

    Article Snippet: After cfDNA extraction, the purity of the cfDNA was measured with an Agilent High Sensitivity DNA kit and a Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA, USA).

    Techniques: Concentration Assay

    Study flow diagram cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer, ADC, adenocarcinoma.

    Journal: Oncotarget

    Article Title: Quantification of circulating cell-free DNA to predict patient survival in non-small-cell lung cancer

    doi: 10.18632/oncotarget.21769

    Figure Lengend Snippet: Study flow diagram cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer, ADC, adenocarcinoma.

    Article Snippet: After cfDNA extraction, the purity of the cfDNA was measured with an Agilent High Sensitivity DNA kit and a Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA, USA).

    Techniques: Flow Cytometry

    Kaplan-Meier estimates of PFS and OS according to the cfDNA concentration in patients with NSCLC (A) PFS and (B) OS according to the baseline cfDNA concentration (≤ 70 ng/mL vs. > 70 ng/mL) in all patients with NSCLC. (C) PFS and (D) OS according to the baseline cfDNA concentration (≤ 70 ng/mL vs. > 70 ng/mL) in chemo-naive patients with stage IV adenocarcinoma. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PFS, progression-free survival; OS, overall survival.

    Journal: Oncotarget

    Article Title: Quantification of circulating cell-free DNA to predict patient survival in non-small-cell lung cancer

    doi: 10.18632/oncotarget.21769

    Figure Lengend Snippet: Kaplan-Meier estimates of PFS and OS according to the cfDNA concentration in patients with NSCLC (A) PFS and (B) OS according to the baseline cfDNA concentration (≤ 70 ng/mL vs. > 70 ng/mL) in all patients with NSCLC. (C) PFS and (D) OS according to the baseline cfDNA concentration (≤ 70 ng/mL vs. > 70 ng/mL) in chemo-naive patients with stage IV adenocarcinoma. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PFS, progression-free survival; OS, overall survival.

    Article Snippet: After cfDNA extraction, the purity of the cfDNA was measured with an Agilent High Sensitivity DNA kit and a Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA, USA).

    Techniques: Concentration Assay

    Circulating cfDNA time points coded by NSCLC patient identification number Graphical presentation of the association between the cfDNA level and the assessment of radiological response in patients with disease progression (A) and without progression (B) Change in the cfDNA concentration from baseline to best response, according to the radiological best response category; x-axis displays the time to clinical tumor progression. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PR, partial response; SD, stable disease; PD, progression of disease * Kruskal-Wallis test among PR, SD and PD groups ** Data are expressed as the median, followed by the interquartile range in parentheses *** Wilcoxon signed rank test between the cfDNA concentration at baseline and at best response.

    Journal: Oncotarget

    Article Title: Quantification of circulating cell-free DNA to predict patient survival in non-small-cell lung cancer

    doi: 10.18632/oncotarget.21769

    Figure Lengend Snippet: Circulating cfDNA time points coded by NSCLC patient identification number Graphical presentation of the association between the cfDNA level and the assessment of radiological response in patients with disease progression (A) and without progression (B) Change in the cfDNA concentration from baseline to best response, according to the radiological best response category; x-axis displays the time to clinical tumor progression. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PR, partial response; SD, stable disease; PD, progression of disease * Kruskal-Wallis test among PR, SD and PD groups ** Data are expressed as the median, followed by the interquartile range in parentheses *** Wilcoxon signed rank test between the cfDNA concentration at baseline and at best response.

    Article Snippet: After cfDNA extraction, the purity of the cfDNA was measured with an Agilent High Sensitivity DNA kit and a Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA, USA).

    Techniques: Concentration Assay

    Circulating cfDNA kinetics in patients with NSCLCQuantitative cfDNA dynamics during treatment for NSCLC (A) Change in the cfDNA concentration from baseline to disease progression, according to the radiological best response category. (B) Change in the cfDNA concentration from the previous level to disease progression, according to the radiological best response category. Colors and symbols in the panel represent individual patient cfDNA kinetics; x-axis displays the time to clinical tumor progression. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PR, partial response; SD, stable disease; PD, progression of disease * Kruskal-Wallis test among PR, SD and PD groups ** Data are expressed as the median, followed by the interquartile range in parentheses. *** Wilcoxon signed rank test between the cfDNA level at disease progression and the baseline or previous cfDNA level.

    Journal: Oncotarget

    Article Title: Quantification of circulating cell-free DNA to predict patient survival in non-small-cell lung cancer

    doi: 10.18632/oncotarget.21769

    Figure Lengend Snippet: Circulating cfDNA kinetics in patients with NSCLCQuantitative cfDNA dynamics during treatment for NSCLC (A) Change in the cfDNA concentration from baseline to disease progression, according to the radiological best response category. (B) Change in the cfDNA concentration from the previous level to disease progression, according to the radiological best response category. Colors and symbols in the panel represent individual patient cfDNA kinetics; x-axis displays the time to clinical tumor progression. cfDNA, cell-free DNA; NSCLC, non-small-cell lung cancer; PR, partial response; SD, stable disease; PD, progression of disease * Kruskal-Wallis test among PR, SD and PD groups ** Data are expressed as the median, followed by the interquartile range in parentheses. *** Wilcoxon signed rank test between the cfDNA level at disease progression and the baseline or previous cfDNA level.

    Article Snippet: After cfDNA extraction, the purity of the cfDNA was measured with an Agilent High Sensitivity DNA kit and a Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA, USA).

    Techniques: Concentration Assay

    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: Concentrated maternal cfDNA was analyzed by Agilent Bioanalyzer 2100 instrument and Agilent DNA High Sensitivity Kit following manufacturer’s recommended protocol.

    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: Concentrated maternal cfDNA was analyzed by Agilent Bioanalyzer 2100 instrument and Agilent DNA High Sensitivity Kit following manufacturer’s recommended protocol.

    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: Concentrated maternal cfDNA was analyzed by Agilent Bioanalyzer 2100 instrument and Agilent DNA High Sensitivity Kit following manufacturer’s recommended protocol.

    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