qubit 2 0 fluorometer  (Thermo Fisher)


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    Structured Review

    Thermo Fisher qubit 2 0 fluorometer
    Comparison of five automated DNA extraction systems. Illustration of relative DNA concentrations of samples 1–10 measured by the NanoDrop 2000c spectrophotometer (A) and Qubit 2.0 fluorometer (B). The concentrations of the Maxwell 16 extracts were set to 100% for each sample.
    Qubit 2 0 Fluorometer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 326 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/qubit 2 0 fluorometer/product/Thermo Fisher
    Average 99 stars, based on 326 article reviews
    Price from $9.99 to $1999.99
    qubit 2 0 fluorometer - by Bioz Stars, 2020-02
    99/100 stars

    Images

    1) Product Images from "Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics"

    Article Title: Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0104566

    Comparison of five automated DNA extraction systems. Illustration of relative DNA concentrations of samples 1–10 measured by the NanoDrop 2000c spectrophotometer (A) and Qubit 2.0 fluorometer (B). The concentrations of the Maxwell 16 extracts were set to 100% for each sample.
    Figure Legend Snippet: Comparison of five automated DNA extraction systems. Illustration of relative DNA concentrations of samples 1–10 measured by the NanoDrop 2000c spectrophotometer (A) and Qubit 2.0 fluorometer (B). The concentrations of the Maxwell 16 extracts were set to 100% for each sample.

    Techniques Used: DNA Extraction, Spectrophotometry

    2) Product Images from "Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics"

    Article Title: Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0104566

    Comparison of five automated DNA extraction systems. Illustration of relative DNA concentrations of samples 1–10 measured by the NanoDrop 2000c spectrophotometer (A) and Qubit 2.0 fluorometer (B). The concentrations of the Maxwell 16 extracts were set to 100% for each sample.
    Figure Legend Snippet: Comparison of five automated DNA extraction systems. Illustration of relative DNA concentrations of samples 1–10 measured by the NanoDrop 2000c spectrophotometer (A) and Qubit 2.0 fluorometer (B). The concentrations of the Maxwell 16 extracts were set to 100% for each sample.

    Techniques Used: DNA Extraction, Spectrophotometry

    3) Product Images from "Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics"

    Article Title: Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0104566

    Comparison of five automated DNA extraction systems. Illustration of relative DNA concentrations of samples 1–10 measured by the NanoDrop 2000c spectrophotometer (A) and Qubit 2.0 fluorometer (B). The concentrations of the Maxwell 16 extracts were set to 100% for each sample.
    Figure Legend Snippet: Comparison of five automated DNA extraction systems. Illustration of relative DNA concentrations of samples 1–10 measured by the NanoDrop 2000c spectrophotometer (A) and Qubit 2.0 fluorometer (B). The concentrations of the Maxwell 16 extracts were set to 100% for each sample.

    Techniques Used: DNA Extraction, Spectrophotometry

    Related Articles

    Centrifugation:

    Article Title: Phase I/II clinical trial of everolimus combined with gemcitabine/cisplatin for metastatic triple-negative breast cancer
    Article Snippet: Sample collection and PI3KCA mutation detection by ddPCR Pre-treatment blood samples (5 mL) were obtained in serum separator tubes (SST), and serum was obtained by centrifugation of the SST at 2000 ×g for 10 min. Serum was aliquoted and stored at -80℃ until analysis. .. CfDNA from 800 µl of serum was extracted with the QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol. cfDNA was quantified using the Qubit 2.0 Fluorometer with the Qubit dsDNA HS (High Sensitivity) Assay Kit (Life Technologies, Carlsbad, CA, USA).

    Amplification:

    Article Title: Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health
    Article Snippet: Paragraph title: PCR amplification and sequencing ... The libraries were further quantified on a Qubit 2.0 fluorometer using Qubit dsDNA HS kit (Life technologies, USA) and by qPCR using KAPA SYBR FAST qPCR Master mix and Illumina standards and primer premix (KAPA Biosystems, Wilmington, MA, USA) following the Illumina suggested protocol.

    Article Title: Dynamics of coral‐associated microbiomes during a thermal bleaching event, et al. Dynamics of coral‐associated microbiomes during a thermal bleaching event
    Article Snippet: Paragraph title: DNA extraction, 16S rRNA gene and ITS amplification, and PacBio sequencing ... Final PCR products were purified, using Agentcourt AMPure XP magnetic beads (Beckman Coulter, Indianapolis, IN) and quantified using the Qubit 2.0 Fluorometer and the Qubit dsDNA BR Assay Kit (Thermo Fisher Scientific).

    Article Title: Exercise training causes differential changes in gene expression in diaphragm arteries and 2A arterioles of obese rats
    Article Snippet: Paragraph title: Illumina library preparation (SMARTer amplification and RNA-seq). ... Library quantitation was performed using the Qubit 2.0 fluorometer and the High Sensitivity DNA assay (Life Tech, cat. no. ).

    Article Title: Identification of Nitrogen-Fixing Bradyrhizobium Associated With Roots of Field-Grown Sorghum by Metagenome and Proteome Analyses
    Article Snippet: In the second round of PCR, the first-round PCR products were amplified using the above sequencing priming sites as PCR priming sites by adding dual-index tag sequences and flow cell binding sites of the Illumina adapter. .. The purified tag-indexed PCR products were quantified by using a Qubit 2.0 Fluorometer and dsDNA HS Assay Kit (Life Technologies, Carlsbad, CA, United States).

    Expressing:

    Article Title: Glial cell type-specific changes in spinal dipeptidyl peptidase 4 expression and effects of its inhibitors in inflammatory and neuropatic pain
    Article Snippet: Concentration of the generated cDNA was determined using the Qubit 2.0 Fluorometer with the Qubit ssDNA Assay Kit (Life Technologies). .. Expression of DPP4 mRNA was measured by real-time quantitative TaqMan RT-PCR reaction with a ViiA 7 Real-Time PCR System (Life Technologies), using commercially available TaqMan probe (Rn00562910_n1) on 10-ng cDNA template in duplicates.

    Polymerase Chain Reaction:

    Article Title: Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health
    Article Snippet: Paragraph title: PCR amplification and sequencing ... The libraries were further quantified on a Qubit 2.0 fluorometer using Qubit dsDNA HS kit (Life technologies, USA) and by qPCR using KAPA SYBR FAST qPCR Master mix and Illumina standards and primer premix (KAPA Biosystems, Wilmington, MA, USA) following the Illumina suggested protocol.

    Article Title: Dynamics of coral‐associated microbiomes during a thermal bleaching event, et al. Dynamics of coral‐associated microbiomes during a thermal bleaching event
    Article Snippet: .. Final PCR products were purified, using Agentcourt AMPure XP magnetic beads (Beckman Coulter, Indianapolis, IN) and quantified using the Qubit 2.0 Fluorometer and the Qubit dsDNA BR Assay Kit (Thermo Fisher Scientific). .. Purified 16S/ITS amplicons were pooled in equimolar concentrations, and 500 ng of DNA was used for library preparation.

    Article Title: Exercise training causes differential changes in gene expression in diaphragm arteries and 2A arterioles of obese rats
    Article Snippet: Ligated DNA was purified (2×) with 1.0 × SPRI to remove adapter dimers and perform gel-free size selection, and then amplified through 14 cycles of PCR. .. Library quantitation was performed using the Qubit 2.0 fluorometer and the High Sensitivity DNA assay (Life Tech, cat. no. ).

    Article Title: Highly multiplexed targeted DNA sequencing from single nuclei
    Article Snippet: .. Bio-Rad T100 thermal cycler (Bio-Rad, cat. no. 186-1096) PCR strips, 0.2 ml: Thermo Scientific 0.2-ml Thermo-Strip (Thermo Scientific, cat. no. AB-1182) Pulse-spinning: Denville mini-mouse II microcentrifuge (Denville, cat. no. C0801-N) Tube, 1.5 ml: Sigma-Aldrich Eppendorf Safe-Lock microcentrifuge tubes (Sigma-Aldrich, cat. no. T9661) Nylon mesh filter, 36 μm (Small Parts, cat. no. CMN-0035-D) Polystyrene round-bottom tube, 5 ml (BD Falcon, cat. no. 352058) Feather disposable scalpel no. 11 (Graham-Field, cat. no. 2975#11) Cell culture dish, 60 × 15mm (Corning, cat. no. 430196) FACSAria II (BD Biosciences) SPHERO Supra rainbow midrange fluorescent particles (Spherotech, cat. no. 556298) PCR plate, 96 well: Thermo-tube plate (Thermo Scientific, cat. no. AB-0731) Adhesive sealing sheets (Thermo Scientific, cat. no. AB-0558) Cold block: Eppendorf PCR cooler iceless cold storage system for a 96-well plate and PCR tubes (Sigma-Aldrich, cat. no. Z606634-1EA) ▲ CRITICAL Place the cold block at −20 °C 1 h before use. accuSpin micro 17 microcentrifuge (Fisher Scientific, cat. no. 13-100-675) Zymo DNA Clean & Concentrator-5 columns kit (Zymo, cat. no. D4004) Qubit 2.0 fluorometer (Invitrogen, cat. no. ) Covaris microTUBE AFA fiber pre-slit snap-cap (Covaris, cat. no. 520045) Covaris S220 sonicator (Covaris) PRISM real-time machine (ABI 7900HT) MicroAmp optical 96-well reaction plate (ABI B8010560) ThermalSeal RT2 film for qPCR (Phenix LMT-RT) Digital dry block heater (VWR International, cat. no. 12621-084) Precision digital circulating water bath (Thermo Scientific, cat. no. 2864) Polypropylene tubes, 0.5 ml (USA Scientific, cat. no. 1405-8100) Magnetic separation rack, six tube (NEB, cat. no. S1506S) Magnetic plate, 96 well (Alpaqua, cat. no. A01322) Digital SpeedVac modular concentrator (Thermo Scientific, cat. no. SPD111V-115) .. Mix 800 ml of NST solution (146 mM NaCl, 10 mM Tris base (pH 7.8), 1 mM CaCl2 , 21 mM MgCl2 , 0.05% (wt/vol) BSA and 0.2% (vol/vol) Nonidet P-40) with 200 ml of DAPI solution (106 mM MgCl2 and 10 mg of DAPI).

    Article Title: Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing
    Article Snippet: DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen, Redwood City, CA, USA) and eluted into 50 μL of PCR-grade water. .. Following extraction, DNA concentrations were determined using a Qubit 2.0 Fluorometer with the Qubit dsDNA High Sensitivity Assay Kit (Life Technologies, Grand Island, NY, USA).

    Article Title: Identification of Nitrogen-Fixing Bradyrhizobium Associated With Roots of Field-Grown Sorghum by Metagenome and Proteome Analyses
    Article Snippet: .. The purified tag-indexed PCR products were quantified by using a Qubit 2.0 Fluorometer and dsDNA HS Assay Kit (Life Technologies, Carlsbad, CA, United States). .. Samples were then pooled in equal amounts and sequenced by using a 250-bp paired-end sequencing protocol with the MiSeq Sequencing Reagent Kit v. 2 (Illumina) at Bioengineering Lab Co., Ltd., (Kanagawa, Japan).

    Construct:

    Article Title: Dynamics of coral‐associated microbiomes during a thermal bleaching event, et al. Dynamics of coral‐associated microbiomes during a thermal bleaching event
    Article Snippet: Final PCR products were purified, using Agentcourt AMPure XP magnetic beads (Beckman Coulter, Indianapolis, IN) and quantified using the Qubit 2.0 Fluorometer and the Qubit dsDNA BR Assay Kit (Thermo Fisher Scientific). .. A total of two SMRTbell libraries were constructed (each containing amplicons from 9 to 10 samples) and sequenced on a PacBio RSII system, using the P6‐C4 polymerase and chemistry with a 360‐min movie time.

    Article Title: Exercise training causes differential changes in gene expression in diaphragm arteries and 2A arterioles of obese rats
    Article Snippet: The final sequencing construct was purified with a 1.0 × SPRI to remove low-molecular-weight adapter dimer artifacts (if any), and libraries were validated to contain ∼330-bp fragments using the Bioanalyzer 2100 High Sensitivity DNA Assay. .. Library quantitation was performed using the Qubit 2.0 fluorometer and the High Sensitivity DNA assay (Life Tech, cat. no. ).

    Electrophoresis:

    Article Title: Methylome Characterization of Burkholderia pseudomallei Strain 982 at Single-Base Resolution
    Article Snippet: .. The quantity and quality of the extracted genomic DNA were measured using a Qubit 2.0 fluorometer and a NanoDrop 2000 spectrophotometer (both Thermo Fisher Scientific, Waltham, MA, USA) and a Pippin Pulse electrophoresis power supply (Sage Science, Beverly, MA, USA), respectively ( ). .. Genomic DNA (10 μg) was sheared using a g-TUBE (Covaris, Woburn, Massachusetts, USA).

    Quantitation Assay:

    Article Title: Exercise training causes differential changes in gene expression in diaphragm arteries and 2A arterioles of obese rats
    Article Snippet: .. Library quantitation was performed using the Qubit 2.0 fluorometer and the High Sensitivity DNA assay (Life Tech, cat. no. ). .. As previously described ( , , ), large-scale multiplexing (48 bar codes) was used to form many library pools that were later sequenced.

    Formalin-fixed Paraffin-Embedded:

    Article Title: Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics
    Article Snippet: DNA quantification methods The DNA of 16 previously extracted FFPE tissue blocks were analysed with five different quantification methods. .. In samples 4, 5, 6 and 7 the Qubit 2.0 fluorometer measured the highest DNA concentrations, in sample 10, 15 and 16 the Quant-iT PicoGreen dsDNA reagent measurement gave the highest values, in sample 2 the qPCR and in all other samples the NanoDrop 2000c spectrophotometer estimated the highest DNA concentrations.

    Article Title: Phase I/II clinical trial of everolimus combined with gemcitabine/cisplatin for metastatic triple-negative breast cancer
    Article Snippet: CfDNA from 800 µl of serum was extracted with the QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol. cfDNA was quantified using the Qubit 2.0 Fluorometer with the Qubit dsDNA HS (High Sensitivity) Assay Kit (Life Technologies, Carlsbad, CA, USA). .. For formalin-fixed paraffin-embedded (FFPE) tumor samples, genomic DNA was extracted using the QIAamp DNA FFPE Tissue kit (Qiagen, Hilden, Germany).

    Cell Culture:

    Article Title: Highly multiplexed targeted DNA sequencing from single nuclei
    Article Snippet: .. Bio-Rad T100 thermal cycler (Bio-Rad, cat. no. 186-1096) PCR strips, 0.2 ml: Thermo Scientific 0.2-ml Thermo-Strip (Thermo Scientific, cat. no. AB-1182) Pulse-spinning: Denville mini-mouse II microcentrifuge (Denville, cat. no. C0801-N) Tube, 1.5 ml: Sigma-Aldrich Eppendorf Safe-Lock microcentrifuge tubes (Sigma-Aldrich, cat. no. T9661) Nylon mesh filter, 36 μm (Small Parts, cat. no. CMN-0035-D) Polystyrene round-bottom tube, 5 ml (BD Falcon, cat. no. 352058) Feather disposable scalpel no. 11 (Graham-Field, cat. no. 2975#11) Cell culture dish, 60 × 15mm (Corning, cat. no. 430196) FACSAria II (BD Biosciences) SPHERO Supra rainbow midrange fluorescent particles (Spherotech, cat. no. 556298) PCR plate, 96 well: Thermo-tube plate (Thermo Scientific, cat. no. AB-0731) Adhesive sealing sheets (Thermo Scientific, cat. no. AB-0558) Cold block: Eppendorf PCR cooler iceless cold storage system for a 96-well plate and PCR tubes (Sigma-Aldrich, cat. no. Z606634-1EA) ▲ CRITICAL Place the cold block at −20 °C 1 h before use. accuSpin micro 17 microcentrifuge (Fisher Scientific, cat. no. 13-100-675) Zymo DNA Clean & Concentrator-5 columns kit (Zymo, cat. no. D4004) Qubit 2.0 fluorometer (Invitrogen, cat. no. ) Covaris microTUBE AFA fiber pre-slit snap-cap (Covaris, cat. no. 520045) Covaris S220 sonicator (Covaris) PRISM real-time machine (ABI 7900HT) MicroAmp optical 96-well reaction plate (ABI B8010560) ThermalSeal RT2 film for qPCR (Phenix LMT-RT) Digital dry block heater (VWR International, cat. no. 12621-084) Precision digital circulating water bath (Thermo Scientific, cat. no. 2864) Polypropylene tubes, 0.5 ml (USA Scientific, cat. no. 1405-8100) Magnetic separation rack, six tube (NEB, cat. no. S1506S) Magnetic plate, 96 well (Alpaqua, cat. no. A01322) Digital SpeedVac modular concentrator (Thermo Scientific, cat. no. SPD111V-115) .. Mix 800 ml of NST solution (146 mM NaCl, 10 mM Tris base (pH 7.8), 1 mM CaCl2 , 21 mM MgCl2 , 0.05% (wt/vol) BSA and 0.2% (vol/vol) Nonidet P-40) with 200 ml of DAPI solution (106 mM MgCl2 and 10 mg of DAPI).

    Mass Spectrometry:

    Article Title: Methylome Characterization of Burkholderia pseudomallei Strain 982 at Single-Base Resolution
    Article Snippet: The bacterial sample was identified using the analytical profile index (API) approach and a Microflex benchtop matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometer (Bruker Daltonik GmbH, Germany) ( ). .. The quantity and quality of the extracted genomic DNA were measured using a Qubit 2.0 fluorometer and a NanoDrop 2000 spectrophotometer (both Thermo Fisher Scientific, Waltham, MA, USA) and a Pippin Pulse electrophoresis power supply (Sage Science, Beverly, MA, USA), respectively ( ).

    Flow Cytometry:

    Article Title: Identification of Nitrogen-Fixing Bradyrhizobium Associated With Roots of Field-Grown Sorghum by Metagenome and Proteome Analyses
    Article Snippet: In the second round of PCR, the first-round PCR products were amplified using the above sequencing priming sites as PCR priming sites by adding dual-index tag sequences and flow cell binding sites of the Illumina adapter. .. The purified tag-indexed PCR products were quantified by using a Qubit 2.0 Fluorometer and dsDNA HS Assay Kit (Life Technologies, Carlsbad, CA, United States).

    Ligation:

    Article Title: Exercise training causes differential changes in gene expression in diaphragm arteries and 2A arterioles of obese rats
    Article Snippet: Fragment cDNA was end repaired and purified with 1.8 × SPRI beads to remove reaction components (Agencourt) and A-tailed in preparation for cohesive ligation to the Illumina specific sequencing adapters (NextFlex DNA Adapters, Bioo Scientific, cat. 514104). .. Library quantitation was performed using the Qubit 2.0 fluorometer and the High Sensitivity DNA assay (Life Tech, cat. no. ).

    Infection:

    Article Title: Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing
    Article Snippet: Universal parasite detection assay Aliquots of parasite-positive human blood samples at a volume of 200 μL were spiked 1:100 with C. felis -infected cat blood at a concentration of 1.7 million parasites per microliter. .. Following extraction, DNA concentrations were determined using a Qubit 2.0 Fluorometer with the Qubit dsDNA High Sensitivity Assay Kit (Life Technologies, Grand Island, NY, USA).

    Digital PCR:

    Article Title: Phase I/II clinical trial of everolimus combined with gemcitabine/cisplatin for metastatic triple-negative breast cancer
    Article Snippet: CfDNA from 800 µl of serum was extracted with the QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol. cfDNA was quantified using the Qubit 2.0 Fluorometer with the Qubit dsDNA HS (High Sensitivity) Assay Kit (Life Technologies, Carlsbad, CA, USA). .. PIK3CA mutations were detected by droplet digital PCR (ddPCR) in singleplex assays using inventoried assays for PIK3CA H1047R (dHsaCP2000077), E545K (dHsaCP2000075), and E542K (dHsaCP2000073) (BioRad, Hercules, CA, USA) on a BioRad QX200 Droplet Digital PCR System.

    Generated:

    Article Title: Glial cell type-specific changes in spinal dipeptidyl peptidase 4 expression and effects of its inhibitors in inflammatory and neuropatic pain
    Article Snippet: .. Concentration of the generated cDNA was determined using the Qubit 2.0 Fluorometer with the Qubit ssDNA Assay Kit (Life Technologies). .. Expression of DPP4 mRNA was measured by real-time quantitative TaqMan RT-PCR reaction with a ViiA 7 Real-Time PCR System (Life Technologies), using commercially available TaqMan probe (Rn00562910_n1) on 10-ng cDNA template in duplicates.

    Sequencing:

    Article Title: Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health
    Article Snippet: Paragraph title: PCR amplification and sequencing ... The libraries were further quantified on a Qubit 2.0 fluorometer using Qubit dsDNA HS kit (Life technologies, USA) and by qPCR using KAPA SYBR FAST qPCR Master mix and Illumina standards and primer premix (KAPA Biosystems, Wilmington, MA, USA) following the Illumina suggested protocol.

    Article Title: Methylome Characterization of Burkholderia pseudomallei Strain 982 at Single-Base Resolution
    Article Snippet: The quantity and quality of the extracted genomic DNA were measured using a Qubit 2.0 fluorometer and a NanoDrop 2000 spectrophotometer (both Thermo Fisher Scientific, Waltham, MA, USA) and a Pippin Pulse electrophoresis power supply (Sage Science, Beverly, MA, USA), respectively ( ). .. A 20-kb template library was prepared using the BluePippin size-selection system and sequenced using a Pacific Biosciences RS II platform in two runs of the same batch by using P5-C3 chemistry following the MagBead loading protocol (all Pacific Biosciences, Menlo Park, CA) ( , ), as this increases sequencing coverage, which will facilitate downstream analysis.

    Article Title: Dynamics of coral‐associated microbiomes during a thermal bleaching event, et al. Dynamics of coral‐associated microbiomes during a thermal bleaching event
    Article Snippet: Paragraph title: DNA extraction, 16S rRNA gene and ITS amplification, and PacBio sequencing ... Final PCR products were purified, using Agentcourt AMPure XP magnetic beads (Beckman Coulter, Indianapolis, IN) and quantified using the Qubit 2.0 Fluorometer and the Qubit dsDNA BR Assay Kit (Thermo Fisher Scientific).

    Article Title: Exercise training causes differential changes in gene expression in diaphragm arteries and 2A arterioles of obese rats
    Article Snippet: The final sequencing construct was purified with a 1.0 × SPRI to remove low-molecular-weight adapter dimer artifacts (if any), and libraries were validated to contain ∼330-bp fragments using the Bioanalyzer 2100 High Sensitivity DNA Assay. .. Library quantitation was performed using the Qubit 2.0 fluorometer and the High Sensitivity DNA assay (Life Tech, cat. no. ).

    Article Title: Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics
    Article Snippet: .. Other studies showed that a combination of fluorescent dye-based quantification systems such as the Qubit 2.0 fluorometer with a spectrophotometric system like the NanoDrop 2000c spectrophotometer is the most accurate method for assessing the quantity and purity of DNA and can also be used for the massively parallel sequencing workflow . .. However, none of the studies gave a comprehensive comparison of more than three quantification methods using UV spectrophotometry, fluorescent dye-based quantification and qPCR.

    Article Title: Identification of Nitrogen-Fixing Bradyrhizobium Associated With Roots of Field-Grown Sorghum by Metagenome and Proteome Analyses
    Article Snippet: In the second round of PCR, the first-round PCR products were amplified using the above sequencing priming sites as PCR priming sites by adding dual-index tag sequences and flow cell binding sites of the Illumina adapter. .. The purified tag-indexed PCR products were quantified by using a Qubit 2.0 Fluorometer and dsDNA HS Assay Kit (Life Technologies, Carlsbad, CA, United States).

    Binding Assay:

    Article Title: Identification of Nitrogen-Fixing Bradyrhizobium Associated With Roots of Field-Grown Sorghum by Metagenome and Proteome Analyses
    Article Snippet: In the second round of PCR, the first-round PCR products were amplified using the above sequencing priming sites as PCR priming sites by adding dual-index tag sequences and flow cell binding sites of the Illumina adapter. .. The purified tag-indexed PCR products were quantified by using a Qubit 2.0 Fluorometer and dsDNA HS Assay Kit (Life Technologies, Carlsbad, CA, United States).

    DNA Extraction:

    Article Title: Genomic Context of Azole Resistance Mutations in Aspergillus fumigatus Determined Using Whole-Genome Sequencing
    Article Snippet: Paragraph title: DNA extraction and quality assessment. ... Harvested conidia were homogenized using 1.0-mm-diameter zirconia/silica beads (BioSpec Products, Bartlesville, OK) in a FastPrep-24 system (MP Biomedicals, Solon, OH) at 4.5 m/s for 45 s. Genomic DNA (gDNA) was quantified using a Qubit 2.0 fluorometer and dsDNA BR (double-stranded DNA, broad-range) assay kit (Life Technologies, Carlsbad, CA).

    Article Title: Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics
    Article Snippet: Samples 5 and 6, which were small biopsies, showed the highest difference between their Qubit 2.0 fluorometer and NanoDrop 2000c spectrophotometer values of the BioRobot M48, the QIAcube, the QIAsymphony SP and the InnuPure C16 extracts in relation to the Maxwell 16 extracts. .. The purity ratio 260/280 nm of all samples except sample 5 and 6 were for all five automated DNA extraction systems around 1.8–2.0.

    Article Title: Selective demethylation of two CpG sites causes postnatal activation of the Dao gene and consequent removal of d-serine within the mouse cerebellum
    Article Snippet: Paragraph title: DNA extraction from tissues ... DNA was quality checked using NanoDrop 2000, (Thermo Scientific) and quantified using Qubit 2.0 Fluorometer with the dsDNA broad range assay kit (Invitrogen, Q32850).

    Article Title: Dynamics of coral‐associated microbiomes during a thermal bleaching event, et al. Dynamics of coral‐associated microbiomes during a thermal bleaching event
    Article Snippet: Paragraph title: DNA extraction, 16S rRNA gene and ITS amplification, and PacBio sequencing ... Final PCR products were purified, using Agentcourt AMPure XP magnetic beads (Beckman Coulter, Indianapolis, IN) and quantified using the Qubit 2.0 Fluorometer and the Qubit dsDNA BR Assay Kit (Thermo Fisher Scientific).

    Article Title: Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics
    Article Snippet: This is the first study comparing different automated DNA extraction systems with FFPE material. .. Other studies showed that a combination of fluorescent dye-based quantification systems such as the Qubit 2.0 fluorometer with a spectrophotometric system like the NanoDrop 2000c spectrophotometer is the most accurate method for assessing the quantity and purity of DNA and can also be used for the massively parallel sequencing workflow .

    Article Title: Development of a Highly Sensitive FcMito qPCR Assay for the Quantification of the Toxigenic Fungal Plant Pathogen Fusarium culmorum
    Article Snippet: Paragraph title: 4.3. DNA Extraction ... A Qubit® 2.0 Fluorometer and a Qubit® dsDNA BR Assay (Invitrogen, Carlsbad, CA, USA) were used to determine fungal and plant DNA concentrations according to the manufacturer’s recommendations.

    RNA Sequencing Assay:

    Article Title: Exercise training causes differential changes in gene expression in diaphragm arteries and 2A arterioles of obese rats
    Article Snippet: Paragraph title: Illumina library preparation (SMARTer amplification and RNA-seq). ... Library quantitation was performed using the Qubit 2.0 fluorometer and the High Sensitivity DNA assay (Life Tech, cat. no. ).

    Sensitive Assay:

    Article Title: Phase I/II clinical trial of everolimus combined with gemcitabine/cisplatin for metastatic triple-negative breast cancer
    Article Snippet: .. CfDNA from 800 µl of serum was extracted with the QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol. cfDNA was quantified using the Qubit 2.0 Fluorometer with the Qubit dsDNA HS (High Sensitivity) Assay Kit (Life Technologies, Carlsbad, CA, USA). .. For formalin-fixed paraffin-embedded (FFPE) tumor samples, genomic DNA was extracted using the QIAamp DNA FFPE Tissue kit (Qiagen, Hilden, Germany).

    Article Title: Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing
    Article Snippet: .. Following extraction, DNA concentrations were determined using a Qubit 2.0 Fluorometer with the Qubit dsDNA High Sensitivity Assay Kit (Life Technologies, Grand Island, NY, USA). .. One hundred fifty nanograms of DNA were subsequently digested via incubation with 20 units of BamHI-HF and 20 units of XmaI in 1X CutSmart Buffer (NEB) in a final volume of 50 μL for 2 h in a 37 °C water bath.

    Magnetic Beads:

    Article Title: Dynamics of coral‐associated microbiomes during a thermal bleaching event, et al. Dynamics of coral‐associated microbiomes during a thermal bleaching event
    Article Snippet: .. Final PCR products were purified, using Agentcourt AMPure XP magnetic beads (Beckman Coulter, Indianapolis, IN) and quantified using the Qubit 2.0 Fluorometer and the Qubit dsDNA BR Assay Kit (Thermo Fisher Scientific). .. Purified 16S/ITS amplicons were pooled in equimolar concentrations, and 500 ng of DNA was used for library preparation.

    Mutagenesis:

    Article Title: Phase I/II clinical trial of everolimus combined with gemcitabine/cisplatin for metastatic triple-negative breast cancer
    Article Snippet: Paragraph title: Sample collection and PI3KCA mutation detection by ddPCR ... CfDNA from 800 µl of serum was extracted with the QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol. cfDNA was quantified using the Qubit 2.0 Fluorometer with the Qubit dsDNA HS (High Sensitivity) Assay Kit (Life Technologies, Carlsbad, CA, USA).

    Isolation:

    Article Title: Glial cell type-specific changes in spinal dipeptidyl peptidase 4 expression and effects of its inhibitors in inflammatory and neuropatic pain
    Article Snippet: Paragraph title: RNA isolation and real-time PCR analyses ... Concentration of the generated cDNA was determined using the Qubit 2.0 Fluorometer with the Qubit ssDNA Assay Kit (Life Technologies).

    Article Title: Methylome Characterization of Burkholderia pseudomallei Strain 982 at Single-Base Resolution
    Article Snippet: This strain was originally isolated from the pus of a 13-year-old male patient on 21 March 2015 in Pahang, Malaysia. .. The quantity and quality of the extracted genomic DNA were measured using a Qubit 2.0 fluorometer and a NanoDrop 2000 spectrophotometer (both Thermo Fisher Scientific, Waltham, MA, USA) and a Pippin Pulse electrophoresis power supply (Sage Science, Beverly, MA, USA), respectively ( ).

    Detection Assay:

    Article Title: Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing
    Article Snippet: Paragraph title: Universal parasite detection assay ... Following extraction, DNA concentrations were determined using a Qubit 2.0 Fluorometer with the Qubit dsDNA High Sensitivity Assay Kit (Life Technologies, Grand Island, NY, USA).

    Purification:

    Article Title: Genomic Context of Azole Resistance Mutations in Aspergillus fumigatus Determined Using Whole-Genome Sequencing
    Article Snippet: Harvested conidia were homogenized using 1.0-mm-diameter zirconia/silica beads (BioSpec Products, Bartlesville, OK) in a FastPrep-24 system (MP Biomedicals, Solon, OH) at 4.5 m/s for 45 s. Genomic DNA (gDNA) was quantified using a Qubit 2.0 fluorometer and dsDNA BR (double-stranded DNA, broad-range) assay kit (Life Technologies, Carlsbad, CA). .. Purified gDNAs were stored at −20°C until further use.

    Article Title: Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health
    Article Snippet: After evaluating the amplified products on 2% w/v agarose gel, the products were purified using Ampure XP kit (Beckman Coulter, Brea, CA USA). .. The libraries were further quantified on a Qubit 2.0 fluorometer using Qubit dsDNA HS kit (Life technologies, USA) and by qPCR using KAPA SYBR FAST qPCR Master mix and Illumina standards and primer premix (KAPA Biosystems, Wilmington, MA, USA) following the Illumina suggested protocol.

    Article Title: Dynamics of coral‐associated microbiomes during a thermal bleaching event, et al. Dynamics of coral‐associated microbiomes during a thermal bleaching event
    Article Snippet: .. Final PCR products were purified, using Agentcourt AMPure XP magnetic beads (Beckman Coulter, Indianapolis, IN) and quantified using the Qubit 2.0 Fluorometer and the Qubit dsDNA BR Assay Kit (Thermo Fisher Scientific). .. Purified 16S/ITS amplicons were pooled in equimolar concentrations, and 500 ng of DNA was used for library preparation.

    Article Title: Exercise training causes differential changes in gene expression in diaphragm arteries and 2A arterioles of obese rats
    Article Snippet: The final sequencing construct was purified with a 1.0 × SPRI to remove low-molecular-weight adapter dimer artifacts (if any), and libraries were validated to contain ∼330-bp fragments using the Bioanalyzer 2100 High Sensitivity DNA Assay. .. Library quantitation was performed using the Qubit 2.0 fluorometer and the High Sensitivity DNA assay (Life Tech, cat. no. ).

    Article Title: Identification of Nitrogen-Fixing Bradyrhizobium Associated With Roots of Field-Grown Sorghum by Metagenome and Proteome Analyses
    Article Snippet: .. The purified tag-indexed PCR products were quantified by using a Qubit 2.0 Fluorometer and dsDNA HS Assay Kit (Life Technologies, Carlsbad, CA, United States). .. Samples were then pooled in equal amounts and sequenced by using a 250-bp paired-end sequencing protocol with the MiSeq Sequencing Reagent Kit v. 2 (Illumina) at Bioengineering Lab Co., Ltd., (Kanagawa, Japan).

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Glial cell type-specific changes in spinal dipeptidyl peptidase 4 expression and effects of its inhibitors in inflammatory and neuropatic pain
    Article Snippet: Concentration of the generated cDNA was determined using the Qubit 2.0 Fluorometer with the Qubit ssDNA Assay Kit (Life Technologies). .. Expression of DPP4 mRNA was measured by real-time quantitative TaqMan RT-PCR reaction with a ViiA 7 Real-Time PCR System (Life Technologies), using commercially available TaqMan probe (Rn00562910_n1) on 10-ng cDNA template in duplicates.

    Blocking Assay:

    Article Title: Highly multiplexed targeted DNA sequencing from single nuclei
    Article Snippet: .. Bio-Rad T100 thermal cycler (Bio-Rad, cat. no. 186-1096) PCR strips, 0.2 ml: Thermo Scientific 0.2-ml Thermo-Strip (Thermo Scientific, cat. no. AB-1182) Pulse-spinning: Denville mini-mouse II microcentrifuge (Denville, cat. no. C0801-N) Tube, 1.5 ml: Sigma-Aldrich Eppendorf Safe-Lock microcentrifuge tubes (Sigma-Aldrich, cat. no. T9661) Nylon mesh filter, 36 μm (Small Parts, cat. no. CMN-0035-D) Polystyrene round-bottom tube, 5 ml (BD Falcon, cat. no. 352058) Feather disposable scalpel no. 11 (Graham-Field, cat. no. 2975#11) Cell culture dish, 60 × 15mm (Corning, cat. no. 430196) FACSAria II (BD Biosciences) SPHERO Supra rainbow midrange fluorescent particles (Spherotech, cat. no. 556298) PCR plate, 96 well: Thermo-tube plate (Thermo Scientific, cat. no. AB-0731) Adhesive sealing sheets (Thermo Scientific, cat. no. AB-0558) Cold block: Eppendorf PCR cooler iceless cold storage system for a 96-well plate and PCR tubes (Sigma-Aldrich, cat. no. Z606634-1EA) ▲ CRITICAL Place the cold block at −20 °C 1 h before use. accuSpin micro 17 microcentrifuge (Fisher Scientific, cat. no. 13-100-675) Zymo DNA Clean & Concentrator-5 columns kit (Zymo, cat. no. D4004) Qubit 2.0 fluorometer (Invitrogen, cat. no. ) Covaris microTUBE AFA fiber pre-slit snap-cap (Covaris, cat. no. 520045) Covaris S220 sonicator (Covaris) PRISM real-time machine (ABI 7900HT) MicroAmp optical 96-well reaction plate (ABI B8010560) ThermalSeal RT2 film for qPCR (Phenix LMT-RT) Digital dry block heater (VWR International, cat. no. 12621-084) Precision digital circulating water bath (Thermo Scientific, cat. no. 2864) Polypropylene tubes, 0.5 ml (USA Scientific, cat. no. 1405-8100) Magnetic separation rack, six tube (NEB, cat. no. S1506S) Magnetic plate, 96 well (Alpaqua, cat. no. A01322) Digital SpeedVac modular concentrator (Thermo Scientific, cat. no. SPD111V-115) .. Mix 800 ml of NST solution (146 mM NaCl, 10 mM Tris base (pH 7.8), 1 mM CaCl2 , 21 mM MgCl2 , 0.05% (wt/vol) BSA and 0.2% (vol/vol) Nonidet P-40) with 200 ml of DAPI solution (106 mM MgCl2 and 10 mg of DAPI).

    Sample Prep:

    Article Title: Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health
    Article Snippet: The metagenomic libraries of the fungal and bacterial metagenomic DNA samples were prepared using Illumina Nextera XT sample preparation kit (Illumina Inc., USA). .. The libraries were further quantified on a Qubit 2.0 fluorometer using Qubit dsDNA HS kit (Life technologies, USA) and by qPCR using KAPA SYBR FAST qPCR Master mix and Illumina standards and primer premix (KAPA Biosystems, Wilmington, MA, USA) following the Illumina suggested protocol.

    Shotgun Sequencing:

    Article Title: Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health
    Article Snippet: Among the 140 subjects, 14 subjects with healthy scalp and 14 with dandruff scalp (28 subjects) were selected for shotgun metagenome sequencing of their bacterial and fungal DNA, based on the minimal DNA concentration ( > 0.2 ng/μl) required to carry out the library preparation for shotgun sequencing. .. The libraries were further quantified on a Qubit 2.0 fluorometer using Qubit dsDNA HS kit (Life technologies, USA) and by qPCR using KAPA SYBR FAST qPCR Master mix and Illumina standards and primer premix (KAPA Biosystems, Wilmington, MA, USA) following the Illumina suggested protocol.

    Real-time Polymerase Chain Reaction:

    Article Title: Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health
    Article Snippet: .. The libraries were further quantified on a Qubit 2.0 fluorometer using Qubit dsDNA HS kit (Life technologies, USA) and by qPCR using KAPA SYBR FAST qPCR Master mix and Illumina standards and primer premix (KAPA Biosystems, Wilmington, MA, USA) following the Illumina suggested protocol. .. Libraries in equal concentrations were loaded on Illumina NextSeq 500 platform using NextSeq 500/550 v2 sequencing reagent kit (Illumina Inc., USA) and 150 bp paired-end sequencing was performed for both types of libraries at the Next-Generation Sequencing (NGS) Facility, IISER Bhopal, India.

    Article Title: Glial cell type-specific changes in spinal dipeptidyl peptidase 4 expression and effects of its inhibitors in inflammatory and neuropatic pain
    Article Snippet: Paragraph title: RNA isolation and real-time PCR analyses ... Concentration of the generated cDNA was determined using the Qubit 2.0 Fluorometer with the Qubit ssDNA Assay Kit (Life Technologies).

    Article Title: Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics
    Article Snippet: .. In samples 4, 5, 6 and 7 the Qubit 2.0 fluorometer measured the highest DNA concentrations, in sample 10, 15 and 16 the Quant-iT PicoGreen dsDNA reagent measurement gave the highest values, in sample 2 the qPCR and in all other samples the NanoDrop 2000c spectrophotometer estimated the highest DNA concentrations. .. This is in contrast to other studies where the NanoDrop 2000c spectrophotometer always overestimated the DNA concentration .

    Article Title: Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics
    Article Snippet: Some studies state that quantitative PCR (qPCR) is the most accurate quantification method and that spectrophotometric analysis is the least reliable method for the detection of intact double stranded DNA . .. Other studies showed that a combination of fluorescent dye-based quantification systems such as the Qubit 2.0 fluorometer with a spectrophotometric system like the NanoDrop 2000c spectrophotometer is the most accurate method for assessing the quantity and purity of DNA and can also be used for the massively parallel sequencing workflow .

    Article Title: Highly multiplexed targeted DNA sequencing from single nuclei
    Article Snippet: .. Bio-Rad T100 thermal cycler (Bio-Rad, cat. no. 186-1096) PCR strips, 0.2 ml: Thermo Scientific 0.2-ml Thermo-Strip (Thermo Scientific, cat. no. AB-1182) Pulse-spinning: Denville mini-mouse II microcentrifuge (Denville, cat. no. C0801-N) Tube, 1.5 ml: Sigma-Aldrich Eppendorf Safe-Lock microcentrifuge tubes (Sigma-Aldrich, cat. no. T9661) Nylon mesh filter, 36 μm (Small Parts, cat. no. CMN-0035-D) Polystyrene round-bottom tube, 5 ml (BD Falcon, cat. no. 352058) Feather disposable scalpel no. 11 (Graham-Field, cat. no. 2975#11) Cell culture dish, 60 × 15mm (Corning, cat. no. 430196) FACSAria II (BD Biosciences) SPHERO Supra rainbow midrange fluorescent particles (Spherotech, cat. no. 556298) PCR plate, 96 well: Thermo-tube plate (Thermo Scientific, cat. no. AB-0731) Adhesive sealing sheets (Thermo Scientific, cat. no. AB-0558) Cold block: Eppendorf PCR cooler iceless cold storage system for a 96-well plate and PCR tubes (Sigma-Aldrich, cat. no. Z606634-1EA) ▲ CRITICAL Place the cold block at −20 °C 1 h before use. accuSpin micro 17 microcentrifuge (Fisher Scientific, cat. no. 13-100-675) Zymo DNA Clean & Concentrator-5 columns kit (Zymo, cat. no. D4004) Qubit 2.0 fluorometer (Invitrogen, cat. no. ) Covaris microTUBE AFA fiber pre-slit snap-cap (Covaris, cat. no. 520045) Covaris S220 sonicator (Covaris) PRISM real-time machine (ABI 7900HT) MicroAmp optical 96-well reaction plate (ABI B8010560) ThermalSeal RT2 film for qPCR (Phenix LMT-RT) Digital dry block heater (VWR International, cat. no. 12621-084) Precision digital circulating water bath (Thermo Scientific, cat. no. 2864) Polypropylene tubes, 0.5 ml (USA Scientific, cat. no. 1405-8100) Magnetic separation rack, six tube (NEB, cat. no. S1506S) Magnetic plate, 96 well (Alpaqua, cat. no. A01322) Digital SpeedVac modular concentrator (Thermo Scientific, cat. no. SPD111V-115) .. Mix 800 ml of NST solution (146 mM NaCl, 10 mM Tris base (pH 7.8), 1 mM CaCl2 , 21 mM MgCl2 , 0.05% (wt/vol) BSA and 0.2% (vol/vol) Nonidet P-40) with 200 ml of DAPI solution (106 mM MgCl2 and 10 mg of DAPI).

    Selection:

    Article Title: Exercise training causes differential changes in gene expression in diaphragm arteries and 2A arterioles of obese rats
    Article Snippet: Ligated DNA was purified (2×) with 1.0 × SPRI to remove adapter dimers and perform gel-free size selection, and then amplified through 14 cycles of PCR. .. Library quantitation was performed using the Qubit 2.0 fluorometer and the High Sensitivity DNA assay (Life Tech, cat. no. ).

    Article Title: Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing
    Article Snippet: Following extraction, DNA concentrations were determined using a Qubit 2.0 Fluorometer with the Qubit dsDNA High Sensitivity Assay Kit (Life Technologies, Grand Island, NY, USA). .. The Monarch kit enables template size selection (protocol dependent), and since there is uncertainty as to what the template size would be post-digestion, in most cases one sample aliquot was cleaned as a > 2 kb sample, and the second was cleaned as a < 2 kb sample according to the manufacturer’s instructions.

    Agarose Gel Electrophoresis:

    Article Title: Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health
    Article Snippet: After evaluating the amplified products on 2% w/v agarose gel, the products were purified using Ampure XP kit (Beckman Coulter, Brea, CA USA). .. The libraries were further quantified on a Qubit 2.0 fluorometer using Qubit dsDNA HS kit (Life technologies, USA) and by qPCR using KAPA SYBR FAST qPCR Master mix and Illumina standards and primer premix (KAPA Biosystems, Wilmington, MA, USA) following the Illumina suggested protocol.

    Article Title: Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics
    Article Snippet: In samples 4, 5, 6 and 7 the Qubit 2.0 fluorometer measured the highest DNA concentrations, in sample 10, 15 and 16 the Quant-iT PicoGreen dsDNA reagent measurement gave the highest values, in sample 2 the qPCR and in all other samples the NanoDrop 2000c spectrophotometer estimated the highest DNA concentrations. .. Relating these findings to a 1% agarose gel of the DNA extracts ( A) it could be seen that sample 6 and 11 have a high level of degraded DNA.

    Next-Generation Sequencing:

    Article Title: Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health
    Article Snippet: The libraries were further quantified on a Qubit 2.0 fluorometer using Qubit dsDNA HS kit (Life technologies, USA) and by qPCR using KAPA SYBR FAST qPCR Master mix and Illumina standards and primer premix (KAPA Biosystems, Wilmington, MA, USA) following the Illumina suggested protocol. .. Libraries in equal concentrations were loaded on Illumina NextSeq 500 platform using NextSeq 500/550 v2 sequencing reagent kit (Illumina Inc., USA) and 150 bp paired-end sequencing was performed for both types of libraries at the Next-Generation Sequencing (NGS) Facility, IISER Bhopal, India.

    Incubation:

    Article Title: Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing
    Article Snippet: Following extraction, DNA concentrations were determined using a Qubit 2.0 Fluorometer with the Qubit dsDNA High Sensitivity Assay Kit (Life Technologies, Grand Island, NY, USA). .. One hundred fifty nanograms of DNA were subsequently digested via incubation with 20 units of BamHI-HF and 20 units of XmaI in 1X CutSmart Buffer (NEB) in a final volume of 50 μL for 2 h in a 37 °C water bath.

    Spectrophotometry:

    Article Title: Glial cell type-specific changes in spinal dipeptidyl peptidase 4 expression and effects of its inhibitors in inflammatory and neuropatic pain
    Article Snippet: The purity and concentration of the RNA were analyzed using a SmartSpec Plus spectrophotometer (Bio-Rad, UK). .. Concentration of the generated cDNA was determined using the Qubit 2.0 Fluorometer with the Qubit ssDNA Assay Kit (Life Technologies).

    Article Title: Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics
    Article Snippet: .. Samples 5 and 6, which were small biopsies, showed the highest difference between their Qubit 2.0 fluorometer and NanoDrop 2000c spectrophotometer values of the BioRobot M48, the QIAcube, the QIAsymphony SP and the InnuPure C16 extracts in relation to the Maxwell 16 extracts. .. One explanation could be that these samples have a very low DNA concentration of below 10 ng/µl and it is commonly known that values below 10 ng/µl are less accurate with the NanoDrop 2000c spectrophotometer .

    Article Title: Methylome Characterization of Burkholderia pseudomallei Strain 982 at Single-Base Resolution
    Article Snippet: .. The quantity and quality of the extracted genomic DNA were measured using a Qubit 2.0 fluorometer and a NanoDrop 2000 spectrophotometer (both Thermo Fisher Scientific, Waltham, MA, USA) and a Pippin Pulse electrophoresis power supply (Sage Science, Beverly, MA, USA), respectively ( ). .. Genomic DNA (10 μg) was sheared using a g-TUBE (Covaris, Woburn, Massachusetts, USA).

    Article Title: Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics
    Article Snippet: .. In samples 4, 5, 6 and 7 the Qubit 2.0 fluorometer measured the highest DNA concentrations, in sample 10, 15 and 16 the Quant-iT PicoGreen dsDNA reagent measurement gave the highest values, in sample 2 the qPCR and in all other samples the NanoDrop 2000c spectrophotometer estimated the highest DNA concentrations. .. This is in contrast to other studies where the NanoDrop 2000c spectrophotometer always overestimated the DNA concentration .

    Article Title: Phase I/II clinical trial of everolimus combined with gemcitabine/cisplatin for metastatic triple-negative breast cancer
    Article Snippet: CfDNA from 800 µl of serum was extracted with the QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol. cfDNA was quantified using the Qubit 2.0 Fluorometer with the Qubit dsDNA HS (High Sensitivity) Assay Kit (Life Technologies, Carlsbad, CA, USA). .. DNA quantification was performed with a NanoDrop spectrophotometer (Thermo Scientific, Waltham, MA, USA).

    Article Title: Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics
    Article Snippet: .. Other studies showed that a combination of fluorescent dye-based quantification systems such as the Qubit 2.0 fluorometer with a spectrophotometric system like the NanoDrop 2000c spectrophotometer is the most accurate method for assessing the quantity and purity of DNA and can also be used for the massively parallel sequencing workflow . .. However, none of the studies gave a comprehensive comparison of more than three quantification methods using UV spectrophotometry, fluorescent dye-based quantification and qPCR.

    Concentration Assay:

    Article Title: Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health
    Article Snippet: Among the 140 subjects, 14 subjects with healthy scalp and 14 with dandruff scalp (28 subjects) were selected for shotgun metagenome sequencing of their bacterial and fungal DNA, based on the minimal DNA concentration ( > 0.2 ng/μl) required to carry out the library preparation for shotgun sequencing. .. The libraries were further quantified on a Qubit 2.0 fluorometer using Qubit dsDNA HS kit (Life technologies, USA) and by qPCR using KAPA SYBR FAST qPCR Master mix and Illumina standards and primer premix (KAPA Biosystems, Wilmington, MA, USA) following the Illumina suggested protocol.

    Article Title: Glial cell type-specific changes in spinal dipeptidyl peptidase 4 expression and effects of its inhibitors in inflammatory and neuropatic pain
    Article Snippet: .. Concentration of the generated cDNA was determined using the Qubit 2.0 Fluorometer with the Qubit ssDNA Assay Kit (Life Technologies). .. Expression of DPP4 mRNA was measured by real-time quantitative TaqMan RT-PCR reaction with a ViiA 7 Real-Time PCR System (Life Technologies), using commercially available TaqMan probe (Rn00562910_n1) on 10-ng cDNA template in duplicates.

    Article Title: Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics
    Article Snippet: Paragraph title: Quantification of DNA purity and concentration ... Samples 5 and 6, which were small biopsies, showed the highest difference between their Qubit 2.0 fluorometer and NanoDrop 2000c spectrophotometer values of the BioRobot M48, the QIAcube, the QIAsymphony SP and the InnuPure C16 extracts in relation to the Maxwell 16 extracts.

    Article Title: Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing
    Article Snippet: Universal parasite detection assay Aliquots of parasite-positive human blood samples at a volume of 200 μL were spiked 1:100 with C. felis -infected cat blood at a concentration of 1.7 million parasites per microliter. .. Following extraction, DNA concentrations were determined using a Qubit 2.0 Fluorometer with the Qubit dsDNA High Sensitivity Assay Kit (Life Technologies, Grand Island, NY, USA).

    DNA Purification:

    Article Title: Genomic Context of Azole Resistance Mutations in Aspergillus fumigatus Determined Using Whole-Genome Sequencing
    Article Snippet: High-molecular-weight DNA was extracted with an optimized MasterPure yeast DNA purification kit (Epicentre Biotechnologies, Cambridge, United Kingdom) with an additional bead-beating step included. .. Harvested conidia were homogenized using 1.0-mm-diameter zirconia/silica beads (BioSpec Products, Bartlesville, OK) in a FastPrep-24 system (MP Biomedicals, Solon, OH) at 4.5 m/s for 45 s. Genomic DNA (gDNA) was quantified using a Qubit 2.0 fluorometer and dsDNA BR (double-stranded DNA, broad-range) assay kit (Life Technologies, Carlsbad, CA).

    Article Title: Methylome Characterization of Burkholderia pseudomallei Strain 982 at Single-Base Resolution
    Article Snippet: This isolate was cultivated in lysogeny broth, and its genomic DNA was extracted using a MasterPure DNA purification kit (Epicentre, Madison, WI, USA). .. The quantity and quality of the extracted genomic DNA were measured using a Qubit 2.0 fluorometer and a NanoDrop 2000 spectrophotometer (both Thermo Fisher Scientific, Waltham, MA, USA) and a Pippin Pulse electrophoresis power supply (Sage Science, Beverly, MA, USA), respectively ( ).

    Randall–Selitto Test:

    Article Title: Glial cell type-specific changes in spinal dipeptidyl peptidase 4 expression and effects of its inhibitors in inflammatory and neuropatic pain
    Article Snippet: Development of inflammatory or neuropathic hyperalgesia was confirmed by the Randall-Selitto test, and then rats were sacrificed by decapitation, with a further 6 animals used as controls. .. Concentration of the generated cDNA was determined using the Qubit 2.0 Fluorometer with the Qubit ssDNA Assay Kit (Life Technologies).

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