quant it dsdna hs assay kit  (Thermo Fisher)


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    Name:
    Quant-iT 1X dsDNA HS Assay
    Description:
    The Quant-iT 1X dsDNA HS (High-Sensitivity) Assay Kit is designed to make DNA quantitation easy and accurate. The assay is highly selective for double-stranded DNA (dsDNA) over RNA and is designed to be accurate for initial sample concentrations from 10 pg/µL to 100 ng/µL. Common contaminants such as salts, free nucleotides, solvents, detergents, and protein are well tolerated in the assay. The "1X" dsDNA assay kit provides reagent and buffer in a formulation that is stable as a ready-to-use solution for up to one year after preparation. Simply add your sample (any volume between 1 µL and 20 µL is acceptable) and read the concentration using a fluorescent-based microplate reader.
    Catalog Number:
    Q33232
    Price:
    None
    Applications:
    DNA & RNA Purification & Analysis|DNA Quantitation|Nucleic Acid Quantitation
    Size:
    1000 assays
    Category:
    Kits and Assays, DNA⁄RNA Quantitation Assay Kits
    Score:
    85
    Buy from Supplier


    Structured Review

    Thermo Fisher quant it dsdna hs assay kit
    The effect of blood inhibitors and enhancers on PCR, melting temperature, and polymerase activity . (A) <t>DNA</t> fragment of NP_001035158.1 gene (Fr. 7; 735 bp; 73.1% GC) was amplified in PCR mix II supplemented with the corresponding primers, 37.5 μM hemoglobin and 0.2 M trehalose alone (T), 1 M 1,2-propanediol alone (P) or their combination (PT). PCR mix supplemented with H 2 O instead of enhancers served as a control (C'). A typical experiment of four performed is shown. (B) Melting temperature of GC-rich <t>dsDNA</t> oligonucleotide primer No 7, reverse, and the anti-primer (72.2% GC; 1 μM final concentration) in the presence (+) or absence (-) of hemoglobin (37.5 μM) and various enhancers (as in A). Melting temperature was determined as in Figure 6, except that SGI was used at higher concentration (1.32 μM). (C) Enzymatic activity of Taq DNA polymerase in PCR mix II buffer supplemented with (+) or without (-) 10% blood and various enhancers (as in A). Samples supplemented with H 2 O instead of enhancers (C') served as controls. Data in B and C indicate means ± S.D. (n = 4). Asterisks indicate statistically significant differences (P
    The Quant-iT 1X dsDNA HS (High-Sensitivity) Assay Kit is designed to make DNA quantitation easy and accurate. The assay is highly selective for double-stranded DNA (dsDNA) over RNA and is designed to be accurate for initial sample concentrations from 10 pg/µL to 100 ng/µL. Common contaminants such as salts, free nucleotides, solvents, detergents, and protein are well tolerated in the assay. The "1X" dsDNA assay kit provides reagent and buffer in a formulation that is stable as a ready-to-use solution for up to one year after preparation. Simply add your sample (any volume between 1 µL and 20 µL is acceptable) and read the concentration using a fluorescent-based microplate reader.
    https://www.bioz.com/result/quant it dsdna hs assay kit/product/Thermo Fisher
    Average 99 stars, based on 8 article reviews
    Price from $9.99 to $1999.99
    quant it dsdna hs assay kit - by Bioz Stars, 2019-10
    99/100 stars

    Images

    1) Product Images from "1,2-propanediol-trehalose mixture as a potent quantitative real-time PCR enhancer"

    Article Title: 1,2-propanediol-trehalose mixture as a potent quantitative real-time PCR enhancer

    Journal: BMC Biotechnology

    doi: 10.1186/1472-6750-11-41

    The effect of blood inhibitors and enhancers on PCR, melting temperature, and polymerase activity . (A) DNA fragment of NP_001035158.1 gene (Fr. 7; 735 bp; 73.1% GC) was amplified in PCR mix II supplemented with the corresponding primers, 37.5 μM hemoglobin and 0.2 M trehalose alone (T), 1 M 1,2-propanediol alone (P) or their combination (PT). PCR mix supplemented with H 2 O instead of enhancers served as a control (C'). A typical experiment of four performed is shown. (B) Melting temperature of GC-rich dsDNA oligonucleotide primer No 7, reverse, and the anti-primer (72.2% GC; 1 μM final concentration) in the presence (+) or absence (-) of hemoglobin (37.5 μM) and various enhancers (as in A). Melting temperature was determined as in Figure 6, except that SGI was used at higher concentration (1.32 μM). (C) Enzymatic activity of Taq DNA polymerase in PCR mix II buffer supplemented with (+) or without (-) 10% blood and various enhancers (as in A). Samples supplemented with H 2 O instead of enhancers (C') served as controls. Data in B and C indicate means ± S.D. (n = 4). Asterisks indicate statistically significant differences (P
    Figure Legend Snippet: The effect of blood inhibitors and enhancers on PCR, melting temperature, and polymerase activity . (A) DNA fragment of NP_001035158.1 gene (Fr. 7; 735 bp; 73.1% GC) was amplified in PCR mix II supplemented with the corresponding primers, 37.5 μM hemoglobin and 0.2 M trehalose alone (T), 1 M 1,2-propanediol alone (P) or their combination (PT). PCR mix supplemented with H 2 O instead of enhancers served as a control (C'). A typical experiment of four performed is shown. (B) Melting temperature of GC-rich dsDNA oligonucleotide primer No 7, reverse, and the anti-primer (72.2% GC; 1 μM final concentration) in the presence (+) or absence (-) of hemoglobin (37.5 μM) and various enhancers (as in A). Melting temperature was determined as in Figure 6, except that SGI was used at higher concentration (1.32 μM). (C) Enzymatic activity of Taq DNA polymerase in PCR mix II buffer supplemented with (+) or without (-) 10% blood and various enhancers (as in A). Samples supplemented with H 2 O instead of enhancers (C') served as controls. Data in B and C indicate means ± S.D. (n = 4). Asterisks indicate statistically significant differences (P

    Techniques Used: Polymerase Chain Reaction, Activity Assay, Gas Chromatography, Amplification, Concentration Assay

    The effect of various DNA dyes and enhancers on ssDNA fluorescence and dsDNA melting temperature . (A) TNF-1 oligonucleotide (ssDNA, 45.5% GC; 1 μM final concentration) in PCR mix II (without dNTPs, Taq DNA polymerase and anti-Taq) was mixed with H 2 O (Control; Co) or enhancers [0.2 M trehalose (T; final concentration), 1 M 1,2-propanediol (P) or both 1 M 1,2-propanediol and 0.2 M trehalose (PT)] and various DNA dyes at final concentrations as indicated in Table 1. After heating at 95°C for 2 min the samples were cooled to 50°C and fluorescence was determined using Mastercycler ep realplex. (B) Oligonucleotide primer No 7, reverse (ssDNA; 72.2% GC; 1 μM final concentration) in PCR mix II was combined with various additives and DNA dyes, and fluorescence at 50°C was determined as in A. (C) Oligonucleotide mixture of TNF-1 and anti-TNF-1 (dsDNA, 45.5% GC; 1 μM final concentration) was prepared in mix II supplemented with various additives and DNA dyes. The samples were heated to 95°C for 2 min, then cooled to 30°C and temperature-dependent changes in fluorescence were obtained during heating from 30 to 95°C (0.2°C increments) in Mastercycler ep realplex. Melting temperatures were determined from the melting curves. (D) Oligonucleotide mixture of the primer No 7, reverse, and the anti-primer 7 (dsDNA, 72.2% GC; final concentration 1 μM) was combined in mix II with additives and DNA dyes and analyzed as in C. Means ± S.D. were calculated from 3 - 5 measurements.
    Figure Legend Snippet: The effect of various DNA dyes and enhancers on ssDNA fluorescence and dsDNA melting temperature . (A) TNF-1 oligonucleotide (ssDNA, 45.5% GC; 1 μM final concentration) in PCR mix II (without dNTPs, Taq DNA polymerase and anti-Taq) was mixed with H 2 O (Control; Co) or enhancers [0.2 M trehalose (T; final concentration), 1 M 1,2-propanediol (P) or both 1 M 1,2-propanediol and 0.2 M trehalose (PT)] and various DNA dyes at final concentrations as indicated in Table 1. After heating at 95°C for 2 min the samples were cooled to 50°C and fluorescence was determined using Mastercycler ep realplex. (B) Oligonucleotide primer No 7, reverse (ssDNA; 72.2% GC; 1 μM final concentration) in PCR mix II was combined with various additives and DNA dyes, and fluorescence at 50°C was determined as in A. (C) Oligonucleotide mixture of TNF-1 and anti-TNF-1 (dsDNA, 45.5% GC; 1 μM final concentration) was prepared in mix II supplemented with various additives and DNA dyes. The samples were heated to 95°C for 2 min, then cooled to 30°C and temperature-dependent changes in fluorescence were obtained during heating from 30 to 95°C (0.2°C increments) in Mastercycler ep realplex. Melting temperatures were determined from the melting curves. (D) Oligonucleotide mixture of the primer No 7, reverse, and the anti-primer 7 (dsDNA, 72.2% GC; final concentration 1 μM) was combined in mix II with additives and DNA dyes and analyzed as in C. Means ± S.D. were calculated from 3 - 5 measurements.

    Techniques Used: Fluorescence, Gas Chromatography, Concentration Assay, Polymerase Chain Reaction

    Related Articles

    Methylation Sequencing:

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    Article Snippet: Paragraph title: Bisulfite sequencing ... Genomic DNA was extracted (DNeasy Blood and Tissue Kit, Qiagen), treated with RNase A and quantified (Quant-IT HS dsDNA kit, Invitrogen) using the manufacturer's recommended protocols.

    Clone Assay:

    Article Title: Extra-coding RNAs regulate neuronal DNA methylation dynamics
    Article Snippet: Genomic DNA was extracted (DNeasy Blood and Tissue Kit, Qiagen), treated with RNase A and quantified (Quant-IT HS dsDNA kit, Invitrogen) using the manufacturer's recommended protocols. .. 450 ng of DNA per sample underwent bisulfite conversion (EZ DNA Methylation Lightning kit, Zymo) and PCR amplification using bisulfite-compatible primer sets targeting the Fos promoter locus ( ).

    Amplification:

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    Article Snippet: The following PCR protocol was used: initial denaturation at 95°C for 3 min; eight cycles of 98°C for 20 s, 60°C for 15 s, and 72°C for 30 s; followed by a final extension at 72°C for 1 min. .. The amplified library was purified using Agencourt AMPure XP beads and quantified using the Qubit fluorometer with a Quant-it dsDNA HS kit (Invitrogen-Thermo Fisher Scientific). .. The quality and size were finally checked using the Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA).

    Article Title: Mutations of KRAS/NRAS/BRAF predict cetuximab resistance in metastatic colorectal cancer patients
    Article Snippet: DNA was quantified using the Quant-iT dsDNA HS Assay (Invitrogen). .. DNA was quantified using the Quant-iT dsDNA HS Assay (Invitrogen).

    Article Title: Mutational Spectrum Analysis of Seven Genes Associated with Thyroid Dyshormonogenesis
    Article Snippet: Isolated DNA was qualitatively and quantitatively analyzed via the Quant-iT™ dsDNA HS Assay (Invitrogen, Carlsbad, CA, USA) and Nanodrop spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA), respectively. .. The Ampliseq design resulted in a total of 174 amplicons per sequencing run.

    Article Title: Reassessment of QTLs for Late Blight Resistance in the Tomato Accession L3708 Using a Restriction Site Associated DNA (RAD) Linkage Map and Highly Aggressive Isolates of Phytophthora infestans
    Article Snippet: The repaired dsDNAs were suspended in 20 µL buffer EB and quantified using the Quant-iT dsDNA HS Assay Kit (Life Technologies, Carlsbad CA, USA). .. The mixture was incubated at 20°C for 3 h. The P2 adapter-ligated dsDNAs were then purified using 35 µL (0.7× volume) Agencourt AMPure XP magnetic beads (Beckman Coulter, Brea CA, USA), suspended in 20 µL EB buffer, and quantified using a Quant-iT dsDNA HS Assay Kit (Life Technologies, Carlsbad CA, USA).

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    Article Snippet: Bands were visualised under blue light transillumination, excised, and DNA purified from the gel slices with the QIAquick gel extraction kit (Qiagen, Hilden, Germany). .. Gel-purified amplicon pools were quantified in triplicate with the Quant-iT dsDNA HS assay kit (Invitrogen). .. The three amplicon pools were normalized to contain 1×109 copies µl−1 and subsequently mixed at a ratio of 5∶1∶1 (Bacteria, Archaea, Protozoa) .

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    Article Snippet: The cDNA template was standardized to a concentration of 0.1μg/μl using a NanoDrop 3300 Fluorospectrometer (Thermo-Scientitific Cat. No. ND3300) with Quant-iT™ dsDNA HS Assay Kit (Invitrogen Cat. No. ). .. The 16S rDNA consisted of a forward Pg -specific primer (5′-TGT AGA TGA CTG ATG GTG AAA ACC-3′and a universal reverse primer (C11R), 5′-ACG TCA TCC CCA CCT TCC TC-3′sequence as previously described ( ).

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    Recovery:

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    Article Snippet: In general, PCR reactions were divided into multiple aliquots with one followed in real time using 0.5× Sybr Green I (Life Technologies); following PCR, the aliquots were recombined, purified by spin column (DNA Clean and Concentrator-5; Zymo Research, Irvine, CA) with elution in 20 µl of water, then separated by agarose gel electrophoresis, followed by band excision and recovery (Zymoclean Gel DNA Recovery Kit), eluting with 20 µl of water unless stated otherwise. .. The concentration of dsDNA was measured by fluorescent dye binding (Quant-iT dsDNA HS Assay kit, Life Technologies) unless stated otherwise.

    Synthesized:

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    Quantitative RT-PCR:

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    Real-time Polymerase Chain Reaction:

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    Incubation:

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    Article Title: DNA methylation regulates associative reward learning
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    Formalin-fixed Paraffin-Embedded:

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    Article Snippet: Genomic DNA was extracted from FFPE tumor samples using the QIAamp DNA FFPE Tissue Kit (Qiagen). .. DNA was quantified using the Quant-iT dsDNA HS Assay (Invitrogen).

    Activity Assay:

    Article Title: Humanized Culture of Periosteal Progenitors in Allogeneic Serum Enhances Osteogenic Differentiation and In Vivo Bone Formation
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    High Throughput Screening Assay:

    Article Title: Identification of genetic linkage group 1-linked sequences in Japanese eel (Anguilla japonica) by single chromosome sorting and sequencing
    Article Snippet: Paragraph title: High-throughput sequencing ... The amplified library was purified using Agencourt AMPure XP beads and quantified using the Qubit fluorometer with a Quant-it dsDNA HS kit (Invitrogen-Thermo Fisher Scientific).

    Mass Spectrometry:

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    Modification:

    Article Title: Reassessment of QTLs for Late Blight Resistance in the Tomato Accession L3708 Using a Restriction Site Associated DNA (RAD) Linkage Map and Highly Aggressive Isolates of Phytophthora infestans
    Article Snippet: The repaired dsDNAs were suspended in 20 µL buffer EB and quantified using the Quant-iT dsDNA HS Assay Kit (Life Technologies, Carlsbad CA, USA). .. The mixture was incubated at 20°C for 3 h. The P2 adapter-ligated dsDNAs were then purified using 35 µL (0.7× volume) Agencourt AMPure XP magnetic beads (Beckman Coulter, Brea CA, USA), suspended in 20 µL EB buffer, and quantified using a Quant-iT dsDNA HS Assay Kit (Life Technologies, Carlsbad CA, USA).

    Article Title: Microbial Carriage State of Peripheral Blood Dendritic cells (DCs) in Chronic Periodontitis Influences DC Differentiation, Atherogenic Potential
    Article Snippet: To detect and quantitate P. gingivalis , genomic DNA (gDNA) and total RNA was isolated from subgingival plaque and mDCs with the RNeasy Micro kit (QIAGEN) according to the manufacturers’ instructions, but with a slight modification. .. The cDNA template was standardized to a concentration of 0.1μg/μl using a NanoDrop 3300 Fluorospectrometer (Thermo-Scientitific Cat. No. ND3300) with Quant-iT™ dsDNA HS Assay Kit (Invitrogen Cat. No. ).

    Allele-specific Oligonucleotide:

    Article Title: Extra-coding RNAs regulate neuronal DNA methylation dynamics
    Article Snippet: DNA methylation at the Fos gene promoter following Fos ecRNA ASO treatment was assayed using bisulfite sequencing. .. Genomic DNA was extracted (DNeasy Blood and Tissue Kit, Qiagen), treated with RNase A and quantified (Quant-IT HS dsDNA kit, Invitrogen) using the manufacturer's recommended protocols.

    Ligation:

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    Article Title: Reassessment of QTLs for Late Blight Resistance in the Tomato Accession L3708 Using a Restriction Site Associated DNA (RAD) Linkage Map and Highly Aggressive Isolates of Phytophthora infestans
    Article Snippet: The repaired dsDNAs were suspended in 20 µL buffer EB and quantified using the Quant-iT dsDNA HS Assay Kit (Life Technologies, Carlsbad CA, USA). .. Adenine was added to the 3′ ends of dsDNA fragments in a 50 µL reaction volume containing 1 µg dsDNAs, 5 µL 10× NEBuffer2, 1 µL 10 mM dATP, and 3 µL of 5 unit µL−1 Klenow Fragment (NEB, Ipswish MA, USA) mixed and incubated at 37°C for 30 min. DNAs were cleaned using 90 µL (1.8× volume) Agencourt AMPure XP magnetic beads (Beckman Coulter, Brea CA, USA), and suspended in 45 µL EB buffer.

    Magnetic Beads:

    Article Title: Reassessment of QTLs for Late Blight Resistance in the Tomato Accession L3708 Using a Restriction Site Associated DNA (RAD) Linkage Map and Highly Aggressive Isolates of Phytophthora infestans
    Article Snippet: The mixture was incubated at 25°C for 30 min. Agencourt AMPure XP magnetic beads (Beckman Coulter, Brea CA, USA) were used for reaction clean-ups with a volume DNA:beads ratio of 1∶1.8; this removed DNA fragments of less than 50 bp. .. The repaired dsDNAs were suspended in 20 µL buffer EB and quantified using the Quant-iT dsDNA HS Assay Kit (Life Technologies, Carlsbad CA, USA).

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    Generated:

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    Article Snippet: Amplicon libraries were generated by targeted amplification of the V1-V3 hypervariable regions of the bacterial 16S rRNA gene. .. Individual libraries were quantified with Quant-iT HS dsDNA assay (Life Technologies, USA) and quality checked on a Tapestation 2200 (Agilent, USA).

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    Article Snippet: PCR products were quantified using a Quant-iT dsDNA HS Assay Kit (Invitrogen) and prepared for sequencing using a Nextera XT DNA library preparation kit (Illumina, Inc.). .. We assembled sequence reads from samples collected 2011–2014 using Bowtie 2 version 2.2.3 [ ] and those from 2015 with Geneious 9.1.3 [ ] using reference data for IAVs obtained from GenBank [ ] to map reads.

    other:

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    Article Snippet: The DNA content was determined using a highly quantitative and selective DNA assay (Quant-iT™ dsDNA HS kit; Life Technologies).

    DNA Sequencing:

    Article Title: Mutations of KRAS/NRAS/BRAF predict cetuximab resistance in metastatic colorectal cancer patients
    Article Snippet: Paragraph title: Sample preparation, DNA sequencing, and data processing ... DNA was quantified using the Quant-iT dsDNA HS Assay (Invitrogen).

    Sequencing:

    Article Title: Identification of genetic linkage group 1-linked sequences in Japanese eel (Anguilla japonica) by single chromosome sorting and sequencing
    Article Snippet: Paragraph title: High-throughput sequencing ... The amplified library was purified using Agencourt AMPure XP beads and quantified using the Qubit fluorometer with a Quant-it dsDNA HS kit (Invitrogen-Thermo Fisher Scientific).

    Article Title: Mutations of KRAS/NRAS/BRAF predict cetuximab resistance in metastatic colorectal cancer patients
    Article Snippet: DNA was quantified using the Quant-iT dsDNA HS Assay (Invitrogen). .. DNA was quantified using the Quant-iT dsDNA HS Assay (Invitrogen).

    Article Title: EZH2 enables germinal centre formation through epigenetic silencing of CDKN1A and an Rb-E2F1 feedback loop
    Article Snippet: Paragraph title: mRNA-seq library preparation and sequencing processing ... Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies), and 2000–2200 hours sequenced on HiSeq2000 sequencer mRNA-seq, single read, 50 bp.

    Article Title: Mutational Spectrum Analysis of Seven Genes Associated with Thyroid Dyshormonogenesis
    Article Snippet: Isolated DNA was qualitatively and quantitatively analyzed via the Quant-iT™ dsDNA HS Assay (Invitrogen, Carlsbad, CA, USA) and Nanodrop spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA), respectively. .. Isolated DNA was qualitatively and quantitatively analyzed via the Quant-iT™ dsDNA HS Assay (Invitrogen, Carlsbad, CA, USA) and Nanodrop spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA), respectively.

    Article Title: miR-181a/b-1 controls thymic selection of Treg cells and tunes their suppressive capacity
    Article Snippet: Paragraph title: TCR sequencing ... Amplicons were purified by agarose gel electrophoresis and QIAquick Gel Extraction Kit (Qiagen) and quantified by Quant-iT dsDNA HS Assay Kit (Invitrogen).

    Article Title: Impact of Bacillus spp. spores and gentamicin on the gastrointestinal microbiota of suckling and newly weaned piglets
    Article Snippet: Paragraph title: 16S rRNA gene amplicon sequencing ... Individual libraries were quantified with Quant-iT HS dsDNA assay (Life Technologies, USA) and quality checked on a Tapestation 2200 (Agilent, USA).

    Article Title: Microbial Carriage State of Peripheral Blood Dendritic cells (DCs) in Chronic Periodontitis Influences DC Differentiation, Atherogenic Potential
    Article Snippet: The cDNA template was standardized to a concentration of 0.1μg/μl using a NanoDrop 3300 Fluorospectrometer (Thermo-Scientitific Cat. No. ND3300) with Quant-iT™ dsDNA HS Assay Kit (Invitrogen Cat. No. ). .. The 16S rDNA consisted of a forward Pg -specific primer (5′-TGT AGA TGA CTG ATG GTG AAA ACC-3′and a universal reverse primer (C11R), 5′-ACG TCA TCC CCA CCT TCC TC-3′sequence as previously described ( ).

    Article Title: Influenza A virus recovery, diversity, and intercontinental exchange: A multi-year assessment of wild bird sampling at Izembek National Wildlife Refuge, Alaska
    Article Snippet: Following product visualization and verification (5μl on a 1.0% agarose gel), excess dNTPs and primers were removed using ExoSAP-IT® (USB Corporation). .. PCR products were quantified using a Quant-iT dsDNA HS Assay Kit (Invitrogen) and prepared for sequencing using a Nextera XT DNA library preparation kit (Illumina, Inc.). .. Indexed libraries were pooled and sequenced on the Illumina MiSeq using a 500 cycle reagent kit with paired-end reads.

    Article Title: Extra-coding RNAs regulate neuronal DNA methylation dynamics
    Article Snippet: Genomic DNA was extracted (DNeasy Blood and Tissue Kit, Qiagen), treated with RNase A and quantified (Quant-IT HS dsDNA kit, Invitrogen) using the manufacturer's recommended protocols. .. 450 ng of DNA per sample underwent bisulfite conversion (EZ DNA Methylation Lightning kit, Zymo) and PCR amplification using bisulfite-compatible primer sets targeting the Fos promoter locus ( ).

    Article Title: Canine Hereditary Ataxia in Old English Sheepdogs and Gordon Setters Is Associated with a Defect in the Autophagy Gene Encoding RAB24
    Article Snippet: Paragraph title: Targeted sequence capture ... Analysis of DNA libraries was done using the Agilent Bioanalyzer DNA 1000 (Agilent Technologies; Santa Clara, CA) and Quant-iT dsDNA HS assay (Life Technologies, Grand Island, NY).

    Article Title: Uncovering the Genome-Wide Transcriptional Responses of the Filamentous Fungus Aspergillus niger to Lignocellulose Using RNA Sequencing
    Article Snippet: The Quant-it HS dsDNA assay kit (Invitrogen) was used to measure the concentration of libraries in order to pool equimolar amounts. .. Emulsion PCR (0.5 pM final concentration of pooled libraries) and bead-based enrichment was carried out according to the SOLiD 4 Templated bead preparation guide containing library.

    Sonication:

    Article Title: DNA methylation regulates associative reward learning
    Article Snippet: Genomic DNA was extracted (DNeasy Blood and Tissue Kit, Qiagen), treated with RNase A, and quantified (Quant-IT HS dsDNA kit, Invitrogen) using the manufacturer’s recommended protocols. .. To increase yields of methylated DNA, purified genomic DNA was pooled across 2 biological samples per IP for in vivo experiments.

    Article Title: Canine Hereditary Ataxia in Old English Sheepdogs and Gordon Setters Is Associated with a Defect in the Autophagy Gene Encoding RAB24
    Article Snippet: DNA samples were fragmented by sonication (Covaris; Woburn, MA) and the fragments end-repaired, A-tailed, and ligated to indexing oligonucleotide adapters using NEBNext reagents (New England Biolabs; Ipswich, MA). .. Analysis of DNA libraries was done using the Agilent Bioanalyzer DNA 1000 (Agilent Technologies; Santa Clara, CA) and Quant-iT dsDNA HS assay (Life Technologies, Grand Island, NY).

    Binding Assay:

    Article Title: A Semi-Synthetic Organism with an Expanded Genetic Alphabet
    Article Snippet: Natural oligonucleotides were purchased from IDT (San Diego, CA). .. The concentration of dsDNA was measured by fluorescent dye binding (Quant-iT dsDNA HS Assay kit, Life Technologies) unless stated otherwise. .. The concentration of ssDNA was determined by UV absorption at 260 nm using a NanoDrop 1000 (Thermo Scientific).

    Methylated DNA Immunoprecipitation:

    Article Title: DNA methylation regulates associative reward learning
    Article Snippet: Paragraph title: Methylated DNA immunoprecipitation (MeDIP) ... Genomic DNA was extracted (DNeasy Blood and Tissue Kit, Qiagen), treated with RNase A, and quantified (Quant-IT HS dsDNA kit, Invitrogen) using the manufacturer’s recommended protocols.

    DNA Extraction:

    Article Title: Mutational Spectrum Analysis of Seven Genes Associated with Thyroid Dyshormonogenesis
    Article Snippet: Paragraph title: 2.2. DNA Extraction and Next-Generation Sequencing ... Isolated DNA was qualitatively and quantitatively analyzed via the Quant-iT™ dsDNA HS Assay (Invitrogen, Carlsbad, CA, USA) and Nanodrop spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA), respectively.

    Article Title: Faecal Microbiota of Forage-Fed Horses in New Zealand and the Population Dynamics of Microbial Communities following Dietary Change
    Article Snippet: Paragraph title: DNA extraction, PCR amplification of target genes and pyrosequencing ... Gel-purified amplicon pools were quantified in triplicate with the Quant-iT dsDNA HS assay kit (Invitrogen).

    In Vivo:

    Article Title: DNA methylation regulates associative reward learning
    Article Snippet: Genomic DNA was extracted (DNeasy Blood and Tissue Kit, Qiagen), treated with RNase A, and quantified (Quant-IT HS dsDNA kit, Invitrogen) using the manufacturer’s recommended protocols. .. 200ng (in vivo experiments) or 400ng (in vitro experiments) of DNA per sample was removed and sonicated (Fisher Sonic Dismembrator 120) to 200–1000bp fragments for methylation analysis.

    RNA Sequencing Assay:

    Article Title: EZH2 enables germinal centre formation through epigenetic silencing of CDKN1A and an Rb-E2F1 feedback loop
    Article Snippet: RNA-seq libraries were prepared using the Illumina TruSeq RNA sample kits, according to the manufacturer. .. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies), and 2000–2200 hours sequenced on HiSeq2000 sequencer mRNA-seq, single read, 50 bp.

    Article Title: Uncovering the Genome-Wide Transcriptional Responses of the Filamentous Fungus Aspergillus niger to Lignocellulose Using RNA Sequencing
    Article Snippet: Paragraph title: RNA-seq ... The Quant-it HS dsDNA assay kit (Invitrogen) was used to measure the concentration of libraries in order to pool equimolar amounts.

    Methylation:

    Article Title: DNA methylation regulates associative reward learning
    Article Snippet: Paragraph title: Methylated DNA immunoprecipitation (MeDIP) ... Genomic DNA was extracted (DNeasy Blood and Tissue Kit, Qiagen), treated with RNase A, and quantified (Quant-IT HS dsDNA kit, Invitrogen) using the manufacturer’s recommended protocols.

    Mutagenesis:

    Article Title: Mutations of KRAS/NRAS/BRAF predict cetuximab resistance in metastatic colorectal cancer patients
    Article Snippet: DNA was quantified using the Quant-iT dsDNA HS Assay (Invitrogen). .. DNA was quantified using the Quant-iT dsDNA HS Assay (Invitrogen).

    Isolation:

    Article Title: Genome-wide meta-analysis identifies five new susceptibility loci for cutaneous malignant melanoma
    Article Snippet: Genomic DNA was isolated from 200 μl peripheral blood using the QIAamp DNA blood mini kit [Qiagen]. .. DNA concentration was quantified in samples prior to genotyping by using Quant-iT dsDNA HS Assay kit [Invitrogen].

    Article Title: Mutational Spectrum Analysis of Seven Genes Associated with Thyroid Dyshormonogenesis
    Article Snippet: Genomic DNA was manually extracted from peripheral blood using the Whole Blood Genomic DNA Isolation Kit (GoldMag, Xi'an, Shannxi, China). .. Isolated DNA was qualitatively and quantitatively analyzed via the Quant-iT™ dsDNA HS Assay (Invitrogen, Carlsbad, CA, USA) and Nanodrop spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA), respectively. .. Patients were genetically screened using a customized Ampliseq panel that included seven DH-associated genes (TPO, TG, DUOX2, DUOXA2, SLC5A5, SLC26A4, and IYD).

    Article Title: miR-181a/b-1 controls thymic selection of Treg cells and tunes their suppressive capacity
    Article Snippet: Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany) from 1 × 105 sorted thymic CD3+ CD4+ CD25+ miR-181a/b-1+/− or miR-181a/b-1−/− Treg cells and 4 × 105 sorted splenic CD3+ CD4+ CD25+ miR-181a/b-1+/− or miR-181a/b-1−/− Treg cells. .. Amplicons were purified by agarose gel electrophoresis and QIAquick Gel Extraction Kit (Qiagen) and quantified by Quant-iT dsDNA HS Assay Kit (Invitrogen).

    Article Title: Microbial Carriage State of Peripheral Blood Dendritic cells (DCs) in Chronic Periodontitis Influences DC Differentiation, Atherogenic Potential
    Article Snippet: Briefly, gDNA Eliminator spin columns were not used during the isolation protocol. .. The cDNA template was standardized to a concentration of 0.1μg/μl using a NanoDrop 3300 Fluorospectrometer (Thermo-Scientitific Cat. No. ND3300) with Quant-iT™ dsDNA HS Assay Kit (Invitrogen Cat. No. ).

    Polymerase Chain Reaction:

    Article Title: A Semi-Synthetic Organism with an Expanded Genetic Alphabet
    Article Snippet: In general, PCR reactions were divided into multiple aliquots with one followed in real time using 0.5× Sybr Green I (Life Technologies); following PCR, the aliquots were recombined, purified by spin column (DNA Clean and Concentrator-5; Zymo Research, Irvine, CA) with elution in 20 µl of water, then separated by agarose gel electrophoresis, followed by band excision and recovery (Zymoclean Gel DNA Recovery Kit), eluting with 20 µl of water unless stated otherwise. .. The concentration of dsDNA was measured by fluorescent dye binding (Quant-iT dsDNA HS Assay kit, Life Technologies) unless stated otherwise.

    Article Title: Genome-wide meta-analysis identifies five new susceptibility loci for cutaneous malignant melanoma
    Article Snippet: DNA concentration was quantified in samples prior to genotyping by using Quant-iT dsDNA HS Assay kit [Invitrogen]. .. Allele detection in this assay was performed using matrix-assisted laser desorption/ionization –time-of-flight mass spectrometry .

    Article Title: Identification of genetic linkage group 1-linked sequences in Japanese eel (Anguilla japonica) by single chromosome sorting and sequencing
    Article Snippet: The following PCR protocol was used: initial denaturation at 95°C for 3 min; eight cycles of 98°C for 20 s, 60°C for 15 s, and 72°C for 30 s; followed by a final extension at 72°C for 1 min. .. The amplified library was purified using Agencourt AMPure XP beads and quantified using the Qubit fluorometer with a Quant-it dsDNA HS kit (Invitrogen-Thermo Fisher Scientific).

    Article Title: Reassessment of QTLs for Late Blight Resistance in the Tomato Accession L3708 Using a Restriction Site Associated DNA (RAD) Linkage Map and Highly Aggressive Isolates of Phytophthora infestans
    Article Snippet: The repaired dsDNAs were suspended in 20 µL buffer EB and quantified using the Quant-iT dsDNA HS Assay Kit (Life Technologies, Carlsbad CA, USA). .. The repaired dsDNAs were suspended in 20 µL buffer EB and quantified using the Quant-iT dsDNA HS Assay Kit (Life Technologies, Carlsbad CA, USA).

    Article Title: Faecal Microbiota of Forage-Fed Horses in New Zealand and the Population Dynamics of Microbial Communities following Dietary Change
    Article Snippet: Paragraph title: DNA extraction, PCR amplification of target genes and pyrosequencing ... Gel-purified amplicon pools were quantified in triplicate with the Quant-iT dsDNA HS assay kit (Invitrogen).

    Article Title: Impact of Bacillus spp. spores and gentamicin on the gastrointestinal microbiota of suckling and newly weaned piglets
    Article Snippet: Thermocycler settings: Initial denaturation at 95°C for 2 min, 30 cycles of 95°C for 20 s, 56°C for 30 s, 72°C for 60 s, and final elongation at 72°C for 5 min. PCR reactions were run in duplicate for each sample and pooled before purification. .. Individual libraries were quantified with Quant-iT HS dsDNA assay (Life Technologies, USA) and quality checked on a Tapestation 2200 (Agilent, USA).

    Article Title: Microbial Carriage State of Peripheral Blood Dendritic cells (DCs) in Chronic Periodontitis Influences DC Differentiation, Atherogenic Potential
    Article Snippet: The cDNA template was standardized to a concentration of 0.1μg/μl using a NanoDrop 3300 Fluorospectrometer (Thermo-Scientitific Cat. No. ND3300) with Quant-iT™ dsDNA HS Assay Kit (Invitrogen Cat. No. ). .. The universal reverse primer was also used to detect non- P. gingivalis amplification products, which were then subjected to genomic blast sequencing.

    Article Title: Influenza A virus recovery, diversity, and intercontinental exchange: A multi-year assessment of wild bird sampling at Izembek National Wildlife Refuge, Alaska
    Article Snippet: Following product visualization and verification (5μl on a 1.0% agarose gel), excess dNTPs and primers were removed using ExoSAP-IT® (USB Corporation). .. PCR products were quantified using a Quant-iT dsDNA HS Assay Kit (Invitrogen) and prepared for sequencing using a Nextera XT DNA library preparation kit (Illumina, Inc.). .. Indexed libraries were pooled and sequenced on the Illumina MiSeq using a 500 cycle reagent kit with paired-end reads.

    Article Title: Extra-coding RNAs regulate neuronal DNA methylation dynamics
    Article Snippet: Genomic DNA was extracted (DNeasy Blood and Tissue Kit, Qiagen), treated with RNase A and quantified (Quant-IT HS dsDNA kit, Invitrogen) using the manufacturer's recommended protocols. .. 450 ng of DNA per sample underwent bisulfite conversion (EZ DNA Methylation Lightning kit, Zymo) and PCR amplification using bisulfite-compatible primer sets targeting the Fos promoter locus ( ).

    Article Title: Canine Hereditary Ataxia in Old English Sheepdogs and Gordon Setters Is Associated with a Defect in the Autophagy Gene Encoding RAB24
    Article Snippet: DNA purification was done using QIAquick and MinElute PCR purification kits (Qiagen; Valencia, CA). .. Analysis of DNA libraries was done using the Agilent Bioanalyzer DNA 1000 (Agilent Technologies; Santa Clara, CA) and Quant-iT dsDNA HS assay (Life Technologies, Grand Island, NY).

    Article Title: Uncovering the Genome-Wide Transcriptional Responses of the Filamentous Fungus Aspergillus niger to Lignocellulose Using RNA Sequencing
    Article Snippet: The Quant-it HS dsDNA assay kit (Invitrogen) was used to measure the concentration of libraries in order to pool equimolar amounts. .. The Quant-it HS dsDNA assay kit (Invitrogen) was used to measure the concentration of libraries in order to pool equimolar amounts.

    Purification:

    Article Title: A Semi-Synthetic Organism with an Expanded Genetic Alphabet
    Article Snippet: In general, PCR reactions were divided into multiple aliquots with one followed in real time using 0.5× Sybr Green I (Life Technologies); following PCR, the aliquots were recombined, purified by spin column (DNA Clean and Concentrator-5; Zymo Research, Irvine, CA) with elution in 20 µl of water, then separated by agarose gel electrophoresis, followed by band excision and recovery (Zymoclean Gel DNA Recovery Kit), eluting with 20 µl of water unless stated otherwise. .. The concentration of dsDNA was measured by fluorescent dye binding (Quant-iT dsDNA HS Assay kit, Life Technologies) unless stated otherwise.

    Article Title: Identification of genetic linkage group 1-linked sequences in Japanese eel (Anguilla japonica) by single chromosome sorting and sequencing
    Article Snippet: The following PCR protocol was used: initial denaturation at 95°C for 3 min; eight cycles of 98°C for 20 s, 60°C for 15 s, and 72°C for 30 s; followed by a final extension at 72°C for 1 min. .. The amplified library was purified using Agencourt AMPure XP beads and quantified using the Qubit fluorometer with a Quant-it dsDNA HS kit (Invitrogen-Thermo Fisher Scientific). .. The quality and size were finally checked using the Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA).

    Article Title: miR-181a/b-1 controls thymic selection of Treg cells and tunes their suppressive capacity
    Article Snippet: Forward and reverse primers contained at their 5′ ends the universal adapter sequences and a multiplex identifier (MID), respectively. .. Amplicons were purified by agarose gel electrophoresis and QIAquick Gel Extraction Kit (Qiagen) and quantified by Quant-iT dsDNA HS Assay Kit (Invitrogen). .. Single PCR amplicon molecules were immobilized onto DNA capture beads within an oil–water emulsion to enable clonal amplification in a second PCR process with universal primers.

    Article Title: Reassessment of QTLs for Late Blight Resistance in the Tomato Accession L3708 Using a Restriction Site Associated DNA (RAD) Linkage Map and Highly Aggressive Isolates of Phytophthora infestans
    Article Snippet: The repaired dsDNAs were suspended in 20 µL buffer EB and quantified using the Quant-iT dsDNA HS Assay Kit (Life Technologies, Carlsbad CA, USA). .. The repaired dsDNAs were suspended in 20 µL buffer EB and quantified using the Quant-iT dsDNA HS Assay Kit (Life Technologies, Carlsbad CA, USA).

    Article Title: RNA-seq Analysis of Host and Viral Gene Expression Highlights Interaction between Varicella Zoster Virus and Keratinocyte Differentiation
    Article Snippet: Unique adaptors were ligated to the cDNA and 200 bp fragments were size selected by agarose gel purification. .. Libraries were validated by using a DNA high sensitivity chip (Agilent, Cheshire, UK) and quantified by Qubit analysis using the Quant-iT dsDNA HS Assay (Life technologies).

    Article Title: Faecal Microbiota of Forage-Fed Horses in New Zealand and the Population Dynamics of Microbial Communities following Dietary Change
    Article Snippet: Bands were visualised under blue light transillumination, excised, and DNA purified from the gel slices with the QIAquick gel extraction kit (Qiagen, Hilden, Germany). .. Gel-purified amplicon pools were quantified in triplicate with the Quant-iT dsDNA HS assay kit (Invitrogen).

    Article Title: Impact of Bacillus spp. spores and gentamicin on the gastrointestinal microbiota of suckling and newly weaned piglets
    Article Snippet: Purification of the amplicon libraries was performed using the Agencourt AMPure XP bead protocol (Beckman Coulter, USA) and eluted in 23 μL nuclease-free water. .. Individual libraries were quantified with Quant-iT HS dsDNA assay (Life Technologies, USA) and quality checked on a Tapestation 2200 (Agilent, USA).

    Article Title: DNA methylation regulates associative reward learning
    Article Snippet: Genomic DNA was extracted (DNeasy Blood and Tissue Kit, Qiagen), treated with RNase A, and quantified (Quant-IT HS dsDNA kit, Invitrogen) using the manufacturer’s recommended protocols. .. 200ng (in vivo experiments) or 400ng (in vitro experiments) of DNA per sample was removed and sonicated (Fisher Sonic Dismembrator 120) to 200–1000bp fragments for methylation analysis.

    Article Title: Canine Hereditary Ataxia in Old English Sheepdogs and Gordon Setters Is Associated with a Defect in the Autophagy Gene Encoding RAB24
    Article Snippet: Size selection and purification was done using Agencourt AMPure XP beads (Beckman Coulter; Beverly, MA). .. Analysis of DNA libraries was done using the Agilent Bioanalyzer DNA 1000 (Agilent Technologies; Santa Clara, CA) and Quant-iT dsDNA HS assay (Life Technologies, Grand Island, NY).

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Influenza A virus recovery, diversity, and intercontinental exchange: A multi-year assessment of wild bird sampling at Izembek National Wildlife Refuge, Alaska
    Article Snippet: IAV genomes were amplified from extracted RNA at the USGS ASC, in a multiplex RT-PCR using Super Script™ III One-Step RT-PCR System with Platinum® Taq High Fidelity (Invitrogen), with 2μl of RNA template and the following primers: MBTuni-12 ( ACG-CGT-GAT-CAG-CAA-AAG-CAG-G ) at 0.1 μM, MBTuni-12(M) ( ACG-CGT-GAT-CAG-CRA-AAG-CAG-G ) at 0.1 μM, and MBTuni-13 ( ACG-CGT-GAT-CAG-TAG-AAA-CAA-GG ) at 0.2 μM. .. PCR products were quantified using a Quant-iT dsDNA HS Assay Kit (Invitrogen) and prepared for sequencing using a Nextera XT DNA library preparation kit (Illumina, Inc.).

    Staining:

    Article Title: A Semi-Synthetic Organism with an Expanded Genetic Alphabet
    Article Snippet: Polyacrylamide gels were stained with 1× Sybr Gold (Life Technologies) for 30 min, agarose gels were cast with 1× Sybr Gold. .. The concentration of dsDNA was measured by fluorescent dye binding (Quant-iT dsDNA HS Assay kit, Life Technologies) unless stated otherwise.

    Article Title: Humanized Culture of Periosteal Progenitors in Allogeneic Serum Enhances Osteogenic Differentiation and In Vivo Bone Formation
    Article Snippet: The DNA content was quantified using the Quant-iT dsDNA HS assay kit (Invitrogen). .. The concentration of DNA was converted to a predicted cell number using a predetermined value of 8.9 pg of DNA per hPDC [ ].

    Concentration Assay:

    Article Title: A Semi-Synthetic Organism with an Expanded Genetic Alphabet
    Article Snippet: Natural oligonucleotides were purchased from IDT (San Diego, CA). .. The concentration of dsDNA was measured by fluorescent dye binding (Quant-iT dsDNA HS Assay kit, Life Technologies) unless stated otherwise. .. The concentration of ssDNA was determined by UV absorption at 260 nm using a NanoDrop 1000 (Thermo Scientific).

    Article Title: Genome-wide meta-analysis identifies five new susceptibility loci for cutaneous malignant melanoma
    Article Snippet: Genomic DNA was isolated from 200 μl peripheral blood using the QIAamp DNA blood mini kit [Qiagen]. .. DNA concentration was quantified in samples prior to genotyping by using Quant-iT dsDNA HS Assay kit [Invitrogen]. .. The concentration of the DNA was adjusted to 5 ng/μl.

    Article Title: Microbial Carriage State of Peripheral Blood Dendritic cells (DCs) in Chronic Periodontitis Influences DC Differentiation, Atherogenic Potential
    Article Snippet: This was done to collect, in addition to total RNA, gDNA for P. gingivalis 16S rDNA detection in the mDCs. cDNA was synthesized using STR1 Enhanced Avian First Strand Synthesis Kit (Sigma-Aldrich Cat. No. STR1-1KT). .. The cDNA template was standardized to a concentration of 0.1μg/μl using a NanoDrop 3300 Fluorospectrometer (Thermo-Scientitific Cat. No. ND3300) with Quant-iT™ dsDNA HS Assay Kit (Invitrogen Cat. No. ). .. Quantitative real time-PCR (qRT-PCR) was used to detect the presence of P. gingivalis (16S rDNA) in MoDCs, mDCs and dental plaque samples.

    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 ... The Quant-iT dsDNA HS Assay (Life Technologies) was used according to the manufacturer's instructions.

    Article Title: Uncovering the Genome-Wide Transcriptional Responses of the Filamentous Fungus Aspergillus niger to Lignocellulose Using RNA Sequencing
    Article Snippet: SOLiD whole transcriptome libraries were made as outlined in the SOLiD Whole transcriptome kit protocol (Applied Biosystems). .. The Quant-it HS dsDNA assay kit (Invitrogen) was used to measure the concentration of libraries in order to pool equimolar amounts. .. Pooled libraries were gel-purified using 2% size-select E-gels to 200–300 bp (Invitrogen).

    Agarose Gel Electrophoresis:

    Article Title: A Semi-Synthetic Organism with an Expanded Genetic Alphabet
    Article Snippet: In general, PCR reactions were divided into multiple aliquots with one followed in real time using 0.5× Sybr Green I (Life Technologies); following PCR, the aliquots were recombined, purified by spin column (DNA Clean and Concentrator-5; Zymo Research, Irvine, CA) with elution in 20 µl of water, then separated by agarose gel electrophoresis, followed by band excision and recovery (Zymoclean Gel DNA Recovery Kit), eluting with 20 µl of water unless stated otherwise. .. The concentration of dsDNA was measured by fluorescent dye binding (Quant-iT dsDNA HS Assay kit, Life Technologies) unless stated otherwise.

    Article Title: miR-181a/b-1 controls thymic selection of Treg cells and tunes their suppressive capacity
    Article Snippet: Forward and reverse primers contained at their 5′ ends the universal adapter sequences and a multiplex identifier (MID), respectively. .. Amplicons were purified by agarose gel electrophoresis and QIAquick Gel Extraction Kit (Qiagen) and quantified by Quant-iT dsDNA HS Assay Kit (Invitrogen). .. Single PCR amplicon molecules were immobilized onto DNA capture beads within an oil–water emulsion to enable clonal amplification in a second PCR process with universal primers.

    Article Title: RNA-seq Analysis of Host and Viral Gene Expression Highlights Interaction between Varicella Zoster Virus and Keratinocyte Differentiation
    Article Snippet: Unique adaptors were ligated to the cDNA and 200 bp fragments were size selected by agarose gel purification. .. Libraries were validated by using a DNA high sensitivity chip (Agilent, Cheshire, UK) and quantified by Qubit analysis using the Quant-iT dsDNA HS Assay (Life technologies).

    Article Title: Faecal Microbiota of Forage-Fed Horses in New Zealand and the Population Dynamics of Microbial Communities following Dietary Change
    Article Snippet: Triplicate PCR products were pooled, and correct sizes of PCR products and signal absence from the negative controls were verified by agarose gel electrophoresis. .. Gel-purified amplicon pools were quantified in triplicate with the Quant-iT dsDNA HS assay kit (Invitrogen).

    Article Title: Influenza A virus recovery, diversity, and intercontinental exchange: A multi-year assessment of wild bird sampling at Izembek National Wildlife Refuge, Alaska
    Article Snippet: Following product visualization and verification (5μl on a 1.0% agarose gel), excess dNTPs and primers were removed using ExoSAP-IT® (USB Corporation). .. PCR products were quantified using a Quant-iT dsDNA HS Assay Kit (Invitrogen) and prepared for sequencing using a Nextera XT DNA library preparation kit (Illumina, Inc.).

    Mouse Assay:

    Article Title: miR-181a/b-1 controls thymic selection of Treg cells and tunes their suppressive capacity
    Article Snippet: Four independent sorts were performed (pooled 4–5 mice/genotype), and so were 2 independent sequencing experiments. cDNA templates were synthesized using SuperScript II reverse transcriptase (Invitrogen) according to the manufacturer’s recommendation. .. Amplicons were purified by agarose gel electrophoresis and QIAquick Gel Extraction Kit (Qiagen) and quantified by Quant-iT dsDNA HS Assay Kit (Invitrogen).

    Chromatin Immunoprecipitation:

    Article Title: Identification of genetic linkage group 1-linked sequences in Japanese eel (Anguilla japonica) by single chromosome sorting and sequencing
    Article Snippet: The amplified library was purified using Agencourt AMPure XP beads and quantified using the Qubit fluorometer with a Quant-it dsDNA HS kit (Invitrogen-Thermo Fisher Scientific). .. Emulsion PCR and Ion Sphere Particle enrichment were carried out using the Ion OneTouch 2 system with an Ion P1 Template OT2 200 kit v3 (Ion Torrent-Thermo Fisher Scientific).

    Article Title: RNA-seq Analysis of Host and Viral Gene Expression Highlights Interaction between Varicella Zoster Virus and Keratinocyte Differentiation
    Article Snippet: Unique adaptors were ligated to the cDNA and 200 bp fragments were size selected by agarose gel purification. .. Libraries were validated by using a DNA high sensitivity chip (Agilent, Cheshire, UK) and quantified by Qubit analysis using the Quant-iT dsDNA HS Assay (Life technologies). .. Libraries were sequenced with a 36 bp paired end read using a GAIIx sequencer (Illumina).

    Software:

    Article Title: A Semi-Synthetic Organism with an Expanded Genetic Alphabet
    Article Snippet: All gels were visualized using a Molecular Imager Gel Doc XR+ equipped with 520DF30 filter (Bio-Rad) and quantified with Quantity One software (Bio-Rad). .. The concentration of dsDNA was measured by fluorescent dye binding (Quant-iT dsDNA HS Assay kit, Life Technologies) unless stated otherwise.

    Article Title: Identification of genetic linkage group 1-linked sequences in Japanese eel (Anguilla japonica) by single chromosome sorting and sequencing
    Article Snippet: The amplified library was purified using Agencourt AMPure XP beads and quantified using the Qubit fluorometer with a Quant-it dsDNA HS kit (Invitrogen-Thermo Fisher Scientific). .. Template samples were sequenced on Ion P1 Chip v2 using the Ion Proton platform with an Ion P1 Sequencing 200 kit v3 (Ion Torrent-Thermo Fisher Scientific).

    SYBR Green Assay:

    Article Title: A Semi-Synthetic Organism with an Expanded Genetic Alphabet
    Article Snippet: In general, PCR reactions were divided into multiple aliquots with one followed in real time using 0.5× Sybr Green I (Life Technologies); following PCR, the aliquots were recombined, purified by spin column (DNA Clean and Concentrator-5; Zymo Research, Irvine, CA) with elution in 20 µl of water, then separated by agarose gel electrophoresis, followed by band excision and recovery (Zymoclean Gel DNA Recovery Kit), eluting with 20 µl of water unless stated otherwise. .. The concentration of dsDNA was measured by fluorescent dye binding (Quant-iT dsDNA HS Assay kit, Life Technologies) unless stated otherwise.

    Article Title: Microbial Carriage State of Peripheral Blood Dendritic cells (DCs) in Chronic Periodontitis Influences DC Differentiation, Atherogenic Potential
    Article Snippet: The cDNA template was standardized to a concentration of 0.1μg/μl using a NanoDrop 3300 Fluorospectrometer (Thermo-Scientitific Cat. No. ND3300) with Quant-iT™ dsDNA HS Assay Kit (Invitrogen Cat. No. ). .. The universal reverse primer was also used to detect non- P. gingivalis amplification products, which were then subjected to genomic blast sequencing.

    Article Title: Canine Hereditary Ataxia in Old English Sheepdogs and Gordon Setters Is Associated with a Defect in the Autophagy Gene Encoding RAB24
    Article Snippet: Analysis of DNA libraries was done using the Agilent Bioanalyzer DNA 1000 (Agilent Technologies; Santa Clara, CA) and Quant-iT dsDNA HS assay (Life Technologies, Grand Island, NY). .. Post-capture amplification was done using the primers 5′-AAT GAT ACG GCG ACC ACC GAG-3′ and 5′-GAA GCA GAA GAC GGC ATA CGA-3′ with Phusion (New England Biolabs; Ipswich, MA) and AccuPrime (Life Technologies; Grand Island, NY) enzymes.

    Multiplex Assay:

    Article Title: miR-181a/b-1 controls thymic selection of Treg cells and tunes their suppressive capacity
    Article Snippet: Forward and reverse primers contained at their 5′ ends the universal adapter sequences and a multiplex identifier (MID), respectively. .. Amplicons were purified by agarose gel electrophoresis and QIAquick Gel Extraction Kit (Qiagen) and quantified by Quant-iT dsDNA HS Assay Kit (Invitrogen).

    Article Title: Influenza A virus recovery, diversity, and intercontinental exchange: A multi-year assessment of wild bird sampling at Izembek National Wildlife Refuge, Alaska
    Article Snippet: IAV genomes were amplified from extracted RNA at the USGS ASC, in a multiplex RT-PCR using Super Script™ III One-Step RT-PCR System with Platinum® Taq High Fidelity (Invitrogen), with 2μl of RNA template and the following primers: MBTuni-12 ( ACG-CGT-GAT-CAG-CAA-AAG-CAG-G ) at 0.1 μM, MBTuni-12(M) ( ACG-CGT-GAT-CAG-CRA-AAG-CAG-G ) at 0.1 μM, and MBTuni-13 ( ACG-CGT-GAT-CAG-TAG-AAA-CAA-GG ) at 0.2 μM. .. PCR products were quantified using a Quant-iT dsDNA HS Assay Kit (Invitrogen) and prepared for sequencing using a Nextera XT DNA library preparation kit (Illumina, Inc.).

    Selection:

    Article Title: Identification of genetic linkage group 1-linked sequences in Japanese eel (Anguilla japonica) by single chromosome sorting and sequencing
    Article Snippet: After size selection, each DNA sample was purified using Agencourt AMPure XP beads and then amplified using KAPA HiFi polymerase (KAPA Biosystems, Woburn, MA, USA) with Library Amplification Primer Mix (Ion Torrent-Thermo Fisher Scientific). .. The amplified library was purified using Agencourt AMPure XP beads and quantified using the Qubit fluorometer with a Quant-it dsDNA HS kit (Invitrogen-Thermo Fisher Scientific).

    Article Title: Canine Hereditary Ataxia in Old English Sheepdogs and Gordon Setters Is Associated with a Defect in the Autophagy Gene Encoding RAB24
    Article Snippet: Size selection and purification was done using Agencourt AMPure XP beads (Beckman Coulter; Beverly, MA). .. Analysis of DNA libraries was done using the Agilent Bioanalyzer DNA 1000 (Agilent Technologies; Santa Clara, CA) and Quant-iT dsDNA HS assay (Life Technologies, Grand Island, NY).

    Sample Prep:

    Article Title: Mutations of KRAS/NRAS/BRAF predict cetuximab resistance in metastatic colorectal cancer patients
    Article Snippet: Paragraph title: Sample preparation, DNA sequencing, and data processing ... DNA was quantified using the Quant-iT dsDNA HS Assay (Invitrogen).

    In Vitro:

    Article Title: Humanized Culture of Periosteal Progenitors in Allogeneic Serum Enhances Osteogenic Differentiation and In Vivo Bone Formation
    Article Snippet: Paragraph title: Analysis of In Vitro Cell Dynamics ... The DNA content was quantified using the Quant-iT dsDNA HS assay kit (Invitrogen).

    ALP Assay:

    Article Title: Humanized Culture of Periosteal Progenitors in Allogeneic Serum Enhances Osteogenic Differentiation and In Vivo Bone Formation
    Article Snippet: The DNA content was quantified using the Quant-iT dsDNA HS assay kit (Invitrogen). .. The DNA content was quantified using the Quant-iT dsDNA HS assay kit (Invitrogen).

    Next-Generation Sequencing:

    Article Title: Mutational Spectrum Analysis of Seven Genes Associated with Thyroid Dyshormonogenesis
    Article Snippet: Paragraph title: 2.2. DNA Extraction and Next-Generation Sequencing ... Isolated DNA was qualitatively and quantitatively analyzed via the Quant-iT™ dsDNA HS Assay (Invitrogen, Carlsbad, CA, USA) and Nanodrop spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA), respectively.

    dsDNA Assay:

    Article Title: Impact of Bacillus spp. spores and gentamicin on the gastrointestinal microbiota of suckling and newly weaned piglets
    Article Snippet: Purification of the amplicon libraries was performed using the Agencourt AMPure XP bead protocol (Beckman Coulter, USA) and eluted in 23 μL nuclease-free water. .. Individual libraries were quantified with Quant-iT HS dsDNA assay (Life Technologies, USA) and quality checked on a Tapestation 2200 (Agilent, USA). .. The library pool was sequenced using a MiSeq (Illumina, USA) and MiSeq reagent kit v3 (2x300 PE).

    Article Title: Uncovering the Genome-Wide Transcriptional Responses of the Filamentous Fungus Aspergillus niger to Lignocellulose Using RNA Sequencing
    Article Snippet: SOLiD whole transcriptome libraries were made as outlined in the SOLiD Whole transcriptome kit protocol (Applied Biosystems). .. The Quant-it HS dsDNA assay kit (Invitrogen) was used to measure the concentration of libraries in order to pool equimolar amounts. .. Pooled libraries were gel-purified using 2% size-select E-gels to 200–300 bp (Invitrogen).

    Spectrophotometry:

    Article Title: Mutational Spectrum Analysis of Seven Genes Associated with Thyroid Dyshormonogenesis
    Article Snippet: Genomic DNA was manually extracted from peripheral blood using the Whole Blood Genomic DNA Isolation Kit (GoldMag, Xi'an, Shannxi, China). .. Isolated DNA was qualitatively and quantitatively analyzed via the Quant-iT™ dsDNA HS Assay (Invitrogen, Carlsbad, CA, USA) and Nanodrop spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA), respectively. .. Patients were genetically screened using a customized Ampliseq panel that included seven DH-associated genes (TPO, TG, DUOX2, DUOXA2, SLC5A5, SLC26A4, and IYD).

    Article Title: Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics
    Article Snippet: The genomic DNA extracted with each system was quantified in duplicates with the NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). .. The Quant-iT dsDNA HS Assay (Life Technologies) was used according to the manufacturer's instructions.

    DNA Methylation Assay:

    Article Title: Extra-coding RNAs regulate neuronal DNA methylation dynamics
    Article Snippet: DNA methylation at the Fos gene promoter following Fos ecRNA ASO treatment was assayed using bisulfite sequencing. .. Genomic DNA was extracted (DNeasy Blood and Tissue Kit, Qiagen), treated with RNase A and quantified (Quant-IT HS dsDNA kit, Invitrogen) using the manufacturer's recommended protocols.

    Immunoprecipitation:

    Article Title: DNA methylation regulates associative reward learning
    Article Snippet: Paragraph title: Methylated DNA immunoprecipitation (MeDIP) ... Genomic DNA was extracted (DNeasy Blood and Tissue Kit, Qiagen), treated with RNase A, and quantified (Quant-IT HS dsDNA kit, Invitrogen) using the manufacturer’s recommended protocols.

    Thin Layer Chromatography:

    Article Title: A Semi-Synthetic Organism with an Expanded Genetic Alphabet
    Article Snippet: The concentration of dsDNA was measured by fluorescent dye binding (Quant-iT dsDNA HS Assay kit, Life Technologies) unless stated otherwise. .. The concentration of dsDNA was measured by fluorescent dye binding (Quant-iT dsDNA HS Assay kit, Life Technologies) unless stated otherwise.

    DNA Purification:

    Article Title: Canine Hereditary Ataxia in Old English Sheepdogs and Gordon Setters Is Associated with a Defect in the Autophagy Gene Encoding RAB24
    Article Snippet: DNA purification was done using QIAquick and MinElute PCR purification kits (Qiagen; Valencia, CA). .. Analysis of DNA libraries was done using the Agilent Bioanalyzer DNA 1000 (Agilent Technologies; Santa Clara, CA) and Quant-iT dsDNA HS assay (Life Technologies, Grand Island, NY).

    CTG Assay:

    Article Title: Microbial Carriage State of Peripheral Blood Dendritic cells (DCs) in Chronic Periodontitis Influences DC Differentiation, Atherogenic Potential
    Article Snippet: The cDNA template was standardized to a concentration of 0.1μg/μl using a NanoDrop 3300 Fluorospectrometer (Thermo-Scientitific Cat. No. ND3300) with Quant-iT™ dsDNA HS Assay Kit (Invitrogen Cat. No. ). .. Quantitative real time-PCR (qRT-PCR) was used to detect the presence of P. gingivalis (16S rDNA) in MoDCs, mDCs and dental plaque samples.

    Gel Extraction:

    Article Title: miR-181a/b-1 controls thymic selection of Treg cells and tunes their suppressive capacity
    Article Snippet: Forward and reverse primers contained at their 5′ ends the universal adapter sequences and a multiplex identifier (MID), respectively. .. Amplicons were purified by agarose gel electrophoresis and QIAquick Gel Extraction Kit (Qiagen) and quantified by Quant-iT dsDNA HS Assay Kit (Invitrogen). .. Single PCR amplicon molecules were immobilized onto DNA capture beads within an oil–water emulsion to enable clonal amplification in a second PCR process with universal primers.

    Article Title: Faecal Microbiota of Forage-Fed Horses in New Zealand and the Population Dynamics of Microbial Communities following Dietary Change
    Article Snippet: Bands were visualised under blue light transillumination, excised, and DNA purified from the gel slices with the QIAquick gel extraction kit (Qiagen, Hilden, Germany). .. Gel-purified amplicon pools were quantified in triplicate with the Quant-iT dsDNA HS assay kit (Invitrogen).

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