kapa library quantification kit  (Kapa Biosystems)


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  • 99
    Name:
    Library Quantification Kit Illumina Universal
    Description:
    Complete kit Universal
    Catalog Number:
    kk4824
    Price:
    None
    Size:
    500 x 20 µL
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    Structured Review

    Kapa Biosystems kapa library quantification kit
    Schematic of the study. (A) )] were harvested by trypsinization and resuspended in medium, as indicated. Cell samples were lysed, generating crude nuclei preparations. Next, the transposition reaction was performed in the presence of Tn5 transposase, which cuts and ligates adapters at <t>DNA</t> regions of increased accessibility. The quality of the transposed DNA fragment libraries was assessed using a Bioanalyzer. Libraries were sequenced, mapped to the genome, and processed bioinformatically, and accessible genomic regions were detected (peak calling). (B) Single-cell (SC) RNA-seq [gel bead-in-emulsion (GEM) Drop-seq] workflow. Following treatment with GnRH or vehicle, cultured LβT2 cells were harvested by trypsinization and resuspended in a PBS BSA-containing buffer. Cell samples were loaded on a microfluidic chip, combined with reagents and barcoded gel beads to form Gel beads in Emulsion (GEMs), and then mixed with oil. The resulting emulsions were collected and reverse transcribed in SC droplets. Oil was removed, and barcoded cDNA was amplified, purified, and subject to quality control (QC) assessment. Amplified cDNA was incorporated into libraries, which were subsequently subject to QC evaluation using <t>Kapa,</t> Bioanalyzer, and Qubit. Libraries were pooled for sequencing and demultiplexed for subsequent analyses.
    Complete kit Universal
    https://www.bioz.com/result/kapa library quantification kit/product/Kapa Biosystems
    Average 99 stars, based on 517 article reviews
    Price from $9.99 to $1999.99
    kapa library quantification kit - by Bioz Stars, 2020-09
    99/100 stars

    Images

    1) Product Images from "Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone"

    Article Title: Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone

    Journal: Frontiers in Endocrinology

    doi: 10.3389/fendo.2018.00034

    Schematic of the study. (A) )] were harvested by trypsinization and resuspended in medium, as indicated. Cell samples were lysed, generating crude nuclei preparations. Next, the transposition reaction was performed in the presence of Tn5 transposase, which cuts and ligates adapters at DNA regions of increased accessibility. The quality of the transposed DNA fragment libraries was assessed using a Bioanalyzer. Libraries were sequenced, mapped to the genome, and processed bioinformatically, and accessible genomic regions were detected (peak calling). (B) Single-cell (SC) RNA-seq [gel bead-in-emulsion (GEM) Drop-seq] workflow. Following treatment with GnRH or vehicle, cultured LβT2 cells were harvested by trypsinization and resuspended in a PBS BSA-containing buffer. Cell samples were loaded on a microfluidic chip, combined with reagents and barcoded gel beads to form Gel beads in Emulsion (GEMs), and then mixed with oil. The resulting emulsions were collected and reverse transcribed in SC droplets. Oil was removed, and barcoded cDNA was amplified, purified, and subject to quality control (QC) assessment. Amplified cDNA was incorporated into libraries, which were subsequently subject to QC evaluation using Kapa, Bioanalyzer, and Qubit. Libraries were pooled for sequencing and demultiplexed for subsequent analyses.
    Figure Legend Snippet: Schematic of the study. (A) )] were harvested by trypsinization and resuspended in medium, as indicated. Cell samples were lysed, generating crude nuclei preparations. Next, the transposition reaction was performed in the presence of Tn5 transposase, which cuts and ligates adapters at DNA regions of increased accessibility. The quality of the transposed DNA fragment libraries was assessed using a Bioanalyzer. Libraries were sequenced, mapped to the genome, and processed bioinformatically, and accessible genomic regions were detected (peak calling). (B) Single-cell (SC) RNA-seq [gel bead-in-emulsion (GEM) Drop-seq] workflow. Following treatment with GnRH or vehicle, cultured LβT2 cells were harvested by trypsinization and resuspended in a PBS BSA-containing buffer. Cell samples were loaded on a microfluidic chip, combined with reagents and barcoded gel beads to form Gel beads in Emulsion (GEMs), and then mixed with oil. The resulting emulsions were collected and reverse transcribed in SC droplets. Oil was removed, and barcoded cDNA was amplified, purified, and subject to quality control (QC) assessment. Amplified cDNA was incorporated into libraries, which were subsequently subject to QC evaluation using Kapa, Bioanalyzer, and Qubit. Libraries were pooled for sequencing and demultiplexed for subsequent analyses.

    Techniques Used: RNA Sequencing Assay, Cell Culture, Chromatin Immunoprecipitation, Amplification, Purification, Sequencing

    2) Product Images from "Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone"

    Article Title: Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone

    Journal: Frontiers in Endocrinology

    doi: 10.3389/fendo.2018.00034

    Schematic of the study. (A) Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) workflow. Following treatment with pulses of gonadotropin-releasing hormone (GnRH), LβT2 cells cultured in coverslips placed in racks [see in Ref. ( 9 )] were harvested by trypsinization and resuspended in medium, as indicated. Cell samples were lysed, generating crude nuclei preparations. Next, the transposition reaction was performed in the presence of Tn5 transposase, which cuts and ligates adapters at DNA regions of increased accessibility. The quality of the transposed DNA fragment libraries was assessed using a Bioanalyzer. Libraries were sequenced, mapped to the genome, and processed bioinformatically, and accessible genomic regions were detected (peak calling). (B) Single-cell (SC) RNA-seq [gel bead-in-emulsion (GEM) Drop-seq] workflow. Following treatment with GnRH or vehicle, cultured LβT2 cells were harvested by trypsinization and resuspended in a PBS BSA-containing buffer. Cell samples were loaded on a microfluidic chip, combined with reagents and barcoded gel beads to form Gel beads in Emulsion (GEMs), and then mixed with oil. The resulting emulsions were collected and reverse transcribed in SC droplets. Oil was removed, and barcoded cDNA was amplified, purified, and subject to quality control (QC) assessment. Amplified cDNA was incorporated into libraries, which were subsequently subject to QC evaluation using Kapa, Bioanalyzer, and Qubit. Libraries were pooled for sequencing and demultiplexed for subsequent analyses.
    Figure Legend Snippet: Schematic of the study. (A) Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) workflow. Following treatment with pulses of gonadotropin-releasing hormone (GnRH), LβT2 cells cultured in coverslips placed in racks [see in Ref. ( 9 )] were harvested by trypsinization and resuspended in medium, as indicated. Cell samples were lysed, generating crude nuclei preparations. Next, the transposition reaction was performed in the presence of Tn5 transposase, which cuts and ligates adapters at DNA regions of increased accessibility. The quality of the transposed DNA fragment libraries was assessed using a Bioanalyzer. Libraries were sequenced, mapped to the genome, and processed bioinformatically, and accessible genomic regions were detected (peak calling). (B) Single-cell (SC) RNA-seq [gel bead-in-emulsion (GEM) Drop-seq] workflow. Following treatment with GnRH or vehicle, cultured LβT2 cells were harvested by trypsinization and resuspended in a PBS BSA-containing buffer. Cell samples were loaded on a microfluidic chip, combined with reagents and barcoded gel beads to form Gel beads in Emulsion (GEMs), and then mixed with oil. The resulting emulsions were collected and reverse transcribed in SC droplets. Oil was removed, and barcoded cDNA was amplified, purified, and subject to quality control (QC) assessment. Amplified cDNA was incorporated into libraries, which were subsequently subject to QC evaluation using Kapa, Bioanalyzer, and Qubit. Libraries were pooled for sequencing and demultiplexed for subsequent analyses.

    Techniques Used: Next-Generation Sequencing, Cell Culture, RNA Sequencing Assay, Chromatin Immunoprecipitation, Amplification, Purification, Sequencing

    Related Articles

    Picogreen Assay:

    Article Title: Chromatin structure analysis enables detection of DNA insertions into the mammalian nuclear genome
    Article Snippet: .. Sequencing libraries were quantified with Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies, CA) and Illumina/Universal Quantification Kit (KAPA Biosystems, MA), and DNA fragment sizes were determined using the Bioanalyzer High Sensitivity ChIP (Agilent Technologies, CA). .. Cluster Generation was performed on the cBot (Illumina, CA) and sequencing was performed on the Genome Analyzer IIx (Illumina, CA), generating 35 bp single end reads ( a).

    Quantitative RT-PCR:

    Article Title: A phenol/chloroform-free method to extract nucleic acids from recalcitrant, woody tropical species for gene expression and sequencing
    Article Snippet: .. Libraries were quantified by qRT-PCR using the Library Quantification Kit for Illumina sequencing platforms (KAPA Biosystems, Boston, USA), using a CFX96 Touch™ Real-Time PCR Detection System (Bio-Rad Laboratories, California, USA). .. The libraries were normalised to a working concentration of 4 nM using the molarity calculated from qRT-PCR, adjusted for fragment size.

    Purification:

    Article Title: Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin-Releasing Hormone
    Article Snippet: .. Libraries were purified with AMPure beads and then quantified using a KAPA Library Quantification Kit (Kapa Biosystems) and High-Sensitivity DNA Bionalyzer kit (Agilent) and sequenced on an Illumina HiSeq 2500 to > 164M reads with 50 bp read length, paired-end. ..

    Article Title: Analysis options for high-throughput sequencing in miRNA expression profiling
    Article Snippet: .. The barcoded libraries were size restricted between 140 and 165 bp, purified and quantified using the Library Quantification Kit - Illumina/Universal (KAPA Biosystems) according to the instructions of the manufacturer. .. High-throughput sequencingA pool of ten libraries was used for cluster generation at a concentration of 10 nM using an Illumina cBot.

    Real-time Polymerase Chain Reaction:

    Article Title: RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study
    Article Snippet: .. The adapter-ligated fragments were quantified by qPCR using the Library quantification kit for Illumina (KAPA Biosystems) on a StepOnePlus instrument (Applied Biosystems/Life Technologies) prior to cluster generation and sequencing. .. Cluster generation and sequencing An 11 pM solution of sequencing library was subjected to cluster generation and paired-end sequencing with 100 bp read length on the HiSeq 2500 system (Illumina Inc.) using v3 chemistry according to the manufacturer’s protocols.

    Article Title: Massive functional mapping of a 5?-UTR by saturation mutagenesis, phenotypic sorting and deep sequencing
    Article Snippet: .. The adapter-ligated fragments were quantified by quantitative PCR (qPCR) using the Library quantification kit for Illumina (KAPA Biosystems) on a StepOnePlus instrument (Applied Biosystems/Life technologies) before cluster generation and sequencing. .. A 16 pM solution of DNA libraries in equimolar amounts was subjected to cluster generation on the cBot instrument (Illumina Inc.) using the TruSeq PE cluster kit v3.

    Article Title: A phenol/chloroform-free method to extract nucleic acids from recalcitrant, woody tropical species for gene expression and sequencing
    Article Snippet: .. Libraries were quantified by qRT-PCR using the Library Quantification Kit for Illumina sequencing platforms (KAPA Biosystems, Boston, USA), using a CFX96 Touch™ Real-Time PCR Detection System (Bio-Rad Laboratories, California, USA). .. The libraries were normalised to a working concentration of 4 nM using the molarity calculated from qRT-PCR, adjusted for fragment size.

    Sequencing:

    Article Title: RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study
    Article Snippet: .. The adapter-ligated fragments were quantified by qPCR using the Library quantification kit for Illumina (KAPA Biosystems) on a StepOnePlus instrument (Applied Biosystems/Life Technologies) prior to cluster generation and sequencing. .. Cluster generation and sequencing An 11 pM solution of sequencing library was subjected to cluster generation and paired-end sequencing with 100 bp read length on the HiSeq 2500 system (Illumina Inc.) using v3 chemistry according to the manufacturer’s protocols.

    Article Title: A systematic comparison of error correction enzymes by next-generation sequencing
    Article Snippet: .. Then, the individually prepared sequencing libraries were quantified using the Library Quantification Kit-Illumina (KAPA Biosystems), according to the provided protocol. .. Barcoded libraries were subsequently mixed to \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$ \sim$\end{document}10 nM concentration, and the mixed libraries were quantified again before being loaded onto an Illumina MiSeq with a V2 300 cycle kit.

    Article Title: Massive functional mapping of a 5?-UTR by saturation mutagenesis, phenotypic sorting and deep sequencing
    Article Snippet: .. The adapter-ligated fragments were quantified by quantitative PCR (qPCR) using the Library quantification kit for Illumina (KAPA Biosystems) on a StepOnePlus instrument (Applied Biosystems/Life technologies) before cluster generation and sequencing. .. A 16 pM solution of DNA libraries in equimolar amounts was subjected to cluster generation on the cBot instrument (Illumina Inc.) using the TruSeq PE cluster kit v3.

    Article Title: A phenol/chloroform-free method to extract nucleic acids from recalcitrant, woody tropical species for gene expression and sequencing
    Article Snippet: .. Libraries were quantified by qRT-PCR using the Library Quantification Kit for Illumina sequencing platforms (KAPA Biosystems, Boston, USA), using a CFX96 Touch™ Real-Time PCR Detection System (Bio-Rad Laboratories, California, USA). .. The libraries were normalised to a working concentration of 4 nM using the molarity calculated from qRT-PCR, adjusted for fragment size.

    Article Title: Chromatin structure analysis enables detection of DNA insertions into the mammalian nuclear genome
    Article Snippet: .. Sequencing libraries were quantified with Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies, CA) and Illumina/Universal Quantification Kit (KAPA Biosystems, MA), and DNA fragment sizes were determined using the Bioanalyzer High Sensitivity ChIP (Agilent Technologies, CA). .. Cluster Generation was performed on the cBot (Illumina, CA) and sequencing was performed on the Genome Analyzer IIx (Illumina, CA), generating 35 bp single end reads ( a).

    Chromatin Immunoprecipitation:

    Article Title: Chromatin structure analysis enables detection of DNA insertions into the mammalian nuclear genome
    Article Snippet: .. Sequencing libraries were quantified with Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies, CA) and Illumina/Universal Quantification Kit (KAPA Biosystems, MA), and DNA fragment sizes were determined using the Bioanalyzer High Sensitivity ChIP (Agilent Technologies, CA). .. Cluster Generation was performed on the cBot (Illumina, CA) and sequencing was performed on the Genome Analyzer IIx (Illumina, CA), generating 35 bp single end reads ( a).

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    Kapa Biosystems library quantification kit illumina
    Schematic of enzymatic error correction and downstream data processing. We assembled our 142 bp product from two 113 nt oligos consisting of a 21 nt primer, a 64 nt payload and a 28 nt overlap region. After annealing and overlap extension, we amplified our template via polymerase chain reaction (PCR), yielding 100 bp of template in-between the primer sites. We then denatured and re-annealed the PCR products to form heteroduplexes, thereby exposing any errors (shown in green). After, we subjected the pool of heteroduplexes to two successive rounds of ten different enzymatic error correction treatments. At each step, we took aliquots and sequenced the products on an <t>Illumina</t> MiSeq with fully overlapping forward and reverse reads. To mitigate sequencing errors, we used BBMerge to merge reads with a perfect agreement between the forward and reverse reads. We then aligned these sequences to the designed reference using an exhaustive Neeleman–Wunsch aligner to minimize alignment artifacts. Finally, we further processed the alignments to quantitate the types and extent of different errors across all conditions.
    Library Quantification Kit Illumina, supplied by Kapa Biosystems, used in various techniques. Bioz Stars score: 99/100, based on 178 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/library quantification kit illumina/product/Kapa Biosystems
    Average 99 stars, based on 178 article reviews
    Price from $9.99 to $1999.99
    library quantification kit illumina - by Bioz Stars, 2020-09
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    93
    Kapa Biosystems qpcr method
    Bland and Altman plot of differences between quantification methods <t>(Qubit</t> and <t>qPCR)</t> versus the mean of those measurements. Dashed lines represent the calculated limits of agreement (95%). In this plot, Qubit measurements were converted using a factor
    Qpcr Method, supplied by Kapa Biosystems, used in various techniques. Bioz Stars score: 93/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/qpcr method/product/Kapa Biosystems
    Average 93 stars, based on 2 article reviews
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    Schematic of enzymatic error correction and downstream data processing. We assembled our 142 bp product from two 113 nt oligos consisting of a 21 nt primer, a 64 nt payload and a 28 nt overlap region. After annealing and overlap extension, we amplified our template via polymerase chain reaction (PCR), yielding 100 bp of template in-between the primer sites. We then denatured and re-annealed the PCR products to form heteroduplexes, thereby exposing any errors (shown in green). After, we subjected the pool of heteroduplexes to two successive rounds of ten different enzymatic error correction treatments. At each step, we took aliquots and sequenced the products on an Illumina MiSeq with fully overlapping forward and reverse reads. To mitigate sequencing errors, we used BBMerge to merge reads with a perfect agreement between the forward and reverse reads. We then aligned these sequences to the designed reference using an exhaustive Neeleman–Wunsch aligner to minimize alignment artifacts. Finally, we further processed the alignments to quantitate the types and extent of different errors across all conditions.

    Journal: Nucleic Acids Research

    Article Title: A systematic comparison of error correction enzymes by next-generation sequencing

    doi: 10.1093/nar/gkx691

    Figure Lengend Snippet: Schematic of enzymatic error correction and downstream data processing. We assembled our 142 bp product from two 113 nt oligos consisting of a 21 nt primer, a 64 nt payload and a 28 nt overlap region. After annealing and overlap extension, we amplified our template via polymerase chain reaction (PCR), yielding 100 bp of template in-between the primer sites. We then denatured and re-annealed the PCR products to form heteroduplexes, thereby exposing any errors (shown in green). After, we subjected the pool of heteroduplexes to two successive rounds of ten different enzymatic error correction treatments. At each step, we took aliquots and sequenced the products on an Illumina MiSeq with fully overlapping forward and reverse reads. To mitigate sequencing errors, we used BBMerge to merge reads with a perfect agreement between the forward and reverse reads. We then aligned these sequences to the designed reference using an exhaustive Neeleman–Wunsch aligner to minimize alignment artifacts. Finally, we further processed the alignments to quantitate the types and extent of different errors across all conditions.

    Article Snippet: Then, the individually prepared sequencing libraries were quantified using the Library Quantification Kit-Illumina (KAPA Biosystems), according to the provided protocol.

    Techniques: Amplification, Polymerase Chain Reaction, Sequencing

    Comparison of Illumina high-throughput sequencing and Illumina miRNA Bead Arrays v2 performance in thyroid tumor samples. Each dot represents the abundance of one mature miRNA in 1 of 20 samples in HTS (x-axis) and the fluorescent intensity of the corresponding spot on the microarray (y-axis) of all 20 samples. Expression values are based on normalized data, assuming perfect matching of microarray probe sequence and HTS sequence reads. The figure illustrates the saturation of microarray signals compared to the number of HTS reads and a lack of specificity of microarray probe hybridizations by the presence of fluorescent signal for miRNA targets without any HTS reads (x-axis position -∞). Because RPM normalization of low read counts generates visual artifact (column-like data structures between 0 and 5 RPM) we excluded all miRNAs with a very low abundance of one or two reads in individual samples. The correlation coefficient between the microarray and HTS data set is 0.67.

    Journal: BMC Research Notes

    Article Title: Analysis options for high-throughput sequencing in miRNA expression profiling

    doi: 10.1186/1756-0500-7-144

    Figure Lengend Snippet: Comparison of Illumina high-throughput sequencing and Illumina miRNA Bead Arrays v2 performance in thyroid tumor samples. Each dot represents the abundance of one mature miRNA in 1 of 20 samples in HTS (x-axis) and the fluorescent intensity of the corresponding spot on the microarray (y-axis) of all 20 samples. Expression values are based on normalized data, assuming perfect matching of microarray probe sequence and HTS sequence reads. The figure illustrates the saturation of microarray signals compared to the number of HTS reads and a lack of specificity of microarray probe hybridizations by the presence of fluorescent signal for miRNA targets without any HTS reads (x-axis position -∞). Because RPM normalization of low read counts generates visual artifact (column-like data structures between 0 and 5 RPM) we excluded all miRNAs with a very low abundance of one or two reads in individual samples. The correlation coefficient between the microarray and HTS data set is 0.67.

    Article Snippet: The barcoded libraries were size restricted between 140 and 165 bp, purified and quantified using the Library Quantification Kit - Illumina/Universal (KAPA Biosystems) according to the instructions of the manufacturer.

    Techniques: Next-Generation Sequencing, Microarray, Expressing, Sequencing

    Effect of DNA extraction method on double stranded DNA yield, nucleic acids quality metrics and quantitative PCR analysis. The CHAO method gave the maximum concentration of amplicons per mass (g) of faecal samples ( a ). While PHEC method had the highest double stranded DNA concentration ( bottom left ) for the probiotic capsule, the absorbance ratio 260/280 indicated that the extracted nucleic acids were of low purity ( top left ). Right panel ( b ) shows the 16S rRNA amplicon copies in qPCR analysis. ED, AB, IM correspond to the three faecal sample and VSL to the proprietary probiotic capsule ID respectively

    Journal: BMC Research Notes

    Article Title: The effect of DNA extraction methodology on gut microbiota research applications

    doi: 10.1186/s13104-016-2171-7

    Figure Lengend Snippet: Effect of DNA extraction method on double stranded DNA yield, nucleic acids quality metrics and quantitative PCR analysis. The CHAO method gave the maximum concentration of amplicons per mass (g) of faecal samples ( a ). While PHEC method had the highest double stranded DNA concentration ( bottom left ) for the probiotic capsule, the absorbance ratio 260/280 indicated that the extracted nucleic acids were of low purity ( top left ). Right panel ( b ) shows the 16S rRNA amplicon copies in qPCR analysis. ED, AB, IM correspond to the three faecal sample and VSL to the proprietary probiotic capsule ID respectively

    Article Snippet: Amplicon concentration was quantified with use of KAPA SYBR® FAST qPCR Kit (Kapa biosystems, KK4824, UK), diluted to 40 pM and spiked with 40 pM of genomic DNA to avoid base-calling issues due to low base diversity.

    Techniques: DNA Extraction, Real-time Polymerase Chain Reaction, Concentration Assay, Amplification

    Bland and Altman plot of differences between quantification methods (Qubit and qPCR) versus the mean of those measurements. Dashed lines represent the calculated limits of agreement (95%). In this plot, Qubit measurements were converted using a factor

    Journal: Forensic science international. Genetics

    Article Title: Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq

    doi: 10.1016/j.fsigen.2014.05.007

    Figure Lengend Snippet: Bland and Altman plot of differences between quantification methods (Qubit and qPCR) versus the mean of those measurements. Dashed lines represent the calculated limits of agreement (95%). In this plot, Qubit measurements were converted using a factor

    Article Snippet: 3.5 Quantification To assess the accuracy of our template quantification step, a subset of samples (n=92) was quantified by two methods, following the manufacture’s recommendations: 1) a dsDNA-specific fluorescent dye method (Qubit), and 2) a qPCR method (KAPA Biosystem library quantification kit).

    Techniques: Real-time Polymerase Chain Reaction