bioanalyzer dna high sensitivity chip  (Agilent technologies)

 
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    Name:
    High Sensitivity DNA BioAnalyzer Kit
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    Catalog Number:
    1806
    Price:
    None
    Score:
    85
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    Agilent technologies bioanalyzer dna high sensitivity chip

    https://www.bioz.com/result/bioanalyzer dna high sensitivity chip/product/Agilent technologies
    Average 99 stars, based on 30 article reviews
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    bioanalyzer dna high sensitivity chip - by Bioz Stars, 2019-10
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    Amplification:

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

    Article Title: Phase-defined complete sequencing of the HLA genes by next-generation sequencing
    Article Snippet: Each amplification reaction contained 20 ng of genomic DNA, 0.25 unit of PrimeSTAR® GXL DNA polymerase (TAKARA BIO INC., Japan), 1× PrimeSTAR® GXL buffer (Mg2+ concentration 1 mM), 0.2 mM of each dNTP, and 0.2 μM of each primer in a 10 μl reaction volume. .. Each sample was dual indexed and equally pooled by evaluating the molar concentration by Agilent High Sensitivity DNA Kit and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

    Article Title: Physiological Expression of Ion Channel Receptors in Human Periodontal Ligament Stem Cells
    Article Snippet: A second PCR amplification was done following the same protocol as that of the first one, except for the cycles (just 10 instead of 15). .. The Bioanalyzer instrument (Agilent High Sensitivity DNA Kit, Richardson, TX, USA) was used to validate the quality of the library.

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

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

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

    Article Title: Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA
    Article Snippet: Seventh, we amplified libraries for as few cycles as necessary using a KAPA Real-Time PCR Library Amplification Kit (Kapa Biosystems) and PCR primers developed by the Broad Institute [Additional file ]. .. Finally, we quantified libraries using a KAPA Library Quantification Kit (Kapa Biosystems) and an Agilent Bioanalyzer High Sensitivity DNA Kit.

    Article Title: Construction and Characterization of Synthetic Bacterial Community for Experimental Ecology and Evolution
    Article Snippet: Samples were pooled together in equal volumes and purified with Agencourt® AMPure® XP beads (Beckman Coulter, Brea, CA, United States) twice using 0.8 × volume of beads compared to the sample pool volume (40 μl). .. The ready amplicon library was diluted to 1:10 and 1:20 and quantified with the Agilent 2100 Bioanalyzer High Sensitivity DNA Analysis Kit (Agilent Genomics, Santa Clara, CA, United States). .. The 16S rRNA gene amplicon pool was sequenced with Illumina MiSeq System using the Illumina MiSeq Reagent Kit v3 600 cycles kit (Illumina, San Diego, CA, United States).

    Whole Genome Amplification:

    Article Title: Aneuploidy of chromosome 8 and mutation of circulating tumor cells predict pathologic complete response in the treatment of locally advanced rectal cancer
    Article Snippet: Paragraph title: WGA quality control on Agilent 2100 ... A BioAnalyzer High Sensitivity DNA kit (Agilent Technologies, Inc.) was used to visualize the size range of MALBAC products.

    Construct:

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

    Article Title: Draft Genome of the Multidrug-Resistant Acinetobacter baumannii Strain A155 Clinical Isolate
    Article Snippet: The Nextera XT kit (Illumina, Inc., San Diego, CA, USA) was used to simultaneously fragment and construct adapter-tagged libraries per the manufacturer’s instructions. .. The Bioanalyzer 2100 High Sensitivity DNA analysis kit (Agilent Technologies, Santa Clara, CA, USA) with version B.02.08.SI648 software was used to determine the fragmentation of the resultant libraries.

    SYBR Green Assay:

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

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

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

    Incubation:

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

    Size-exclusion Chromatography:

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

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

    Expressing:

    Article Title: Exosomes impact survival to radiation exposure in cell line models of nervous system cancer
    Article Snippet: Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies). .. De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) were quality trimmed/filtered using The FASTX-Toolkit ( ).

    Modification:

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

    Hybridization:

    Article Title: Optimization of Extraction of Circulating RNAs from Plasma – Enabling Small RNA Sequencing
    Article Snippet: Multiplex adaptor ligations, reverse transcription primer hybridization, reverse transcription reaction and the PCR amplification were processed with regard to the protocol for library preparation (Protocol E7330, New England BioLabs Inc., USA). .. A concluding Bioanalyzer 2100 run with the High Sensitivity DNA Kit (Agilent Technologies, Germany) that allows the analysis of DNA libraries regarding size, purity and concentration completed the workflow of library preparation.

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

    Article Title: Next-generation sequencing using a pre-designed gene panel for the molecular diagnosis of congenital disorders in pediatric patients
    Article Snippet: During the 16-h hybridization process, HaloPlex ION Barcodes and Ion Torrent sequencing motifs were incorporated into the targeted fragments. .. Amplicons ranging from 150 to 550 bp were then quantified using an Agilent BioAnalyzer High Sensitivity DNA Assay kit on the 2100 Bioanalyzer to validate the enrichment of the libraries.

    Flow Cytometry:

    Article Title: Next-generation sequencing using a pre-designed gene panel for the molecular diagnosis of congenital disorders in pediatric patients
    Article Snippet: Amplicons ranging from 150 to 550 bp were then quantified using an Agilent BioAnalyzer High Sensitivity DNA Assay kit on the 2100 Bioanalyzer to validate the enrichment of the libraries. .. The template-positive Ion Sphere Particles (ISPs) were then enriched with the Ion OneTouchTM ES and loaded on an Ion 318TM Chip v1.

    Article Title: Exosomes impact survival to radiation exposure in cell line models of nervous system cancer
    Article Snippet: Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions. .. Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).

    Sequencing:

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

    Article Title: Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing
    Article Snippet: For gDNA sequencing, we sheared gDNA with Covaris S220 AFA (Covaris) according to the manufacturer’s instructions prior to Illumina library preparation. .. We assessed library quality and quantity on the 2100 Bioanalyzer (Agilent) using the High Sensitivity DNA Kit (Agilent), and by qPCR with the Kapa Library quantification Kit (KapaBiosystems).

    Article Title: Current Protocols in Molecular Biology Unit 4.23
    Article Snippet: After purification by an 8% polyacrylamide gel, a DNA library can be quantified by Agilent Bioanalyzer analysis (High-sensitivity DNA Kit) as well as by Quantitative-PCR (Q-PCR) analysis by comparison to previously calibrated/sequenced DNA libraries using Q-PCR checking primers F and R ( ). .. After purification by an 8% polyacrylamide gel, a DNA library can be quantified by Agilent Bioanalyzer analysis (High-sensitivity DNA Kit) as well as by Quantitative-PCR (Q-PCR) analysis by comparison to previously calibrated/sequenced DNA libraries using Q-PCR checking primers F and R ( ).

    Article Title: Phase-defined complete sequencing of the HLA genes by next-generation sequencing
    Article Snippet: Paragraph title: Sequencing of HLA genes ... Each sample was dual indexed and equally pooled by evaluating the molar concentration by Agilent High Sensitivity DNA Kit and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

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

    Article Title: Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs
    Article Snippet: To adjust loading amount of total RNA as 10 pg per IFC chamber, we prepared the 20 μL of Lysis Mix (2.4 μL of 3′ SMART-Seq CDS Primer II A (12 μM), 2 μL ES total RNA (11.11 ng/μL), 2 μL of 1:4500 ERCC RNA Spikes, 2.6 μL of 10× Reaction Buffer, 1 μL of C1 Loading Reagent, and 10 μL of RNase-free water). .. When we performed quality control of RamDA-seq library DNA using the Bioanalyzer Agilent High-Sensitivity DNA Kit, the typical yield of the sequencing library DNA obtained from one mESC or 10 pg of total RNA was 120–150 ng. .. To investigate the possibility of generating library DNAs derived from genomic DNA or environmental DNAs, we prepared transcriptase-minus and non-template control samples.

    Article Title: Physiological Expression of Ion Channel Receptors in Human Periodontal Ligament Stem Cells
    Article Snippet: The Bioanalyzer instrument (Agilent High Sensitivity DNA Kit, Richardson, TX, USA) was used to validate the quality of the library. .. A denaturation step through 2N NaOH was performed, and then it was diluted until it reached a concentration of 12 pM.

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

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

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

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

    Article Title: Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA
    Article Snippet: Paragraph title: Strand-specific, Non-polyA-selected, library preparation and sequencing ... Finally, we quantified libraries using a KAPA Library Quantification Kit (Kapa Biosystems) and an Agilent Bioanalyzer High Sensitivity DNA Kit.

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

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

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

    Ligation:

    Article Title: Optimization of Extraction of Circulating RNAs from Plasma – Enabling Small RNA Sequencing
    Article Snippet: These modifications are increasing the ligation efficiency of methylated RNAs such as piRNAs. .. A concluding Bioanalyzer 2100 run with the High Sensitivity DNA Kit (Agilent Technologies, Germany) that allows the analysis of DNA libraries regarding size, purity and concentration completed the workflow of library preparation.

    Magnetic Beads:

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

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

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

    Generated:

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

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

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

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

    DNA Sequencing:

    Article Title: Current Protocols in Molecular Biology Unit 4.23
    Article Snippet: Paragraph title: Quantification of DNA sequencing library ... After purification by an 8% polyacrylamide gel, a DNA library can be quantified by Agilent Bioanalyzer analysis (High-sensitivity DNA Kit) as well as by Quantitative-PCR (Q-PCR) analysis by comparison to previously calibrated/sequenced DNA libraries using Q-PCR checking primers F and R ( ).

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

    Reverse Transcription Polymerase Chain Reaction:

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

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

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

    Binding Assay:

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

    DNA Extraction:

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

    RNA Sequencing Assay:

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

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

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

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

    Fluorescence:

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

    Methylation:

    Article Title: Optimization of Extraction of Circulating RNAs from Plasma – Enabling Small RNA Sequencing
    Article Snippet: These modifications are increasing the ligation efficiency of methylated RNAs such as piRNAs. .. A concluding Bioanalyzer 2100 run with the High Sensitivity DNA Kit (Agilent Technologies, Germany) that allows the analysis of DNA libraries regarding size, purity and concentration completed the workflow of library preparation.

    Isolation:

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

    Multiplex Assay:

    Article Title: Optimization of Extraction of Circulating RNAs from Plasma – Enabling Small RNA Sequencing
    Article Snippet: Multiplex adaptor ligations, reverse transcription primer hybridization, reverse transcription reaction and the PCR amplification were processed with regard to the protocol for library preparation (Protocol E7330, New England BioLabs Inc., USA). .. A concluding Bioanalyzer 2100 run with the High Sensitivity DNA Kit (Agilent Technologies, Germany) that allows the analysis of DNA libraries regarding size, purity and concentration completed the workflow of library preparation.

    Article Title: Phase-defined complete sequencing of the HLA genes by next-generation sequencing
    Article Snippet: Each sample was dual indexed and equally pooled by evaluating the molar concentration by Agilent High Sensitivity DNA Kit and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). .. Each sample was dual indexed and equally pooled by evaluating the molar concentration by Agilent High Sensitivity DNA Kit and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

    Purification:

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

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

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

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

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

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

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

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

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

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

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

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

    Polymerase Chain Reaction:

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

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

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

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

    Article Title: Phase-defined complete sequencing of the HLA genes by next-generation sequencing
    Article Snippet: Briefly, PCR product was treated with the Tn5 transposase artificially loaded with synthetic oligonucleotides, enabling simultaneous fragmentation and addition of an adaptor. .. Each sample was dual indexed and equally pooled by evaluating the molar concentration by Agilent High Sensitivity DNA Kit and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

    Article Title: Haplotyping germline and cancer genomes using high-throughput linked-read sequencing
    Article Snippet: Two ul of lysate was used for a 20 ul PCR reaction. .. The PCR products were visualized using the BioAnalyzer High Sensitivity DNA Kit (Agilent), with respectively the amplicons ACTB diluted 1:50, EML4/ALK 1:20, and ALK/PTPN3 diluted 1:3. .. The primers for the EML4/ALK amplicon are (F) 5′-GCATAAAGATGTCATCATCAACCAAG; (R) 5′-CGGAGCTTGCTCAGCTTGTA.

    Article Title: Physiological Expression of Ion Channel Receptors in Human Periodontal Ligament Stem Cells
    Article Snippet: A second PCR amplification was done following the same protocol as that of the first one, except for the cycles (just 10 instead of 15). .. The Bioanalyzer instrument (Agilent High Sensitivity DNA Kit, Richardson, TX, USA) was used to validate the quality of the library.

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

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

    Article Title: Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA
    Article Snippet: Each library except for T6, T14, and TT8 required only four PCR cycles, while T14 and TT8 required eight PCR cycles, and T6 required twelve PCR cycles. .. Finally, we quantified libraries using a KAPA Library Quantification Kit (Kapa Biosystems) and an Agilent Bioanalyzer High Sensitivity DNA Kit.

    Article Title: Construction and Characterization of Synthetic Bacterial Community for Experimental Ecology and Evolution
    Article Snippet: After PCR, random samples were measured with LabChip GX Touch HT DNA High Sensitivity Reagent Kit (Perkin Elmer, Waltham, MA, United States) to check that the PCR was successful with the correct product size. .. The ready amplicon library was diluted to 1:10 and 1:20 and quantified with the Agilent 2100 Bioanalyzer High Sensitivity DNA Analysis Kit (Agilent Genomics, Santa Clara, CA, United States).

    Quantitative RT-PCR:

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

    Gel Extraction:

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

    cDNA Library Assay:

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

    Agarose Gel Electrophoresis:

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

    Chromatin Immunoprecipitation:

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

    RNA Extraction:

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

    Software:

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

    Real-time Polymerase Chain Reaction:

    Article Title: Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing
    Article Snippet: For gDNA sequencing, we sheared gDNA with Covaris S220 AFA (Covaris) according to the manufacturer’s instructions prior to Illumina library preparation. .. We assessed library quality and quantity on the 2100 Bioanalyzer (Agilent) using the High Sensitivity DNA Kit (Agilent), and by qPCR with the Kapa Library quantification Kit (KapaBiosystems). .. We generated clusters on the Illumina flow cell using the automatic cBot station and the TruSeq PE Cluster Kit v3-cBot-HS.

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

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

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

    Negative Control:

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

    Selection:

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

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

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

    Sample Prep:

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

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

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

    Electrophoresis:

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

    Next-Generation Sequencing:

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

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

    Multiple Annealing and Looping–Based Amplification Cycles:

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

    Spectrophotometry:

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

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

    Concentration Assay:

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

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

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

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

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

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

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

    Gel Purification:

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

    FACS:

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

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    Agilent technologies bioanalyzer dna high sensitivity chip kit
    Inter-individual variability of cell-free <t>DNA</t> (cfDNA) concentration. Plasma from circulating tumor cell (CTC)-depleted (depl.)_blood (by AdnaTest EMT-2/StemCell Select) and matched plasma from whole blood were used in the same volume for cfDNA isolation with a QIAamp MinElute ccfDNA Kit, and cfDNA was quantified using an <t>Agilent</t> High Sensitivity Chip (fragments between 100–700 bp).
    Bioanalyzer Dna High Sensitivity Chip Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 17 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Inter-individual variability of cell-free DNA (cfDNA) concentration. Plasma from circulating tumor cell (CTC)-depleted (depl.)_blood (by AdnaTest EMT-2/StemCell Select) and matched plasma from whole blood were used in the same volume for cfDNA isolation with a QIAamp MinElute ccfDNA Kit, and cfDNA was quantified using an Agilent High Sensitivity Chip (fragments between 100–700 bp).

    Journal: Cancers

    Article Title: Cell-Free DNA Variant Sequencing Using CTC-Depleted Blood for Comprehensive Liquid Biopsy Testing in Metastatic Breast Cancer

    doi: 10.3390/cancers11020238

    Figure Lengend Snippet: Inter-individual variability of cell-free DNA (cfDNA) concentration. Plasma from circulating tumor cell (CTC)-depleted (depl.)_blood (by AdnaTest EMT-2/StemCell Select) and matched plasma from whole blood were used in the same volume for cfDNA isolation with a QIAamp MinElute ccfDNA Kit, and cfDNA was quantified using an Agilent High Sensitivity Chip (fragments between 100–700 bp).

    Article Snippet: Capillary electrophoresis using the Agilent High Sensitivity DNA Chip resolved the fragment length of the cfDNA.

    Techniques: Concentration Assay, Isolation, Chromatin Immunoprecipitation

    Size distribution of cfDNA. Matched cfDNA samples isolated from CTC-depl. blood ( B , D ; CTC isolation using AdnaTest EMT-2/StemCell Select) and from whole blood ( A , C ) of two exemplary patients ( A + B ; C + D ) displayed a large mononucleosomal fraction and, in general, a similar size distribution without high-molecular-weight DNA (700–10,000 bp). Capillary electrophoresis was performed with an Agilent High Sensitivity Chip. (A) Cell-free DNA eluate from whole blood of patient 2, diluted 1:40; ( B ) cfDNA eluate from CTC-depl. blood of patient 2, diluted 1:40; ( C ) cfDNA eluate from whole blood of patient 3, diluted 1:5; (D) cfDNA eluate from CTC-depl. blood of patient 3, diluted 1:20.

    Journal: Cancers

    Article Title: Cell-Free DNA Variant Sequencing Using CTC-Depleted Blood for Comprehensive Liquid Biopsy Testing in Metastatic Breast Cancer

    doi: 10.3390/cancers11020238

    Figure Lengend Snippet: Size distribution of cfDNA. Matched cfDNA samples isolated from CTC-depl. blood ( B , D ; CTC isolation using AdnaTest EMT-2/StemCell Select) and from whole blood ( A , C ) of two exemplary patients ( A + B ; C + D ) displayed a large mononucleosomal fraction and, in general, a similar size distribution without high-molecular-weight DNA (700–10,000 bp). Capillary electrophoresis was performed with an Agilent High Sensitivity Chip. (A) Cell-free DNA eluate from whole blood of patient 2, diluted 1:40; ( B ) cfDNA eluate from CTC-depl. blood of patient 2, diluted 1:40; ( C ) cfDNA eluate from whole blood of patient 3, diluted 1:5; (D) cfDNA eluate from CTC-depl. blood of patient 3, diluted 1:20.

    Article Snippet: Capillary electrophoresis using the Agilent High Sensitivity DNA Chip resolved the fragment length of the cfDNA.

    Techniques: Isolation, Molecular Weight, Electrophoresis, Chromatin Immunoprecipitation

    L-EVs isolated from plasma of mCRPC patients contain large size DNA with tumour aberrations . (a) DNA quantitation in plasma-derived L-EVs and S-EVs, as well as EV-free DNA obtained from mCRPC patients ( n = 4) indicates that a significant portion of circulating DNA is enclosed in L-EVs. The EV-free DNA was extracted from EV-depleted plasma. (b) Chip-based capillary electrophoresis (Bioanalyzer) showing that L-EVs isolated from 1 ml of mCRPC patient plasma ( n = 3) contain high-quality, large size DNA. (c) EVs were isolated from 1 ml of plasma obtained from mCRPC patients ( n = 4), EV DNA was extracted in agarose plugs by incubation in lysis buffer for 48 h, and high molecular weight DNA was resolved by PFGE. Similar to L-EVs in vitro , patient plasma-derived L-EVs contain high molecular weight DNA (100 kbp–2 Mbp) (indicated by red dashed lines). (d) MYC/PTEN copy number imbalance in PC3 L-EVs was analysed by digital PCR (dPCR) using different amounts of DNA template. (e) MYC/PTEN copy number imbalance was evaluated in L-EVs isolated from 1 ml of mCRPC patient plasma ( n = 6) and compared to MYC/PTEN copy number in normal DNA extracted from the indicated benign cell lines. * p

    Journal: Journal of Extracellular Vesicles

    Article Title: Large extracellular vesicles carry most of the tumour DNA circulating in prostate cancer patient plasma

    doi: 10.1080/20013078.2018.1505403

    Figure Lengend Snippet: L-EVs isolated from plasma of mCRPC patients contain large size DNA with tumour aberrations . (a) DNA quantitation in plasma-derived L-EVs and S-EVs, as well as EV-free DNA obtained from mCRPC patients ( n = 4) indicates that a significant portion of circulating DNA is enclosed in L-EVs. The EV-free DNA was extracted from EV-depleted plasma. (b) Chip-based capillary electrophoresis (Bioanalyzer) showing that L-EVs isolated from 1 ml of mCRPC patient plasma ( n = 3) contain high-quality, large size DNA. (c) EVs were isolated from 1 ml of plasma obtained from mCRPC patients ( n = 4), EV DNA was extracted in agarose plugs by incubation in lysis buffer for 48 h, and high molecular weight DNA was resolved by PFGE. Similar to L-EVs in vitro , patient plasma-derived L-EVs contain high molecular weight DNA (100 kbp–2 Mbp) (indicated by red dashed lines). (d) MYC/PTEN copy number imbalance in PC3 L-EVs was analysed by digital PCR (dPCR) using different amounts of DNA template. (e) MYC/PTEN copy number imbalance was evaluated in L-EVs isolated from 1 ml of mCRPC patient plasma ( n = 6) and compared to MYC/PTEN copy number in normal DNA extracted from the indicated benign cell lines. * p

    Article Snippet: DNA quality was assessed using the Bioanalyzer DNA High Sensitivity Chip Kit (Agilent).

    Techniques: Isolation, Quantitation Assay, Derivative Assay, Chromatin Immunoprecipitation, Electrophoresis, Incubation, Lysis, Molecular Weight, In Vitro, Digital PCR

    Most extracellular DNA is packaged into L-EVs . (a) Tunable resistive pulse sensing (TRPS, qNano) using two different pore membranes (NP4000 and NP200) identified as L-EVs (left) and S-EVs (right) derived from PC3 cells. NP4000 membrane, which can detect particles with a diameter between 1.0 and 6.0 μm, was used for quantitation of L-EVs, while NP200 membrane, which can detect particles with a diameter between 60 and 400 nm, was used for quantitation of S-EVs. (b) Protein lysates from L-EVs and S-EVs purified by iodixanol density gradient (at 1.10 and 1.15 g/ml) were blotted with LO markers HSPA5 and CK18, and with Exo marker CD81. (c) Total DNA was quantified by Qubit Fluorometer in L-EVs and S-EVs isolated from PC3 and U87 cell lines. The plot shows the DNA ratio between L-EVs and S-EVs. (d) Double stranded (ds)DNA was quantified by High Sensitivity (HS) dsDNA Qubit Assay in L-EVs and S-EVs isolated from 1 ml of plasma from patients with mCRPC ( n = 40) and cancer-free individuals ( n = 6). (e) Quantification of both protein and DNA content in L-EVs and S-EVs isolated from conditioned media of 12.6 × 10 7 PC3 cells. (f) Single stranded (ss) and dsDNA in PC3-derived L-EVs and S-EVs, with or without treatment with DNase I and Exonuclease III, were quantified by Qubit. (g) Chip-based capillary electrophoresis (Bioanalyzer) showing the presence of dsDNA in PC3-derived L-EVs and S-EVs, with or without treatment with DNase I and Endonuclease III. L-EVs contain abundant DNA with a large peak around 10 kbp. Conversely, the amount of DNA in S-EVs is negligible. (h) ss- and dsDNA in PC3-derived L-EVs and S-EVs were quantified by Qubit after treatment with nucleases (DNase I and Exonuclease III) with or without addition of a detergent (Triton X-100) prior to nuclease treatment. (i) Chip-based capillary electrophoresis (Bioanalyzer) showing that only miniscule amounts of dsDNA could be detected after EV lysis using a detergent prior to treatment with nucleases.

    Journal: Journal of Extracellular Vesicles

    Article Title: Large extracellular vesicles carry most of the tumour DNA circulating in prostate cancer patient plasma

    doi: 10.1080/20013078.2018.1505403

    Figure Lengend Snippet: Most extracellular DNA is packaged into L-EVs . (a) Tunable resistive pulse sensing (TRPS, qNano) using two different pore membranes (NP4000 and NP200) identified as L-EVs (left) and S-EVs (right) derived from PC3 cells. NP4000 membrane, which can detect particles with a diameter between 1.0 and 6.0 μm, was used for quantitation of L-EVs, while NP200 membrane, which can detect particles with a diameter between 60 and 400 nm, was used for quantitation of S-EVs. (b) Protein lysates from L-EVs and S-EVs purified by iodixanol density gradient (at 1.10 and 1.15 g/ml) were blotted with LO markers HSPA5 and CK18, and with Exo marker CD81. (c) Total DNA was quantified by Qubit Fluorometer in L-EVs and S-EVs isolated from PC3 and U87 cell lines. The plot shows the DNA ratio between L-EVs and S-EVs. (d) Double stranded (ds)DNA was quantified by High Sensitivity (HS) dsDNA Qubit Assay in L-EVs and S-EVs isolated from 1 ml of plasma from patients with mCRPC ( n = 40) and cancer-free individuals ( n = 6). (e) Quantification of both protein and DNA content in L-EVs and S-EVs isolated from conditioned media of 12.6 × 10 7 PC3 cells. (f) Single stranded (ss) and dsDNA in PC3-derived L-EVs and S-EVs, with or without treatment with DNase I and Exonuclease III, were quantified by Qubit. (g) Chip-based capillary electrophoresis (Bioanalyzer) showing the presence of dsDNA in PC3-derived L-EVs and S-EVs, with or without treatment with DNase I and Endonuclease III. L-EVs contain abundant DNA with a large peak around 10 kbp. Conversely, the amount of DNA in S-EVs is negligible. (h) ss- and dsDNA in PC3-derived L-EVs and S-EVs were quantified by Qubit after treatment with nucleases (DNase I and Exonuclease III) with or without addition of a detergent (Triton X-100) prior to nuclease treatment. (i) Chip-based capillary electrophoresis (Bioanalyzer) showing that only miniscule amounts of dsDNA could be detected after EV lysis using a detergent prior to treatment with nucleases.

    Article Snippet: DNA quality was assessed using the Bioanalyzer DNA High Sensitivity Chip Kit (Agilent).

    Techniques: Tunable Resistive Pulse Sensing, Derivative Assay, Quantitation Assay, Purification, Marker, Isolation, HS DSDNA Qubit Assay, Chromatin Immunoprecipitation, Electrophoresis, Lysis