s2 ultrasonicator  (Covaris)


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    Covaris s2 ultrasonicator
    S2 Ultrasonicator, supplied by Covaris, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/s2 ultrasonicator/product/Covaris
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    s2 ultrasonicator - by Bioz Stars, 2020-02
    95/100 stars

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    Related Articles

    Amplification:

    Article Title: TMEM231, mutated in orofaciodigital and Meckel syndromes, organizes the ciliary transition zone
    Article Snippet: All coding exons and exon–intron boundaries of TMEM231 were amplified in 1,056 patients with nephronophthisis-related ciliopathies in a large-scale microfluidic multiplex PCR by using a Fluidigm Access Array system (48.48). .. In brief, SureSelect libraries (Agilent Technologies) were prepared from 3 µg of genomic DNA sheared with an S2 Ultrasonicator (Covaris) according to the manufacturers’ instructions.

    Article Title: The Cost of Metabolic Interactions in Symbioses between Insects and Bacteria with Reduced Genomes
    Article Snippet: The extracted DNA (1 to 2 µg per sample) was fragmented using an S2 ultrasonicator (Covaris) to obtain 700-bp fragments, which were end repaired with the End repair mix LC (Enzymatics) and A-tailed with the Klenow 3′→5′ exo-enzyme (Enzymatics). .. Universal Y-shaped adaptors were ligated using A-T ligation, adaptor-ligated DNA was purified and size-selected using AMPure XP beads (Agencourt), and DNA was subjected to 14 cycles of PCR amplification with barcoded Illumina index primers (see in the supplemental material).

    Article Title: Essential role of Nr2f nuclear receptors in patterning the vertebrate upper jaw
    Article Snippet: The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip (Agilent, Santa Clara, CA) and then reverse-transcribed into cDNA using the SMARTer kit (Clontech, Mountain View, CA). cDNA amplification was adjusted based on the RNA input quantity, and the size and amount of generated cDNA was measured by BioAnalyzer. .. The samples were sonicated on a S2 ultrasonicator (Covaris, Woburn, MA) according to Clontech’s recommendations.

    Filtration:

    Article Title: Deeper Insight in Beehives: Metagenomes of Royal Jelly, Pollen, and Honey from Lavender, Chestnut, and Fir Honeydew and Epiphytic and Endophytic Microbiota of Lavender and Rose Flowers
    Article Snippet: DNA of epiphytic microbiota from lavender and rose flowers were extracted by incubating flowers in PBS (1×) 0.15% Tween 20 with shaking (400 rpm) for 10 min, followed by a 5-min sonication step, shaking for 10 min (400 rpm) prior to prefiltration, and filtration on a 0.22-µm sterile filter (Millipore, Germany). .. For each sample, 0.1 to 1 µg of DNA was sheared in an AFA microTUBE (Covaris, USA) in an S2 ultrasonicator (Covaris) to achieve an average fragment size of 350 bp.

    Real-time Polymerase Chain Reaction:

    Article Title: Essential role of Nr2f nuclear receptors in patterning the vertebrate upper jaw
    Article Snippet: The samples were sonicated on a S2 ultrasonicator (Covaris, Woburn, MA) according to Clontech’s recommendations. .. DNA libraries were assembled using the Kapa Hyper Prep kit (Kapa Biosystems, Wilmington, MA) with NextFlex adapters (Bioo Scientific, Austin, TX), assessed by Bioanalyzer, and quantified using qPCR (Kapa Library Quantification kit, Kapa Biosystems).

    Article Title: Evidence for a pre-malignant cell line in a skin biopsy from a patient with Nijmegen breakage syndrome
    Article Snippet: The qPCR products were checked by agarose gel electrophoresis, visualized by UV-transilluminator and photographed. .. Genomic DNA was sheared using an S2 Ultrasonicator (Covaris, Woburn, MA, USA).

    Incubation:

    Article Title: Use of a Primary Epithelial Cell Screening Tool to Investigate Phage Therapy in Cystic Fibrosis
    Article Snippet: A 200 μL aliquot containing ∼1011 PFU of phage was incubated for 30 min at 37°C with 1 U of DNase I from the Invitrogen PureLink RNA Mini Kit. .. The sample (10 ng) was sheared using a S2 ultrasonicator (Covaris) and sequencing libraries prepared using a NEBnext Ultra library kit (New England Biosciences).

    Western Blot:

    Article Title: Use of a Primary Epithelial Cell Screening Tool to Investigate Phage Therapy in Cystic Fibrosis
    Article Snippet: DNA was subsequently extracted using a QIAamp DNA mini spin column kit (QIAGEN) per manufacturer’s instructions and sequenced (LotteryWest Sequencing Facility, University of Western Australia, Perth, WA, Australia). .. The sample (10 ng) was sheared using a S2 ultrasonicator (Covaris) and sequencing libraries prepared using a NEBnext Ultra library kit (New England Biosciences).

    Derivative Assay:

    Article Title: Global deceleration of gene evolution following recent genome hybridizations in fungi
    Article Snippet: .. Paired-end DNA libraries with insert size of 200–300 bp were derived from 1 µg genomic DNA followed by fragmentation with an S2 ultrasonicator (Covaris) and sequencing with Illumina HiSeq 2500 (Illumina). .. Mate pair libraries with insert size of ∼3 kb were prepared with Nextera Mate Pair Sample Prep Kit (Illumina) according to the manufacturer's protocol with some modifications ( ) and sequenced using HiSeq 2500 to generate 151-bp paired-end reads.

    Ligation:

    Article Title: The Cost of Metabolic Interactions in Symbioses between Insects and Bacteria with Reduced Genomes
    Article Snippet: The extracted DNA (1 to 2 µg per sample) was fragmented using an S2 ultrasonicator (Covaris) to obtain 700-bp fragments, which were end repaired with the End repair mix LC (Enzymatics) and A-tailed with the Klenow 3′→5′ exo-enzyme (Enzymatics). .. Universal Y-shaped adaptors were ligated using A-T ligation, adaptor-ligated DNA was purified and size-selected using AMPure XP beads (Agencourt), and DNA was subjected to 14 cycles of PCR amplification with barcoded Illumina index primers (see in the supplemental material).

    Generated:

    Article Title: TMEM231, mutated in orofaciodigital and Meckel syndromes, organizes the ciliary transition zone
    Article Snippet: Consecutively, generated amplicons from 1,056 patients were pooled and submitted to next generation sequencing, performed on a Genome Analyzer II platform (Illumina). .. In brief, SureSelect libraries (Agilent Technologies) were prepared from 3 µg of genomic DNA sheared with an S2 Ultrasonicator (Covaris) according to the manufacturers’ instructions.

    Article Title: Essential role of Nr2f nuclear receptors in patterning the vertebrate upper jaw
    Article Snippet: The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip (Agilent, Santa Clara, CA) and then reverse-transcribed into cDNA using the SMARTer kit (Clontech, Mountain View, CA). cDNA amplification was adjusted based on the RNA input quantity, and the size and amount of generated cDNA was measured by BioAnalyzer. .. The samples were sonicated on a S2 ultrasonicator (Covaris, Woburn, MA) according to Clontech’s recommendations.

    DNA HS Assay:

    Article Title: The Cost of Metabolic Interactions in Symbioses between Insects and Bacteria with Reduced Genomes
    Article Snippet: The extracted DNA (1 to 2 µg per sample) was fragmented using an S2 ultrasonicator (Covaris) to obtain 700-bp fragments, which were end repaired with the End repair mix LC (Enzymatics) and A-tailed with the Klenow 3′→5′ exo-enzyme (Enzymatics). .. Concentrations were determined by Qubit 2.0 fluorometer (Thermo Fisher) with the DNA HS assay, yielding 5.8 to 14.1 ng DNA µl−1 .

    Polymerase Chain Reaction:

    Article Title: Illuminating Choices for Library Prep: A Comparison of Library Preparation Methods for Whole Genome Sequencing of Cryptococcus neoformans Using Illumina HiSeq
    Article Snippet: Fifty-four microlitres of gDNA was sheared using an S2 Ultrasonicator (Covaris) using the same settings as for the TruSeq DNA protocol. .. Adaptor enrichment was performed using eight cycles of PCR according to the manufacturer's instructions.

    Article Title: Genetic Control of Myelin Plasticity after Chronic Psychosocial Stress
    Article Snippet: RNA was fragmented using the S2 ultrasonicator (Covaris Inc.) and sequencing libraries were prepared with Nextera (Illumina; vHPC), ScriptSeq v2 (Epicentre; mPFC), or Ovation Universal RNA-Seq System (NuGEN; BNST) RNA-seq library preparation kits. .. The RNA-seq reads were trimmed for adapters with Cutadapt v1.8.3 (vHPC) and FastX toolkit (mPFC, BNST) and PCR duplicates were removed with PRINSEQ v0.20.4.

    Article Title: TMEM231, mutated in orofaciodigital and Meckel syndromes, organizes the ciliary transition zone
    Article Snippet: In a second PCR reaction, amplicons were barcoded by adding a patient-specific 10-bp nucleotide sequence. .. In brief, SureSelect libraries (Agilent Technologies) were prepared from 3 µg of genomic DNA sheared with an S2 Ultrasonicator (Covaris) according to the manufacturers’ instructions.

    Article Title: The Cost of Metabolic Interactions in Symbioses between Insects and Bacteria with Reduced Genomes
    Article Snippet: The extracted DNA (1 to 2 µg per sample) was fragmented using an S2 ultrasonicator (Covaris) to obtain 700-bp fragments, which were end repaired with the End repair mix LC (Enzymatics) and A-tailed with the Klenow 3′→5′ exo-enzyme (Enzymatics). .. Universal Y-shaped adaptors were ligated using A-T ligation, adaptor-ligated DNA was purified and size-selected using AMPure XP beads (Agencourt), and DNA was subjected to 14 cycles of PCR amplification with barcoded Illumina index primers (see in the supplemental material).

    Article Title: Deeper Insight in Beehives: Metagenomes of Royal Jelly, Pollen, and Honey from Lavender, Chestnut, and Fir Honeydew and Epiphytic and Endophytic Microbiota of Lavender and Rose Flowers
    Article Snippet: For each sample, 0.1 to 1 µg of DNA was sheared in an AFA microTUBE (Covaris, USA) in an S2 ultrasonicator (Covaris) to achieve an average fragment size of 350 bp. .. Libraries were created using the TruSeq DNA PCR-free and TruSeq Nano DNA library preparation kits (Illumina, USA), and the insert size was checked in a Fragment analyzer (Advanced Analytical Technologies, Inc., USA).

    Article Title: Whole-Genome Sequence of Mesorhizobium hungaricum sp. nov. Strain UASWS1009, a Potential Resource for Agricultural and Environmental Uses
    Article Snippet: Genomic DNA was extracted ( ) and fragmented to an average size of 350 bp in a 50-µl Adaptive Focused Acoustics (AFA) microTUBE (Covaris, USA) in an S2 ultrasonicator (Covaris). .. The TruSeq DNA PCR-free library preparation kits (Illumina, USA) produced a library, of which insert sizes were checked in a fragment analyzer (Advanced Analytical Technologies, Inc.).

    Sonication:

    Article Title: Deeper Insight in Beehives: Metagenomes of Royal Jelly, Pollen, and Honey from Lavender, Chestnut, and Fir Honeydew and Epiphytic and Endophytic Microbiota of Lavender and Rose Flowers
    Article Snippet: DNA of epiphytic microbiota from lavender and rose flowers were extracted by incubating flowers in PBS (1×) 0.15% Tween 20 with shaking (400 rpm) for 10 min, followed by a 5-min sonication step, shaking for 10 min (400 rpm) prior to prefiltration, and filtration on a 0.22-µm sterile filter (Millipore, Germany). .. For each sample, 0.1 to 1 µg of DNA was sheared in an AFA microTUBE (Covaris, USA) in an S2 ultrasonicator (Covaris) to achieve an average fragment size of 350 bp.

    Article Title: Essential role of Nr2f nuclear receptors in patterning the vertebrate upper jaw
    Article Snippet: .. The samples were sonicated on a S2 ultrasonicator (Covaris, Woburn, MA) according to Clontech’s recommendations. .. DNA libraries were assembled using the Kapa Hyper Prep kit (Kapa Biosystems, Wilmington, MA) with NextFlex adapters (Bioo Scientific, Austin, TX), assessed by Bioanalyzer, and quantified using qPCR (Kapa Library Quantification kit, Kapa Biosystems).

    Article Title: High-resolution melting analysis for molecular detection of multidrug resistance tuberculosis in Peruvian isolates
    Article Snippet: .. Extraction of DNA Bacteria, grown on Lowenstein Jensen solid medium, were resuspended in molecular biology grade water and sonicated using S2 ultrasonicator (Covaris Inc, USA). .. Finally, the DNA was extracted using the PureLink™ Genomic DNA kit (ThermoFisher Scientific, USA) according to manufacturer’s procedure.

    DNA Extraction:

    Article Title: Use of a Primary Epithelial Cell Screening Tool to Investigate Phage Therapy in Cystic Fibrosis
    Article Snippet: Paragraph title: Phage DNA Extraction and Genome Sequencing ... The sample (10 ng) was sheared using a S2 ultrasonicator (Covaris) and sequencing libraries prepared using a NEBnext Ultra library kit (New England Biosciences).

    Article Title: Global deceleration of gene evolution following recent genome hybridizations in fungi
    Article Snippet: Culture and DNA extraction from freeze-dried cell masses were performed as described ( ; ). .. Paired-end DNA libraries with insert size of 200–300 bp were derived from 1 µg genomic DNA followed by fragmentation with an S2 ultrasonicator (Covaris) and sequencing with Illumina HiSeq 2500 (Illumina).

    RNA Sequencing Assay:

    Article Title: Genetic Control of Myelin Plasticity after Chronic Psychosocial Stress
    Article Snippet: .. RNA was fragmented using the S2 ultrasonicator (Covaris Inc.) and sequencing libraries were prepared with Nextera (Illumina; vHPC), ScriptSeq v2 (Epicentre; mPFC), or Ovation Universal RNA-Seq System (NuGEN; BNST) RNA-seq library preparation kits. .. Libraries were size-selected with Pippin Prep (Sage Science) and sequencing was conducted on HighSeq 2000 (vHPC, paired-end 91 bp, Illumina) or NextSeq 500 platforms (mPFC and BNST, single-end 96 bp; Illumina).

    Article Title: Essential role of Nr2f nuclear receptors in patterning the vertebrate upper jaw
    Article Snippet: Paragraph title: RNA sequencing ... The samples were sonicated on a S2 ultrasonicator (Covaris, Woburn, MA) according to Clontech’s recommendations.

    Mutagenesis:

    Article Title: TMEM231, mutated in orofaciodigital and Meckel syndromes, organizes the ciliary transition zone
    Article Snippet: Paragraph title: Mutation analysis of ciliopathy patients ... In brief, SureSelect libraries (Agilent Technologies) were prepared from 3 µg of genomic DNA sheared with an S2 Ultrasonicator (Covaris) according to the manufacturers’ instructions.

    Isolation:

    Article Title: Whole-Genome Sequence of Mesorhizobium hungaricum sp. nov. Strain UASWS1009, a Potential Resource for Agricultural and Environmental Uses
    Article Snippet: Strain UASWS1009 was isolated from the sewage sludge of a coking plant in Hungary through a selection experiment for highly ammonia-tolerant nitrifying bacteria. .. Genomic DNA was extracted ( ) and fragmented to an average size of 350 bp in a 50-µl Adaptive Focused Acoustics (AFA) microTUBE (Covaris, USA) in an S2 ultrasonicator (Covaris).

    Purification:

    Article Title: Defective DNA damage repair leads to frequent catastrophic genomic events in murine and human tumors
    Article Snippet: Purified DNA was quantified using the Qubit Broad Range double-stranded DNA assay (Life Technologies, Carlsbad, CA, USA). .. Genomic DNA was sheared using an S2 Ultrasonicator (Covaris, Woburn, MA, USA).

    Article Title: The Cost of Metabolic Interactions in Symbioses between Insects and Bacteria with Reduced Genomes
    Article Snippet: The extracted DNA (1 to 2 µg per sample) was fragmented using an S2 ultrasonicator (Covaris) to obtain 700-bp fragments, which were end repaired with the End repair mix LC (Enzymatics) and A-tailed with the Klenow 3′→5′ exo-enzyme (Enzymatics). .. Universal Y-shaped adaptors were ligated using A-T ligation, adaptor-ligated DNA was purified and size-selected using AMPure XP beads (Agencourt), and DNA was subjected to 14 cycles of PCR amplification with barcoded Illumina index primers (see in the supplemental material).

    Article Title: Essential role of Nr2f nuclear receptors in patterning the vertebrate upper jaw
    Article Snippet: The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip (Agilent, Santa Clara, CA) and then reverse-transcribed into cDNA using the SMARTer kit (Clontech, Mountain View, CA). cDNA amplification was adjusted based on the RNA input quantity, and the size and amount of generated cDNA was measured by BioAnalyzer. .. The samples were sonicated on a S2 ultrasonicator (Covaris, Woburn, MA) according to Clontech’s recommendations.

    Article Title: Evidence for a pre-malignant cell line in a skin biopsy from a patient with Nijmegen breakage syndrome
    Article Snippet: Purified DNA was quantified using the Qubit Broad Range double-stranded DNA assay (Life Technologies, Carlsbad, CA, USA). .. Genomic DNA was sheared using an S2 Ultrasonicator (Covaris, Woburn, MA, USA).

    Article Title: Global deceleration of gene evolution following recent genome hybridizations in fungi
    Article Snippet: Genomic DNA was purified using Genomic-tip 100/G (Qiagen) according to the manufacturer's instructions. .. Paired-end DNA libraries with insert size of 200–300 bp were derived from 1 µg genomic DNA followed by fragmentation with an S2 ultrasonicator (Covaris) and sequencing with Illumina HiSeq 2500 (Illumina).

    Sequencing:

    Article Title: Genetic Control of Myelin Plasticity after Chronic Psychosocial Stress
    Article Snippet: .. RNA was fragmented using the S2 ultrasonicator (Covaris Inc.) and sequencing libraries were prepared with Nextera (Illumina; vHPC), ScriptSeq v2 (Epicentre; mPFC), or Ovation Universal RNA-Seq System (NuGEN; BNST) RNA-seq library preparation kits. .. Libraries were size-selected with Pippin Prep (Sage Science) and sequencing was conducted on HighSeq 2000 (vHPC, paired-end 91 bp, Illumina) or NextSeq 500 platforms (mPFC and BNST, single-end 96 bp; Illumina).

    Article Title: Defective DNA damage repair leads to frequent catastrophic genomic events in murine and human tumors
    Article Snippet: Paragraph title: Library preparation and sequencing ... Genomic DNA was sheared using an S2 Ultrasonicator (Covaris, Woburn, MA, USA).

    Article Title: TMEM231, mutated in orofaciodigital and Meckel syndromes, organizes the ciliary transition zone
    Article Snippet: Whole exome sequencing and variant filtering was conducted as described previously ( ). .. In brief, SureSelect libraries (Agilent Technologies) were prepared from 3 µg of genomic DNA sheared with an S2 Ultrasonicator (Covaris) according to the manufacturers’ instructions.

    Article Title: The Cost of Metabolic Interactions in Symbioses between Insects and Bacteria with Reduced Genomes
    Article Snippet: Paragraph title: DNA library preparation and sequencing of bacterial genomes. ... The extracted DNA (1 to 2 µg per sample) was fragmented using an S2 ultrasonicator (Covaris) to obtain 700-bp fragments, which were end repaired with the End repair mix LC (Enzymatics) and A-tailed with the Klenow 3′→5′ exo-enzyme (Enzymatics).

    Article Title: Use of a Primary Epithelial Cell Screening Tool to Investigate Phage Therapy in Cystic Fibrosis
    Article Snippet: .. The sample (10 ng) was sheared using a S2 ultrasonicator (Covaris) and sequencing libraries prepared using a NEBnext Ultra library kit (New England Biosciences). .. Sequencing was performed on a 318 chip using an Ion Torrent PGM semiconductor sequencer for 820 flows.

    Article Title: Essential role of Nr2f nuclear receptors in patterning the vertebrate upper jaw
    Article Snippet: The samples were sonicated on a S2 ultrasonicator (Covaris, Woburn, MA) according to Clontech’s recommendations. .. Sequencing was performed on a NextSeq500, using 75-bp paired end reads (Illumina, San Diego, CA).

    Article Title: Global deceleration of gene evolution following recent genome hybridizations in fungi
    Article Snippet: .. Paired-end DNA libraries with insert size of 200–300 bp were derived from 1 µg genomic DNA followed by fragmentation with an S2 ultrasonicator (Covaris) and sequencing with Illumina HiSeq 2500 (Illumina). .. Mate pair libraries with insert size of ∼3 kb were prepared with Nextera Mate Pair Sample Prep Kit (Illumina) according to the manufacturer's protocol with some modifications ( ) and sequenced using HiSeq 2500 to generate 151-bp paired-end reads.

    Article Title: Whole-Genome Sequence of Mesorhizobium hungaricum sp. nov. Strain UASWS1009, a Potential Resource for Agricultural and Environmental Uses
    Article Snippet: Initially identified as a Mesorhizobium species by 16S sequencing, it shared 98 to 99% identity with many Mesorhizobium strains in GenBank ( ). .. Genomic DNA was extracted ( ) and fragmented to an average size of 350 bp in a 50-µl Adaptive Focused Acoustics (AFA) microTUBE (Covaris, USA) in an S2 ultrasonicator (Covaris).

    Agarose Gel Electrophoresis:

    Article Title: Evidence for a pre-malignant cell line in a skin biopsy from a patient with Nijmegen breakage syndrome
    Article Snippet: The qPCR products were checked by agarose gel electrophoresis, visualized by UV-transilluminator and photographed. .. Genomic DNA was sheared using an S2 Ultrasonicator (Covaris, Woburn, MA, USA).

    Shotgun Sequencing:

    Article Title: Deeper Insight in Beehives: Metagenomes of Royal Jelly, Pollen, and Honey from Lavender, Chestnut, and Fir Honeydew and Epiphytic and Endophytic Microbiota of Lavender and Rose Flowers
    Article Snippet: For each sample, 0.1 to 1 µg of DNA was sheared in an AFA microTUBE (Covaris, USA) in an S2 ultrasonicator (Covaris) to achieve an average fragment size of 350 bp. .. Whole-metagenome shotgun sequencing was carried out within three high-output (300 cycles) Illumina MiniSeq runs with a 2 × 151-bp paired-end read length.

    Chromatin Immunoprecipitation:

    Article Title: Genetic Control of Myelin Plasticity after Chronic Psychosocial Stress
    Article Snippet: RNA-sequencing (RNA-seq) Total RNA was extracted with TriReagent (Molecular Research Center Inc.) and RNA quality was assessed with a 2100 Bioanalyzer (Agilent Technologies) using Agilent RNA 600 Nano Chip kit (Agilent Technologies). rRNA was depleted with Ribo-Zero Gold rRNA Removal kit (Illumina Inc; mPFC and vHPC) or custom Insert Dependent Adaptor Cleavage (InDA-C) primers (BNST). .. RNA was fragmented using the S2 ultrasonicator (Covaris Inc.) and sequencing libraries were prepared with Nextera (Illumina; vHPC), ScriptSeq v2 (Epicentre; mPFC), or Ovation Universal RNA-Seq System (NuGEN; BNST) RNA-seq library preparation kits.

    Article Title: Use of a Primary Epithelial Cell Screening Tool to Investigate Phage Therapy in Cystic Fibrosis
    Article Snippet: The sample (10 ng) was sheared using a S2 ultrasonicator (Covaris) and sequencing libraries prepared using a NEBnext Ultra library kit (New England Biosciences). .. Sequencing was performed on a 318 chip using an Ion Torrent PGM semiconductor sequencer for 820 flows.

    Article Title: Essential role of Nr2f nuclear receptors in patterning the vertebrate upper jaw
    Article Snippet: The purified RNA was evaluated for quality and quantity on a BioAnalyzer Pico RNA chip (Agilent, Santa Clara, CA) and then reverse-transcribed into cDNA using the SMARTer kit (Clontech, Mountain View, CA). cDNA amplification was adjusted based on the RNA input quantity, and the size and amount of generated cDNA was measured by BioAnalyzer. .. The samples were sonicated on a S2 ultrasonicator (Covaris, Woburn, MA) according to Clontech’s recommendations.

    Software:

    Article Title: Evidence for a pre-malignant cell line in a skin biopsy from a patient with Nijmegen breakage syndrome
    Article Snippet: All PCRs were performed on Applied Biosystem prism 7500 (software DSD V1.2.3). .. Genomic DNA was sheared using an S2 Ultrasonicator (Covaris, Woburn, MA, USA).

    Multiplex Assay:

    Article Title: TMEM231, mutated in orofaciodigital and Meckel syndromes, organizes the ciliary transition zone
    Article Snippet: All coding exons and exon–intron boundaries of TMEM231 were amplified in 1,056 patients with nephronophthisis-related ciliopathies in a large-scale microfluidic multiplex PCR by using a Fluidigm Access Array system (48.48). .. In brief, SureSelect libraries (Agilent Technologies) were prepared from 3 µg of genomic DNA sheared with an S2 Ultrasonicator (Covaris) according to the manufacturers’ instructions.

    Article Title: Illuminating Choices for Library Prep: A Comparison of Library Preparation Methods for Whole Genome Sequencing of Cryptococcus neoformans Using Illumina HiSeq
    Article Snippet: Fifty-four microlitres of gDNA was sheared using an S2 Ultrasonicator (Covaris) using the same settings as for the TruSeq DNA protocol. .. Adaptor enrichment was performed using eight cycles of PCR, and using the NEBNext Multiplex oligos for Illumina (New England Biolabs).

    Selection:

    Article Title: Illuminating Choices for Library Prep: A Comparison of Library Preparation Methods for Whole Genome Sequencing of Cryptococcus neoformans Using Illumina HiSeq
    Article Snippet: Fifty-four microlitres of gDNA was sheared using an S2 Ultrasonicator (Covaris) using the same settings as for the TruSeq DNA protocol. .. Library preparation was performed according to the manufacturer's instructions, with size selection performed using AMPure XP beads (45 µl beads for the initial step, and 25 µl for the second step).

    Article Title: Whole-Genome Sequence of Mesorhizobium hungaricum sp. nov. Strain UASWS1009, a Potential Resource for Agricultural and Environmental Uses
    Article Snippet: Strain UASWS1009 was isolated from the sewage sludge of a coking plant in Hungary through a selection experiment for highly ammonia-tolerant nitrifying bacteria. .. Genomic DNA was extracted ( ) and fragmented to an average size of 350 bp in a 50-µl Adaptive Focused Acoustics (AFA) microTUBE (Covaris, USA) in an S2 ultrasonicator (Covaris).

    Sample Prep:

    Article Title: Global deceleration of gene evolution following recent genome hybridizations in fungi
    Article Snippet: Paired-end DNA libraries with insert size of 200–300 bp were derived from 1 µg genomic DNA followed by fragmentation with an S2 ultrasonicator (Covaris) and sequencing with Illumina HiSeq 2500 (Illumina). .. Mate pair libraries with insert size of ∼3 kb were prepared with Nextera Mate Pair Sample Prep Kit (Illumina) according to the manufacturer's protocol with some modifications ( ) and sequenced using HiSeq 2500 to generate 151-bp paired-end reads.

    Next-Generation Sequencing:

    Article Title: TMEM231, mutated in orofaciodigital and Meckel syndromes, organizes the ciliary transition zone
    Article Snippet: Consecutively, generated amplicons from 1,056 patients were pooled and submitted to next generation sequencing, performed on a Genome Analyzer II platform (Illumina). .. In brief, SureSelect libraries (Agilent Technologies) were prepared from 3 µg of genomic DNA sheared with an S2 Ultrasonicator (Covaris) according to the manufacturers’ instructions.

    dsDNA Assay:

    Article Title: Defective DNA damage repair leads to frequent catastrophic genomic events in murine and human tumors
    Article Snippet: Purified DNA was quantified using the Qubit Broad Range double-stranded DNA assay (Life Technologies, Carlsbad, CA, USA). .. Genomic DNA was sheared using an S2 Ultrasonicator (Covaris, Woburn, MA, USA).

    Article Title: Evidence for a pre-malignant cell line in a skin biopsy from a patient with Nijmegen breakage syndrome
    Article Snippet: Purified DNA was quantified using the Qubit Broad Range double-stranded DNA assay (Life Technologies, Carlsbad, CA, USA). .. Genomic DNA was sheared using an S2 Ultrasonicator (Covaris, Woburn, MA, USA).

    Produced:

    Article Title: Whole-Genome Sequence of Mesorhizobium hungaricum sp. nov. Strain UASWS1009, a Potential Resource for Agricultural and Environmental Uses
    Article Snippet: Genomic DNA was extracted ( ) and fragmented to an average size of 350 bp in a 50-µl Adaptive Focused Acoustics (AFA) microTUBE (Covaris, USA) in an S2 ultrasonicator (Covaris). .. The TruSeq DNA PCR-free library preparation kits (Illumina, USA) produced a library, of which insert sizes were checked in a fragment analyzer (Advanced Analytical Technologies, Inc.).

    Concentration Assay:

    Article Title: Use of a Primary Epithelial Cell Screening Tool to Investigate Phage Therapy in Cystic Fibrosis
    Article Snippet: The concentration of DNA was determined using a Qubit fluorometer according to manufacturer’s instructions. .. The sample (10 ng) was sheared using a S2 ultrasonicator (Covaris) and sequencing libraries prepared using a NEBnext Ultra library kit (New England Biosciences).

    Variant Assay:

    Article Title: TMEM231, mutated in orofaciodigital and Meckel syndromes, organizes the ciliary transition zone
    Article Snippet: Whole exome sequencing and variant filtering was conducted as described previously ( ). .. In brief, SureSelect libraries (Agilent Technologies) were prepared from 3 µg of genomic DNA sheared with an S2 Ultrasonicator (Covaris) according to the manufacturers’ instructions.

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