le220  (Covaris)


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  • 99
    Name:
    LE220 Focused ultrasonicator
    Description:
    Plate batch or single sample processing includes computer requires recirculating chiller not included
    Catalog Number:
    500219
    Product Aliases:
    LE220, Ultrasonicator
    Price:
    None
    Size:
    24 W x 30 D x 19 H
    Category:
    Instrument
    Score:
    85
    Quantity:
    1
    Buy from Supplier


    Structured Review

    Covaris le220
    LE220 Focused ultrasonicator
    Plate batch or single sample processing includes computer requires recirculating chiller not included
    https://www.bioz.com/result/le220/product/Covaris
    Average 99 stars, based on 59 article reviews
    Price from $9.99 to $1999.99
    le220 - by Bioz Stars, 2019-10
    99/100 stars

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    Related Articles

    Amplification:

    Article Title: Detecting eukaryotic microbiota with single-cell sensitivity in human tissue
    Article Snippet: Cherrypicked plates were sheared to 450 bp using a Covaris LE220 instrument (Covaris, Woburn, Massachusetts, USA). .. The PCR was carried out with KapaHiFi Hot start mix (Kapa Biosystems, Wilmington, Massachusetts, USA) and IDT 96 iPCR tag barcodes (Integrated DNA Technologies, Coralville, Iowa, USA) using the Agilent Bravo WS automation system (Agilent).

    Article Title: Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates
    Article Snippet: Each RNA sample was reverse-transcribed and amplified with a modified random amplification (Round AB) protocol as described previously [ ]. .. PCR amplicons obtained from the pre-amplification were purified with Agencourt AmPure XP (Beckman Coulter) and subsequently fragmented by sonication using a Covaris LE220 focused-ultrasonicator (Covaris) in order to achieve efficient library generation.

    Article Title: Radon Exposure-induced Genetic Variations in Lung Cancers among Never Smokers
    Article Snippet: Diluted in EB buffer, 1 μg of DNA was sheared to a target peak size of 150–200 bp using a Covaris LE220 focused-ultrasonicator (Covaris, Woburnm, MA, USA), according to the manufacturer's instructions. .. Diluted in EB buffer, 1 μg of DNA was sheared to a target peak size of 150–200 bp using a Covaris LE220 focused-ultrasonicator (Covaris, Woburnm, MA, USA), according to the manufacturer's instructions.

    Article Title: Complete Genome Sequence of Thermus aquaticus Y51MC23
    Article Snippet: Fragment libraries were constructed by shearing genomic DNA to approximately 300–400 with a Covaris LE220 Focused-Ultrasonicator (Covaris, Woburn, MA), end repairing, A-tailing and ligating Illumina compatible adaptors. .. An eight kb mate pair library was constructed by shearing genomic DNA with a g-TUBE (Covaris), followed by end repair, A-tailing and ligation of adaptors.

    Article Title: Defective mitochondrial DNA homeostasis in the substantia nigra in Parkinson disease
    Article Snippet: Amplification of each sample was performed in a 50 μl reaction using 5 μl of cell lysate as template, forward primer 5′-TTAAAACTCAAAGGACCTGGC-3′ and reverse primer 5′-GACCTAGTCAACGGTCGGCGAAC-3′. .. Subsequently, samples were normalized in 50 μl of nuclease-free water using 0.30–1.00 μg of stock DNA material and sonicated on a Covaris LE220 (Covaris) to a target insert size of ∼400 bp.

    Positive Control:

    Article Title: Detecting eukaryotic microbiota with single-cell sensitivity in human tissue
    Article Snippet: The same positive control samples used for the MiSeq 18S experiments were also analyzed by whole genome sequencing using the Illumina HiSeq X Ten. .. Cherrypicked plates were sheared to 450 bp using a Covaris LE220 instrument (Covaris, Woburn, Massachusetts, USA).

    Picogreen Assay:

    Article Title: Detection of functional protein domains by unbiased genome-wide forward genetic screening
    Article Snippet: Extracted DNA was tested for total volume, concentration and total amount by using gel electrophoresis and the Quant-iTTM PicoGreen® dsDNA Assay Kit (ThermoFisher Scientific). .. Genomic DNA −500 µg (yeast) or 1–3 μg (mouse) – was fragmented to an average size of 100–400 bp (mouse) or 400–600 bp (yeast) by using a Covaris E210 or LE220 device (Covaris, Woburn, MA, USA), size-selected and subjected to DNA library creation via established Illumina paired-end protocols.

    Construct:

    Article Title: Breast cancer diagnosed during pregnancy is associated with enrichment of non-silent mutations, mismatch repair deficiency signature and mucin mutations
    Article Snippet: Briefly, manual dual indexed libraries were constructed with 1μg of FFPE genomic DNA for the 53 tumor/normal pairs using the Accel-NGS 2S Plus Library Kit (Swift, MI, USA). .. Samples were fragmented on the Covaris LE220 instrument with 350bp target insert size.

    Article Title: Complete Genome Sequence of Thermus aquaticus Y51MC23
    Article Snippet: Both fragment and 8 kb mate pair libraries were constructed for sequencing using NxSeq® DNA Sample Prep and Long Mate Pair Library Kits (Lucigen, Middleton, WI), respectively. .. Fragment libraries were constructed by shearing genomic DNA to approximately 300–400 with a Covaris LE220 Focused-Ultrasonicator (Covaris, Woburn, MA), end repairing, A-tailing and ligating Illumina compatible adaptors. .. The adapted DNA was then size selected with AMPure XP beads (Beckman Coulter, Brea CA).

    Real-time Polymerase Chain Reaction:

    Article Title: Breast cancer diagnosed during pregnancy is associated with enrichment of non-silent mutations, mismatch repair deficiency signature and mucin mutations
    Article Snippet: Samples were fragmented on the Covaris LE220 instrument with 350bp target insert size. .. PCR cycle optimization was performed to prevent over-amplification of the libraries.

    Article Title: The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease
    Article Snippet: Briefly, 650 ng of DNA was sheared using a Covaris LE220 sonicator (adaptive focused acoustics). .. DNA fragments underwent bead-based size selection and were subsequently end-repaired, adenylated, and ligated to Illumina sequencing adapters.

    Article Title: Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population
    Article Snippet: The genomic DNA (2 μg in 100 μL) was sonicated using a Covaris LE220 (Covaris Inc., Woburn, MA) to an average target size of 550 bp. .. The sheared DNA was used for library construction with the TruSeq DNA PCR-free sample preparation kit (Illumina, San Diego, CA) on a Bravo liquid-handling instrument (Agilent Technologies, Santa Clara, CA).

    Article Title: Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum
    Article Snippet: Both the libraries were quantified using KAPA Biosystem's next-generation sequencing library quantitative PCR (qPCR) kit and run on a Roche LightCycler 480 real-time PCR instrument. .. To fill gaps in Illumina genome assembly of C. geophilum , an unamplified library was generated using Pacific Biosciences standard template preparation protocol, where 5 μg of gDNA was used to generate the library and the DNA was sheared using a Covaris LE220 focused-ultrasonicator with their Blue 3.0 kb miniTUBES to generate sheared fragments of 3 kb in length.

    Article Title: Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils
    Article Snippet: DNA was mechanically sheared to a median length of 270 bp using a Covaris LE220 and then size-selected using solid-phase reversible immobilization. .. DNA was mechanically sheared to a median length of 270 bp using a Covaris LE220 and then size-selected using solid-phase reversible immobilization.

    Article Title: A high-throughput molecular data resource for cutaneous neurofibromas
    Article Snippet: The samples were then sonicated on the Covaris LE220 (Covaris Inc, Woburn, MA, USA) to achieve an average target size of 400 bp. .. Library quality was assessed using the Qubit 2.0 Fluorometer, and the library concentration was estimated by utilizing a DNA 1,000 Chip on an Agilent 2,100 Bioanalyzer.

    Incubation:

    Article Title: Stage-specific epigenetic regulation of CD4 expression by coordinated enhancer elements during T cell development
    Article Snippet: 3C libraries were prepared from sorted populations from the thymus and spleen/lymph nodes as described previously with the following changes: Dpn II enzymes were used for restriction digest, with a total of 500 U fresh restriction enzyme added every 5–7 h, for a total incubation of 16–24 h after initial addition of restriction enzyme. .. Two aliquots of 5 µg of 3C library was then sonicated to 200 bp using a Covaris LE220 instrument (190 s shearing time; 30% duty factor; 450PIP, 200 cycles per burst).

    Article Title: Static and dynamic DNA loops form AP-1 bound activation hubs during macrophage development
    Article Snippet: The resulting pellet was resuspended in 130 ul of 10mM Tric-HCl, pH8 and incubated at 37’C for 15 minutes. .. DNA was sheared using an LE220 Covaris Focused-ultrasonicator to a fragment size of 300–500 bp.

    Article Title: Nine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphila, and C. cf. spartinae, pseudomolecules for the pitch canker pathogen Fusarium circinatum, draft genome of Davidsoniella eucalypti, Grosmannia galeiformis, Quambalaria eucalypti, and Teratosphaeria destructansNine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphil
    Article Snippet: The protocol was modified to remove RNA by adding extra RNase and incubating for longer time as follows: (1) after homogenization of ground fungal tissues with 700 μl 2X CTAB, 140 μl RNase CocktailTM Enzyme Mix (4x recommended volume ratio: 2.5 μl / 50 μl sample; Invitrogen by Thermo Fisher Scientific), and 28 μl RNASE A (4x recommended volume ratio: 1 μl / 100 μl sample) was added, and digested for 6–7 h at room temperature. (2) Afterwards, 10 μl Proteinase K (50 μg/μL stock; Fisher Scientific by Thermo Fisher Scientific) was added to the suspension and incubated for 2 h at 55 °C. (3) Before DNA precipitation, another 35ul RNase Cocktail (recommended volume ratio without extra) was added into the supernatant, incubated for 45 min – 1 h at room temperature, followed by adding 650 μL CHCl4 and centrifuging at 13 000 rpm for 15 min. .. The extracted gDNAs were normalized to 400 ng and sheared to a 300 bp insert using a Covaris LE220 instrument.

    Formalin-fixed Paraffin-Embedded:

    Article Title: Breast cancer diagnosed during pregnancy is associated with enrichment of non-silent mutations, mismatch repair deficiency signature and mucin mutations
    Article Snippet: Briefly, manual dual indexed libraries were constructed with 1μg of FFPE genomic DNA for the 53 tumor/normal pairs using the Accel-NGS 2S Plus Library Kit (Swift, MI, USA). .. Samples were fragmented on the Covaris LE220 instrument with 350bp target insert size.

    Modification:

    Article Title: Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates
    Article Snippet: Each RNA sample was reverse-transcribed and amplified with a modified random amplification (Round AB) protocol as described previously [ ]. .. PCR amplicons obtained from the pre-amplification were purified with Agencourt AmPure XP (Beckman Coulter) and subsequently fragmented by sonication using a Covaris LE220 focused-ultrasonicator (Covaris) in order to achieve efficient library generation.

    Article Title: Nine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphila, and C. cf. spartinae, pseudomolecules for the pitch canker pathogen Fusarium circinatum, draft genome of Davidsoniella eucalypti, Grosmannia galeiformis, Quambalaria eucalypti, and Teratosphaeria destructansNine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphil
    Article Snippet: The protocol was modified to remove RNA by adding extra RNase and incubating for longer time as follows: (1) after homogenization of ground fungal tissues with 700 μl 2X CTAB, 140 μl RNase CocktailTM Enzyme Mix (4x recommended volume ratio: 2.5 μl / 50 μl sample; Invitrogen by Thermo Fisher Scientific), and 28 μl RNASE A (4x recommended volume ratio: 1 μl / 100 μl sample) was added, and digested for 6–7 h at room temperature. (2) Afterwards, 10 μl Proteinase K (50 μg/μL stock; Fisher Scientific by Thermo Fisher Scientific) was added to the suspension and incubated for 2 h at 55 °C. (3) Before DNA precipitation, another 35ul RNase Cocktail (recommended volume ratio without extra) was added into the supernatant, incubated for 45 min – 1 h at room temperature, followed by adding 650 μL CHCl4 and centrifuging at 13 000 rpm for 15 min. .. The extracted gDNAs were normalized to 400 ng and sheared to a 300 bp insert using a Covaris LE220 instrument.

    Article Title: Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils
    Article Snippet: Unamplified libraries were prepared for each sample using a modified version of the Illumina TruSeq protocol with 500 ng of purified soil DNA. .. DNA was mechanically sheared to a median length of 270 bp using a Covaris LE220 and then size-selected using solid-phase reversible immobilization.

    Hybridization:

    Article Title: Radon Exposure-induced Genetic Variations in Lung Cancers among Never Smokers
    Article Snippet: Diluted in EB buffer, 1 μg of DNA was sheared to a target peak size of 150–200 bp using a Covaris LE220 focused-ultrasonicator (Covaris, Woburnm, MA, USA), according to the manufacturer's instructions. .. After the ligation, the adapter-ligated library went through polymerase chain reaction (PCR) amplification.

    Flow Cytometry:

    Article Title: Breast cancer diagnosed during pregnancy is associated with enrichment of non-silent mutations, mismatch repair deficiency signature and mucin mutations
    Article Snippet: Samples were fragmented on the Covaris LE220 instrument with 350bp target insert size. .. Samples were fragmented on the Covaris LE220 instrument with 350bp target insert size.

    Inverse PCR:

    Article Title: Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum
    Article Snippet: The self-ligated products were immobilized on beads and inverse PCR was used to enrich for the final library (NEB). .. To fill gaps in Illumina genome assembly of C. geophilum , an unamplified library was generated using Pacific Biosciences standard template preparation protocol, where 5 μg of gDNA was used to generate the library and the DNA was sheared using a Covaris LE220 focused-ultrasonicator with their Blue 3.0 kb miniTUBES to generate sheared fragments of 3 kb in length.

    Ligation:

    Article Title: Stage-specific epigenetic regulation of CD4 expression by coordinated enhancer elements during T cell development
    Article Snippet: After digest, Dpn II was heat inactivated and a ligation reaction with 200 U of T4 DNA ligase (NEB) was set up overnight at room temperature with gentle rotation. .. Two aliquots of 5 µg of 3C library was then sonicated to 200 bp using a Covaris LE220 instrument (190 s shearing time; 30% duty factor; 450PIP, 200 cycles per burst).

    Article Title: Static and dynamic DNA loops form AP-1 bound activation hubs during macrophage development
    Article Snippet: Ligation was performed by adding 667 ul of water, 120 ul of 10× NEB T4 DNA ligase buffer, 100 ul of 10% Triton X-100, 12 ul of 10 mg/ml BSA, and 1 ul of 2000 U/ul T4 DNA Ligase and incubating at room temperature for 4 hours. .. DNA was sheared using an LE220 Covaris Focused-ultrasonicator to a fragment size of 300–500 bp.

    Article Title: Detecting eukaryotic microbiota with single-cell sensitivity in human tissue
    Article Snippet: Cherrypicked plates were sheared to 450 bp using a Covaris LE220 instrument (Covaris, Woburn, Massachusetts, USA). .. Post-sheared samples were purified using Agencourt AMPure XP SPRI beads (Beckman Coulter, Brea, CA, USA) on an Agilent Bravo WS (Agilent).

    Article Title: Radon Exposure-induced Genetic Variations in Lung Cancers among Never Smokers
    Article Snippet: Diluted in EB buffer, 1 μg of DNA was sheared to a target peak size of 150–200 bp using a Covaris LE220 focused-ultrasonicator (Covaris, Woburnm, MA, USA), according to the manufacturer's instructions. .. Diluted in EB buffer, 1 μg of DNA was sheared to a target peak size of 150–200 bp using a Covaris LE220 focused-ultrasonicator (Covaris, Woburnm, MA, USA), according to the manufacturer's instructions.

    Generated:

    Article Title: Breast cancer diagnosed during pregnancy is associated with enrichment of non-silent mutations, mismatch repair deficiency signature and mucin mutations
    Article Snippet: Samples were fragmented on the Covaris LE220 instrument with 350bp target insert size. .. For the normal samples, each library was loaded on one lane of a HiSeqX flow cell, whereas for tumor samples, each library was loaded across two lanes of a HiSeqX flow cell.

    Article Title: Similarities and Differences between Exome Sequences Found in a Variety of Tissues from the Same Individual
    Article Snippet: 3×10−6 g of genomic DNA was fragmented to an average size of 200 bp using a Covaris LE220 instrument. .. Exonic sequences were enriched using NimbleGen Sequence Capture Human Exome 2.1 M Array.

    Article Title: Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates
    Article Snippet: PCR amplicons obtained from the pre-amplification were purified with Agencourt AmPure XP (Beckman Coulter) and subsequently fragmented by sonication using a Covaris LE220 focused-ultrasonicator (Covaris) in order to achieve efficient library generation. .. Library construction was done either manually or on an automated NGS workstation, Zephyr G3 NGS Workstation (PerkinElmer).

    Article Title: Comparative genomics and transcriptomics of Pichia pastoris
    Article Snippet: Illumina fragment libraries were generated as previously described [ ] with the following modifications. .. For each sample, 100 ng of genomic DNA was sheared to 200 bp in size using a Covaris LE220 instrument (Covaris, MA) with the following parameters: temperature: 7–9 °C; duty cycle: 20 %; intensity: 5; cycles per burst: 200; time: 90 s; shearing tubes: Crimp Cap microTUBES with AFA fibers Covaris, MA).

    Article Title: Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum
    Article Snippet: Genomic data from five libraries were filtered and assembled with AllPathsLG . .. To fill gaps in Illumina genome assembly of C. geophilum , an unamplified library was generated using Pacific Biosciences standard template preparation protocol, where 5 μg of gDNA was used to generate the library and the DNA was sheared using a Covaris LE220 focused-ultrasonicator with their Blue 3.0 kb miniTUBES to generate sheared fragments of 3 kb in length. .. The sheared DNA fragments were then prepared according to the Pacific Biosciences protocol and using their SMRTbell template preparation kit, where the fragments were treated with DNA damage repair, had their ends repaired so that they were blunt-ended, and 5′ phosphorylated.

    Capture-C:

    Article Title: Stage-specific epigenetic regulation of CD4 expression by coordinated enhancer elements during T cell development
    Article Snippet: Paragraph title: Capture C sample preparation ... Two aliquots of 5 µg of 3C library was then sonicated to 200 bp using a Covaris LE220 instrument (190 s shearing time; 30% duty factor; 450PIP, 200 cycles per burst).

    Sequencing:

    Article Title: Breast cancer diagnosed during pregnancy is associated with enrichment of non-silent mutations, mismatch repair deficiency signature and mucin mutations
    Article Snippet: Paragraph title: Library preparation and whole genome sequencing ... Samples were fragmented on the Covaris LE220 instrument with 350bp target insert size.

    Article Title: Stage-specific epigenetic regulation of CD4 expression by coordinated enhancer elements during T cell development
    Article Snippet: Two aliquots of 5 µg of 3C library was then sonicated to 200 bp using a Covaris LE220 instrument (190 s shearing time; 30% duty factor; 450PIP, 200 cycles per burst). .. Two aliquots of 5 µg of 3C library was then sonicated to 200 bp using a Covaris LE220 instrument (190 s shearing time; 30% duty factor; 450PIP, 200 cycles per burst).

    Article Title: The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease
    Article Snippet: Whole genome sequencing (WGS) libraries were prepared at the New York Genome Center (NYGC) using the KAPA Hyper Library Preparation Kit (PCR-free) in accordance with the manufacturer’s instructions. .. Briefly, 650 ng of DNA was sheared using a Covaris LE220 sonicator (adaptive focused acoustics).

    Article Title: Detecting eukaryotic microbiota with single-cell sensitivity in human tissue
    Article Snippet: The same positive control samples used for the MiSeq 18S experiments were also analyzed by whole genome sequencing using the Illumina HiSeq X Ten. .. Cherrypicked plates were sheared to 450 bp using a Covaris LE220 instrument (Covaris, Woburn, Massachusetts, USA).

    Article Title: Detection of functional protein domains by unbiased genome-wide forward genetic screening
    Article Snippet: Paragraph title: Illumina library preparation and sequencing ... Genomic DNA −500 µg (yeast) or 1–3 μg (mouse) – was fragmented to an average size of 100–400 bp (mouse) or 400–600 bp (yeast) by using a Covaris E210 or LE220 device (Covaris, Woburn, MA, USA), size-selected and subjected to DNA library creation via established Illumina paired-end protocols.

    Article Title: High-Quality Complete and Draft Genome Sequences for Three Escherichia spp. and Three Shigella spp. Generated with Pacific Biosciences and Illumina Sequencing and Optical Mapping
    Article Snippet: Aliquots of DNA were also used for MiSeq sequencing according to the manufacturer’s protocols (Illumina, San Diego, CA, USA). .. DNA samples were sheared to a mean size of 600 bp utilizing a Covaris LE220 focused ultrasonicator (Covaris Inc., Woburn, MA, USA) and cleaned with AMPure (Beckman Coulter, Inc., Indianapolis, IN, USA).

    Article Title: Similarities and Differences between Exome Sequences Found in a Variety of Tissues from the Same Individual
    Article Snippet: Paragraph title: Sample processing for exome sequencing ... 3×10−6 g of genomic DNA was fragmented to an average size of 200 bp using a Covaris LE220 instrument.

    Article Title: Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates
    Article Snippet: Paragraph title: Pre-amplification, library construction and Illumina HiSeq sequencing ... PCR amplicons obtained from the pre-amplification were purified with Agencourt AmPure XP (Beckman Coulter) and subsequently fragmented by sonication using a Covaris LE220 focused-ultrasonicator (Covaris) in order to achieve efficient library generation.

    Article Title: Radon Exposure-induced Genetic Variations in Lung Cancers among Never Smokers
    Article Snippet: With 1 μg of input gDNA, we applied the Agilent SureSelect Target Enrichment protocol for Illumina paired-end sequencing (ver. .. Diluted in EB buffer, 1 μg of DNA was sheared to a target peak size of 150–200 bp using a Covaris LE220 focused-ultrasonicator (Covaris, Woburnm, MA, USA), according to the manufacturer's instructions.

    Article Title: Nine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphila, and C. cf. spartinae, pseudomolecules for the pitch canker pathogen Fusarium circinatum, draft genome of Davidsoniella eucalypti, Grosmannia galeiformis, Quambalaria eucalypti, and Teratosphaeria destructansNine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphil
    Article Snippet: The extracted gDNAs were normalized to 400 ng and sheared to a 300 bp insert using a Covaris LE220 instrument. .. The fragmented inserts were used as a template to construct PCR free Libraries with a NxSeq AmpFREE Low DNA Library kit (Lucigen) following the manufacturer’s instructions.

    Article Title: Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population
    Article Snippet: Paragraph title: PCR-free whole-genome sequencing with the HiSeq 2500 sequencer ... The genomic DNA (2 μg in 100 μL) was sonicated using a Covaris LE220 (Covaris Inc., Woburn, MA) to an average target size of 550 bp.

    Article Title: Complete Genome Sequence of Thermus aquaticus Y51MC23
    Article Snippet: Paragraph title: Genome Sequencing and Assembly ... Fragment libraries were constructed by shearing genomic DNA to approximately 300–400 with a Covaris LE220 Focused-Ultrasonicator (Covaris, Woburn, MA), end repairing, A-tailing and ligating Illumina compatible adaptors.

    Article Title: Comparative genomics and transcriptomics of Pichia pastoris
    Article Snippet: Paragraph title: Genome sequencing ... For each sample, 100 ng of genomic DNA was sheared to 200 bp in size using a Covaris LE220 instrument (Covaris, MA) with the following parameters: temperature: 7–9 °C; duty cycle: 20 %; intensity: 5; cycles per burst: 200; time: 90 s; shearing tubes: Crimp Cap microTUBES with AFA fibers Covaris, MA).

    Article Title: Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum
    Article Snippet: Paragraph title: Genome sequencing and assembly ... To fill gaps in Illumina genome assembly of C. geophilum , an unamplified library was generated using Pacific Biosciences standard template preparation protocol, where 5 μg of gDNA was used to generate the library and the DNA was sheared using a Covaris LE220 focused-ultrasonicator with their Blue 3.0 kb miniTUBES to generate sheared fragments of 3 kb in length.

    Article Title: Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils
    Article Snippet: Shotgun metagenome library preparation, sequencing, assembly, and annotation were completed at the Joint Genome Institute using standard operating procedures and pipelines. .. DNA was mechanically sheared to a median length of 270 bp using a Covaris LE220 and then size-selected using solid-phase reversible immobilization.

    Article Title: Defective mitochondrial DNA homeostasis in the substantia nigra in Parkinson disease
    Article Snippet: Paragraph title: Single-neuron ultra-deep mtDNA sequencing ... Subsequently, samples were normalized in 50 μl of nuclease-free water using 0.30–1.00 μg of stock DNA material and sonicated on a Covaris LE220 (Covaris) to a target insert size of ∼400 bp.

    Article Title: A high-throughput molecular data resource for cutaneous neurofibromas
    Article Snippet: Paragraph title: Whole genome sequencing ... The samples were then sonicated on the Covaris LE220 (Covaris Inc, Woburn, MA, USA) to achieve an average target size of 400 bp.

    Sonication:

    Article Title: Stage-specific epigenetic regulation of CD4 expression by coordinated enhancer elements during T cell development
    Article Snippet: After digest, Dpn II was heat inactivated and a ligation reaction with 200 U of T4 DNA ligase (NEB) was set up overnight at room temperature with gentle rotation. .. Two aliquots of 5 µg of 3C library was then sonicated to 200 bp using a Covaris LE220 instrument (190 s shearing time; 30% duty factor; 450PIP, 200 cycles per burst). .. We indexed libraries with Illumina Truseq indexed sequencing adaptors using NEBnext reagents (E6000, E6040, E7335, or E7500) for end repair, dA labeling, adaptor ligation, and PCR indexing, primarily following the manufacturer’s instructions.

    Article Title: Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates
    Article Snippet: Each RNA sample was reverse-transcribed and amplified with a modified random amplification (Round AB) protocol as described previously [ ]. .. PCR amplicons obtained from the pre-amplification were purified with Agencourt AmPure XP (Beckman Coulter) and subsequently fragmented by sonication using a Covaris LE220 focused-ultrasonicator (Covaris) in order to achieve efficient library generation. .. Library construction for Illumina sequencing was carried out for each sample individually using NEB Ultra II DNA Library Prep Kit (New England Biolabs) with dual index barcoding according to the manufacturer’s instructions.

    Article Title: Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population
    Article Snippet: We omitted the RNase treatment, measured the concentration of the double-stranded DNA with PicoGreen (Life Technologies, Carlsbad, CA), and adjusted the concentration of the DNA to 200 ng/μL in Elution Buffer (Qiagen, Germany). .. The genomic DNA (2 μg in 100 μL) was sonicated using a Covaris LE220 (Covaris Inc., Woburn, MA) to an average target size of 550 bp. .. The sheared DNA was used for library construction with the TruSeq DNA PCR-free sample preparation kit (Illumina, San Diego, CA) on a Bravo liquid-handling instrument (Agilent Technologies, Santa Clara, CA).

    Article Title: Defective mitochondrial DNA homeostasis in the substantia nigra in Parkinson disease
    Article Snippet: Thermal cycling comprised one cycle at 92 °C for 2 min and 35 cycles of 92 °C for 10 s, 63 °C for 30 s and 68 °C for 8 min. PCR products were quality controlled by agarose gel electrophoresis using 5 μl sample and quantitated via picogreen fluorometric assay using 2 μl sample at 1:100 dilution. .. Subsequently, samples were normalized in 50 μl of nuclease-free water using 0.30–1.00 μg of stock DNA material and sonicated on a Covaris LE220 (Covaris) to a target insert size of ∼400 bp. .. Libraries were prepared using the GSL standard whole-genome library prep protocol with 1.8 × clean-up to retain all fragments ≤400 bp insert size and quality controlled by qPCR (KA PA SYBR FAST qPCR, Kapa Biosystems).

    Article Title: A high-throughput molecular data resource for cutaneous neurofibromas
    Article Snippet: One microgram gDNA was required for downstream whole genome library preparation applications. .. The samples were then sonicated on the Covaris LE220 (Covaris Inc, Woburn, MA, USA) to achieve an average target size of 400 bp. .. QC analysis of the post-sonicated material was done using Caliper LabChip GX (Perkin Elmer, Hopkinton, MA, USA).

    Binding Assay:

    Article Title: High-Quality Complete and Draft Genome Sequences for Three Escherichia spp. and Three Shigella spp. Generated with Pacific Biosciences and Illumina Sequencing and Optical Mapping
    Article Snippet: Libraries were bound to polymerase using the DNA/polymerase binding kit P5 or P6v2 and were then loaded on single-molecule real-time (SMRT) cells and sequenced with C3 (P5 polymerase) or C4v2 chemistry (P6v2 polymerase) for 270-min (10-kb libraries) or 360-min (20-kb libraries) movies on the RSII instrument (PacBio). .. DNA samples were sheared to a mean size of 600 bp utilizing a Covaris LE220 focused ultrasonicator (Covaris Inc., Woburn, MA, USA) and cleaned with AMPure (Beckman Coulter, Inc., Indianapolis, IN, USA).

    Hi-C:

    Article Title: Static and dynamic DNA loops form AP-1 bound activation hubs during macrophage development
    Article Snippet: Paragraph title: in situ Hi-C protocol ... DNA was sheared using an LE220 Covaris Focused-ultrasonicator to a fragment size of 300–500 bp.

    DNA Extraction:

    Article Title: Nine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphila, and C. cf. spartinae, pseudomolecules for the pitch canker pathogen Fusarium circinatum, draft genome of Davidsoniella eucalypti, Grosmannia galeiformis, Quambalaria eucalypti, and Teratosphaeria destructansNine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphil
    Article Snippet: Mycelia of 1–2 dishes were harvested and ground using liquid N2 , followed by genomic DNA extraction using a modified cetyltrimethyl ammonium bromide (CTAB) protocol ( ). .. The extracted gDNAs were normalized to 400 ng and sheared to a 300 bp insert using a Covaris LE220 instrument.

    Nucleic Acid Electrophoresis:

    Article Title: Detection of functional protein domains by unbiased genome-wide forward genetic screening
    Article Snippet: Extracted DNA was tested for total volume, concentration and total amount by using gel electrophoresis and the Quant-iTTM PicoGreen® dsDNA Assay Kit (ThermoFisher Scientific). .. Genomic DNA −500 µg (yeast) or 1–3 μg (mouse) – was fragmented to an average size of 100–400 bp (mouse) or 400–600 bp (yeast) by using a Covaris E210 or LE220 device (Covaris, Woburn, MA, USA), size-selected and subjected to DNA library creation via established Illumina paired-end protocols.

    Purification:

    Article Title: Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates
    Article Snippet: Each RNA sample was reverse-transcribed and amplified with a modified random amplification (Round AB) protocol as described previously [ ]. .. PCR amplicons obtained from the pre-amplification were purified with Agencourt AmPure XP (Beckman Coulter) and subsequently fragmented by sonication using a Covaris LE220 focused-ultrasonicator (Covaris) in order to achieve efficient library generation. .. Library construction for Illumina sequencing was carried out for each sample individually using NEB Ultra II DNA Library Prep Kit (New England Biolabs) with dual index barcoding according to the manufacturer’s instructions.

    Article Title: Complete Genome Sequence of Thermus aquaticus Y51MC23
    Article Snippet: Fragment libraries were constructed by shearing genomic DNA to approximately 300–400 with a Covaris LE220 Focused-Ultrasonicator (Covaris, Woburn, MA), end repairing, A-tailing and ligating Illumina compatible adaptors. .. An eight kb mate pair library was constructed by shearing genomic DNA with a g-TUBE (Covaris), followed by end repair, A-tailing and ligation of adaptors.

    Article Title: Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum
    Article Snippet: To fill gaps in Illumina genome assembly of C. geophilum , an unamplified library was generated using Pacific Biosciences standard template preparation protocol, where 5 μg of gDNA was used to generate the library and the DNA was sheared using a Covaris LE220 focused-ultrasonicator with their Blue 3.0 kb miniTUBES to generate sheared fragments of 3 kb in length. .. Pacific Biosciences hairpin adaptors were then ligated to the fragments to create the SMRTbell template for sequencing.

    Article Title: Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils
    Article Snippet: Unamplified libraries were prepared for each sample using a modified version of the Illumina TruSeq protocol with 500 ng of purified soil DNA. .. DNA was mechanically sheared to a median length of 270 bp using a Covaris LE220 and then size-selected using solid-phase reversible immobilization.

    Polymerase Chain Reaction:

    Article Title: The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease
    Article Snippet: Whole genome sequencing (WGS) libraries were prepared at the New York Genome Center (NYGC) using the KAPA Hyper Library Preparation Kit (PCR-free) in accordance with the manufacturer’s instructions. .. Briefly, 650 ng of DNA was sheared using a Covaris LE220 sonicator (adaptive focused acoustics).

    Article Title: Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture
    Article Snippet: The cost for technician time is $3 per sample, assuming that an individual makes 480 libraries on five plates per week. .. Capital costs are difficult to compute (because some laboratories may already have the necessary equipment), but if one computes the cost of a Covaris LE220 instrument, a PCR machine, and an Agilent Bravo liquid handling platform, and divides by the cost of 100,000 libraries produced over the 2–3-yr lifetime of these instruments, this would add about $3 more to the cost per sample. .. This accounting does not include administrative overhead, space rental, process management, quality control on the preparation of reagents, bioinformatic support, data analysis, and research and development, all of which could add significantly to cost.

    Article Title: Detecting eukaryotic microbiota with single-cell sensitivity in human tissue
    Article Snippet: Cherrypicked plates were sheared to 450 bp using a Covaris LE220 instrument (Covaris, Woburn, Massachusetts, USA). .. Cherrypicked plates were sheared to 450 bp using a Covaris LE220 instrument (Covaris, Woburn, Massachusetts, USA).

    Article Title: Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates
    Article Snippet: Each RNA sample was reverse-transcribed and amplified with a modified random amplification (Round AB) protocol as described previously [ ]. .. PCR amplicons obtained from the pre-amplification were purified with Agencourt AmPure XP (Beckman Coulter) and subsequently fragmented by sonication using a Covaris LE220 focused-ultrasonicator (Covaris) in order to achieve efficient library generation. .. Library construction for Illumina sequencing was carried out for each sample individually using NEB Ultra II DNA Library Prep Kit (New England Biolabs) with dual index barcoding according to the manufacturer’s instructions.

    Article Title: Radon Exposure-induced Genetic Variations in Lung Cancers among Never Smokers
    Article Snippet: Diluted in EB buffer, 1 μg of DNA was sheared to a target peak size of 150–200 bp using a Covaris LE220 focused-ultrasonicator (Covaris, Woburnm, MA, USA), according to the manufacturer's instructions. .. Diluted in EB buffer, 1 μg of DNA was sheared to a target peak size of 150–200 bp using a Covaris LE220 focused-ultrasonicator (Covaris, Woburnm, MA, USA), according to the manufacturer's instructions.

    Article Title: Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population
    Article Snippet: Paragraph title: PCR-free whole-genome sequencing with the HiSeq 2500 sequencer ... The genomic DNA (2 μg in 100 μL) was sonicated using a Covaris LE220 (Covaris Inc., Woburn, MA) to an average target size of 550 bp.

    Article Title: Complete Genome Sequence of Thermus aquaticus Y51MC23
    Article Snippet: Fragment libraries were constructed by shearing genomic DNA to approximately 300–400 with a Covaris LE220 Focused-Ultrasonicator (Covaris, Woburn, MA), end repairing, A-tailing and ligating Illumina compatible adaptors. .. An eight kb mate pair library was constructed by shearing genomic DNA with a g-TUBE (Covaris), followed by end repair, A-tailing and ligation of adaptors.

    Article Title: Defective mitochondrial DNA homeostasis in the substantia nigra in Parkinson disease
    Article Snippet: Thermal cycling comprised one cycle at 92 °C for 2 min and 35 cycles of 92 °C for 10 s, 63 °C for 30 s and 68 °C for 8 min. PCR products were quality controlled by agarose gel electrophoresis using 5 μl sample and quantitated via picogreen fluorometric assay using 2 μl sample at 1:100 dilution. .. Subsequently, samples were normalized in 50 μl of nuclease-free water using 0.30–1.00 μg of stock DNA material and sonicated on a Covaris LE220 (Covaris) to a target insert size of ∼400 bp.

    Blocking Assay:

    Article Title: Radon Exposure-induced Genetic Variations in Lung Cancers among Never Smokers
    Article Snippet: Diluted in EB buffer, 1 μg of DNA was sheared to a target peak size of 150–200 bp using a Covaris LE220 focused-ultrasonicator (Covaris, Woburnm, MA, USA), according to the manufacturer's instructions. .. After the ligation, the adapter-ligated library went through polymerase chain reaction (PCR) amplification.

    IA:

    Article Title: Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population
    Article Snippet: The genomic DNA (2 μg in 100 μL) was sonicated using a Covaris LE220 (Covaris Inc., Woburn, MA) to an average target size of 550 bp. .. The sheared DNA was used for library construction with the TruSeq DNA PCR-free sample preparation kit (Illumina, San Diego, CA) on a Bravo liquid-handling instrument (Agilent Technologies, Santa Clara, CA).

    Sample Prep:

    Article Title: Stage-specific epigenetic regulation of CD4 expression by coordinated enhancer elements during T cell development
    Article Snippet: Paragraph title: Capture C sample preparation ... Two aliquots of 5 µg of 3C library was then sonicated to 200 bp using a Covaris LE220 instrument (190 s shearing time; 30% duty factor; 450PIP, 200 cycles per burst).

    Article Title: Complete Genome Sequence of Thermus aquaticus Y51MC23
    Article Snippet: Both fragment and 8 kb mate pair libraries were constructed for sequencing using NxSeq® DNA Sample Prep and Long Mate Pair Library Kits (Lucigen, Middleton, WI), respectively. .. Fragment libraries were constructed by shearing genomic DNA to approximately 300–400 with a Covaris LE220 Focused-Ultrasonicator (Covaris, Woburn, MA), end repairing, A-tailing and ligating Illumina compatible adaptors.

    Chromatin Immunoprecipitation:

    Article Title: A high-throughput molecular data resource for cutaneous neurofibromas
    Article Snippet: The samples were then sonicated on the Covaris LE220 (Covaris Inc, Woburn, MA, USA) to achieve an average target size of 400 bp. .. The samples were then sonicated on the Covaris LE220 (Covaris Inc, Woburn, MA, USA) to achieve an average target size of 400 bp.

    Software:

    Article Title: Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture
    Article Snippet: Fifth, when using our internal barcodes, it is important to pool samples in each lane in such a way that the base composition of the barcodes is balanced, because the Illumina base-calling software assumes balanced nucleotide composition especially during the first few cycles. .. Capital costs are difficult to compute (because some laboratories may already have the necessary equipment), but if one computes the cost of a Covaris LE220 instrument, a PCR machine, and an Agilent Bravo liquid handling platform, and divides by the cost of 100,000 libraries produced over the 2–3-yr lifetime of these instruments, this would add about $3 more to the cost per sample.

    Article Title: High-Quality Complete and Draft Genome Sequences for Three Escherichia spp. and Three Shigella spp. Generated with Pacific Biosciences and Illumina Sequencing and Optical Mapping
    Article Snippet: Sequence reads were assembled de novo using the Hierarchical Genome Assembly Process (HGAP3) from the SMRT Analysis Software suite (PacBio) ( ). .. DNA samples were sheared to a mean size of 600 bp utilizing a Covaris LE220 focused ultrasonicator (Covaris Inc., Woburn, MA, USA) and cleaned with AMPure (Beckman Coulter, Inc., Indianapolis, IN, USA).

    Article Title: Nine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphila, and C. cf. spartinae, pseudomolecules for the pitch canker pathogen Fusarium circinatum, draft genome of Davidsoniella eucalypti, Grosmannia galeiformis, Quambalaria eucalypti, and Teratosphaeria destructansNine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphil
    Article Snippet: The extracted gDNAs were normalized to 400 ng and sheared to a 300 bp insert using a Covaris LE220 instrument. .. Indexed libraries were pooled into two individual pools and sequencing runs were carried on a NextSeq (Illumina; Molecular Technologies Laboratory, Ottawa Research & Development Centre, Agriculture and Agri-Food Canada) using 2x150 bp NextSeq Mid Output Reagent Kits (Illumina).

    Selection:

    Article Title: Defective mitochondrial DNA homeostasis in the substantia nigra in Parkinson disease
    Article Snippet: Subsequently, samples were normalized in 50 μl of nuclease-free water using 0.30–1.00 μg of stock DNA material and sonicated on a Covaris LE220 (Covaris) to a target insert size of ∼400 bp. .. Subsequently, samples were normalized in 50 μl of nuclease-free water using 0.30–1.00 μg of stock DNA material and sonicated on a Covaris LE220 (Covaris) to a target insert size of ∼400 bp.

    Agarose Gel Electrophoresis:

    Article Title: Radon Exposure-induced Genetic Variations in Lung Cancers among Never Smokers
    Article Snippet: PicoGreen and agarose gel electrophoresis was used to evaluate the quantity and quality of DNA samples. .. Diluted in EB buffer, 1 μg of DNA was sheared to a target peak size of 150–200 bp using a Covaris LE220 focused-ultrasonicator (Covaris, Woburnm, MA, USA), according to the manufacturer's instructions.

    Article Title: Defective mitochondrial DNA homeostasis in the substantia nigra in Parkinson disease
    Article Snippet: Thermal cycling comprised one cycle at 92 °C for 2 min and 35 cycles of 92 °C for 10 s, 63 °C for 30 s and 68 °C for 8 min. PCR products were quality controlled by agarose gel electrophoresis using 5 μl sample and quantitated via picogreen fluorometric assay using 2 μl sample at 1:100 dilution. .. Subsequently, samples were normalized in 50 μl of nuclease-free water using 0.30–1.00 μg of stock DNA material and sonicated on a Covaris LE220 (Covaris) to a target insert size of ∼400 bp.

    Article Title: A high-throughput molecular data resource for cutaneous neurofibromas
    Article Snippet: The integrity of the gDNA was assessed by running an aliquot of the gDNA on 0–8% agarose gel to confirm absence of RNA or protein bands as well as absence of a smear that would indicate degradation. .. The samples were then sonicated on the Covaris LE220 (Covaris Inc, Woburn, MA, USA) to achieve an average target size of 400 bp.

    In Situ:

    Article Title: Static and dynamic DNA loops form AP-1 bound activation hubs during macrophage development
    Article Snippet: Paragraph title: in situ Hi-C protocol ... DNA was sheared using an LE220 Covaris Focused-ultrasonicator to a fragment size of 300–500 bp.

    Homogenization:

    Article Title: Nine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphila, and C. cf. spartinae, pseudomolecules for the pitch canker pathogen Fusarium circinatum, draft genome of Davidsoniella eucalypti, Grosmannia galeiformis, Quambalaria eucalypti, and Teratosphaeria destructansNine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphil
    Article Snippet: The protocol was modified to remove RNA by adding extra RNase and incubating for longer time as follows: (1) after homogenization of ground fungal tissues with 700 μl 2X CTAB, 140 μl RNase CocktailTM Enzyme Mix (4x recommended volume ratio: 2.5 μl / 50 μl sample; Invitrogen by Thermo Fisher Scientific), and 28 μl RNASE A (4x recommended volume ratio: 1 μl / 100 μl sample) was added, and digested for 6–7 h at room temperature. (2) Afterwards, 10 μl Proteinase K (50 μg/μL stock; Fisher Scientific by Thermo Fisher Scientific) was added to the suspension and incubated for 2 h at 55 °C. (3) Before DNA precipitation, another 35ul RNase Cocktail (recommended volume ratio without extra) was added into the supernatant, incubated for 45 min – 1 h at room temperature, followed by adding 650 μL CHCl4 and centrifuging at 13 000 rpm for 15 min. .. The extracted gDNAs were normalized to 400 ng and sheared to a 300 bp insert using a Covaris LE220 instrument.

    Next-Generation Sequencing:

    Article Title: Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates
    Article Snippet: PCR amplicons obtained from the pre-amplification were purified with Agencourt AmPure XP (Beckman Coulter) and subsequently fragmented by sonication using a Covaris LE220 focused-ultrasonicator (Covaris) in order to achieve efficient library generation. .. Library construction for Illumina sequencing was carried out for each sample individually using NEB Ultra II DNA Library Prep Kit (New England Biolabs) with dual index barcoding according to the manufacturer’s instructions.

    Article Title: Radon Exposure-induced Genetic Variations in Lung Cancers among Never Smokers
    Article Snippet: Paragraph title: Targeted next generation sequencing ... Diluted in EB buffer, 1 μg of DNA was sheared to a target peak size of 150–200 bp using a Covaris LE220 focused-ultrasonicator (Covaris, Woburnm, MA, USA), according to the manufacturer's instructions.

    Article Title: Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum
    Article Snippet: Both the libraries were quantified using KAPA Biosystem's next-generation sequencing library quantitative PCR (qPCR) kit and run on a Roche LightCycler 480 real-time PCR instrument. .. To fill gaps in Illumina genome assembly of C. geophilum , an unamplified library was generated using Pacific Biosciences standard template preparation protocol, where 5 μg of gDNA was used to generate the library and the DNA was sheared using a Covaris LE220 focused-ultrasonicator with their Blue 3.0 kb miniTUBES to generate sheared fragments of 3 kb in length.

    dsDNA Assay:

    Article Title: Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils
    Article Snippet: DNA was quantified using the Quant-iT PicoGreen double-stranded DNA (dsDNA) assay kit (Invitrogen), according to the product instructions. .. DNA was mechanically sheared to a median length of 270 bp using a Covaris LE220 and then size-selected using solid-phase reversible immobilization.

    Spectrophotometry:

    Article Title: Nine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphila, and C. cf. spartinae, pseudomolecules for the pitch canker pathogen Fusarium circinatum, draft genome of Davidsoniella eucalypti, Grosmannia galeiformis, Quambalaria eucalypti, and Teratosphaeria destructansNine draft genome sequences of Claviceps purpurea s.lat., including C. arundinis, C. humidiphil
    Article Snippet: Potential RNA contamination in the DNA samples was checked by running the samples on 1 % agarose gels, and determining the 260/280 ratio using NanoDrop 1000 Spectrophotometer v3.8 (Thermo Fisher Scientific) to ensure no RNA was present. gDNA was quantified using Qubit® 2 .0 Fluorometer (Invitrogen by Life Technologies). .. The extracted gDNAs were normalized to 400 ng and sheared to a 300 bp insert using a Covaris LE220 instrument.

    Produced:

    Article Title: Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture
    Article Snippet: The cost for technician time is $3 per sample, assuming that an individual makes 480 libraries on five plates per week. .. Capital costs are difficult to compute (because some laboratories may already have the necessary equipment), but if one computes the cost of a Covaris LE220 instrument, a PCR machine, and an Agilent Bravo liquid handling platform, and divides by the cost of 100,000 libraries produced over the 2–3-yr lifetime of these instruments, this would add about $3 more to the cost per sample. .. This accounting does not include administrative overhead, space rental, process management, quality control on the preparation of reagents, bioinformatic support, data analysis, and research and development, all of which could add significantly to cost.

    Concentration Assay:

    Article Title: Breast cancer diagnosed during pregnancy is associated with enrichment of non-silent mutations, mismatch repair deficiency signature and mucin mutations
    Article Snippet: Samples were fragmented on the Covaris LE220 instrument with 350bp target insert size. .. PCR cycle optimization was performed to prevent over-amplification of the libraries.

    Article Title: Detection of functional protein domains by unbiased genome-wide forward genetic screening
    Article Snippet: Extracted DNA was tested for total volume, concentration and total amount by using gel electrophoresis and the Quant-iTTM PicoGreen® dsDNA Assay Kit (ThermoFisher Scientific). .. Genomic DNA −500 µg (yeast) or 1–3 μg (mouse) – was fragmented to an average size of 100–400 bp (mouse) or 400–600 bp (yeast) by using a Covaris E210 or LE220 device (Covaris, Woburn, MA, USA), size-selected and subjected to DNA library creation via established Illumina paired-end protocols.

    Article Title: High-Quality Complete and Draft Genome Sequences for Three Escherichia spp. and Three Shigella spp. Generated with Pacific Biosciences and Illumina Sequencing and Optical Mapping
    Article Snippet: DNA samples were sheared to a mean size of 600 bp utilizing a Covaris LE220 focused ultrasonicator (Covaris Inc., Woburn, MA, USA) and cleaned with AMPure (Beckman Coulter, Inc., Indianapolis, IN, USA). .. Dual-indexed sequencing libraries were prepared with NEBNext ultra DNA library prep kits for Illumina (New England Biolabs, Ipswich, MA, USA), and barcoding indices were synthesized in-house.

    Article Title: A high-throughput molecular data resource for cutaneous neurofibromas
    Article Snippet: The concentration of the gDNA was estimated using the Qubit 2.0 Fluorometer (Invitrogen); samples with less than 500 ng were discarded. .. The samples were then sonicated on the Covaris LE220 (Covaris Inc, Woburn, MA, USA) to achieve an average target size of 400 bp.

    Stripping Membranes:

    Article Title: Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers
    Article Snippet: DNA quality was quantified as the difference between the Ct (cycle threshold) value of the test FFPE-extracted DNA against the Ct value of the control DNA template. .. 2.3 DNA samples of different concentrations (4-500 ng) were diluted in water to a final volume of 15 μl in Covaris microTUBE-15 8 strip tubes (Covaris, USA) and fragmented to an average size distribution of 150-180 bp with Covaris LE220 Focused Ultrasonicator with Adaptive Focused Acoustics technology. .. The following parameters were used for shearing: Peak Incident Power: 180 W; Duty Factor: 30%; Cycles per Burst: 50; with the fragmentation time: 250 s for DNA with ΔCt < 10, and 200 s for DNA with ΔCt ≥10.

    DNA Purification:

    Article Title: Radon Exposure-induced Genetic Variations in Lung Cancers among Never Smokers
    Article Snippet: To extract DNA, the Maxwell® 16 Tissue DNA Purification Kit (Promega, Madison, WI, USA) was used for tissue samples, and the Maxwell® 16 LEV Blood DNA Kit (Promega) was used for blood samples. .. Diluted in EB buffer, 1 μg of DNA was sheared to a target peak size of 150–200 bp using a Covaris LE220 focused-ultrasonicator (Covaris, Woburnm, MA, USA), according to the manufacturer's instructions.

    Hood:

    Article Title: Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates
    Article Snippet: To minimize the issue of contamination, we have run sample processing, pre-amplification, library preparation, and sequencing in a contained hood in separate rooms. .. PCR amplicons obtained from the pre-amplification were purified with Agencourt AmPure XP (Beckman Coulter) and subsequently fragmented by sonication using a Covaris LE220 focused-ultrasonicator (Covaris) in order to achieve efficient library generation.

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    Covaris le220 instrument
    Le220 Instrument, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 64 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/le220 instrument/product/Covaris
    Average 99 stars, based on 64 article reviews
    Price from $9.99 to $1999.99
    le220 instrument - by Bioz Stars, 2019-10
    99/100 stars
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    80
    Covaris fragment size 300 nucleotides
    Fragment Size 300 Nucleotides, supplied by Covaris, used in various techniques. Bioz Stars score: 80/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/fragment size 300 nucleotides/product/Covaris
    Average 80 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    fragment size 300 nucleotides - by Bioz Stars, 2019-10
    80/100 stars
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