e210  (Covaris)


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    Name:
    E220 Focused ultrasonicator
    Description:
    High performance Ultrasonicator for samples of mass 1000mg and or volume 10ml Automated batch sample preparation system serial process
    Catalog Number:
    500239
    Product Aliases:
    E220, Ultrasonicator
    Price:
    None
    Size:
    24 W x 30 D x 19 H
    Category:
    Instrument
    Score:
    85
    Quantity:
    1
    Buy from Supplier


    Structured Review

    Covaris e210
    E220 Focused ultrasonicator
    High performance Ultrasonicator for samples of mass 1000mg and or volume 10ml Automated batch sample preparation system serial process
    https://www.bioz.com/result/e210/product/Covaris
    Average 99 stars, based on 118 article reviews
    Price from $9.99 to $1999.99
    e210 - by Bioz Stars, 2019-10
    99/100 stars

    Images

    1) Product Images from "A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454"

    Article Title: A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454

    Journal: Genome Biology

    doi: 10.1186/gb-2010-11-2-r15

    Robust, optimized plate-based acoustic shearing of genomic DNA . (a) Effect of time on shearing profile. Agilent Bioanalyzer traces of 3 μg human genomic DNA (Promega) diluted in 100 μl, aliquoted into an ABI PRISM™ Optical Reaction plate and sheared in the Covaris™ E210 under standard plate conditions (duty cycle = 5, intensity = 5, cycles per burst = 500) for increasing amounts of time (n = 3 for each timepoint). (b) Incomplete shears recovered by re-shearing. (i) Average shearing distribution (n = 27) of samples sheared for 100 seconds under standard conditions. (ii) An example of incomplete shearing seen in three attempts under standard conditions. (iii) Resultant fragment pattern after reshearing from (ii) with standard conditions. Each shear profile signal is plotted normalized to the maximum ladder fluorescence for the Bioanalyzer chip upon which the sample was run. (c) Dual high and low cutoff size-selection using para-magnetic beads (SPRI). Human genomic DNA (3 μg) was sheared under standard conditions, producing fragments ranging in size from less than 100 bp to approximately 4 kb (i). This shear product then underwent a 0.5× Solid Phase Reversible Immobilization (SPRI) reaction in which high molecular weight fragments were preferentially bound (ii). The supernatant was removed to a second tube and underwent a second 0.7× SPRI reaction where fragments below 300 bp were removed in the supernatant (iii). Fragments in the desired size range of 300 to 1,000 bp were eluted from the beads (iv).
    Figure Legend Snippet: Robust, optimized plate-based acoustic shearing of genomic DNA . (a) Effect of time on shearing profile. Agilent Bioanalyzer traces of 3 μg human genomic DNA (Promega) diluted in 100 μl, aliquoted into an ABI PRISM™ Optical Reaction plate and sheared in the Covaris™ E210 under standard plate conditions (duty cycle = 5, intensity = 5, cycles per burst = 500) for increasing amounts of time (n = 3 for each timepoint). (b) Incomplete shears recovered by re-shearing. (i) Average shearing distribution (n = 27) of samples sheared for 100 seconds under standard conditions. (ii) An example of incomplete shearing seen in three attempts under standard conditions. (iii) Resultant fragment pattern after reshearing from (ii) with standard conditions. Each shear profile signal is plotted normalized to the maximum ladder fluorescence for the Bioanalyzer chip upon which the sample was run. (c) Dual high and low cutoff size-selection using para-magnetic beads (SPRI). Human genomic DNA (3 μg) was sheared under standard conditions, producing fragments ranging in size from less than 100 bp to approximately 4 kb (i). This shear product then underwent a 0.5× Solid Phase Reversible Immobilization (SPRI) reaction in which high molecular weight fragments were preferentially bound (ii). The supernatant was removed to a second tube and underwent a second 0.7× SPRI reaction where fragments below 300 bp were removed in the supernatant (iii). Fragments in the desired size range of 300 to 1,000 bp were eluted from the beads (iv).

    Techniques Used: Fluorescence, Chromatin Immunoprecipitation, Selection, Magnetic Beads, Molecular Weight

    2) Product Images from "Genome wide copy number analysis of single cells"

    Article Title: Genome wide copy number analysis of single cells

    Journal:

    doi: 10.1038/nprot.2012.039

    Sonication profiles of WGA DNA using different sonication programs on the Covaris E210 instrument. (a) Sonication profiles as measured on the Bioanalyzer S1: non-sonicated WGA DNA. S1 400 / S1 300 / S1 200: WGA DNA sonicated using 400+/− ∣300+/−
    Figure Legend Snippet: Sonication profiles of WGA DNA using different sonication programs on the Covaris E210 instrument. (a) Sonication profiles as measured on the Bioanalyzer S1: non-sonicated WGA DNA. S1 400 / S1 300 / S1 200: WGA DNA sonicated using 400+/− ∣300+/−

    Techniques Used: Sonication, Whole Genome Amplification

    Related Articles

    Clone Assay:

    Article Title: Legume Cytosolic and Plastid Acetyl-Coenzyme—A Carboxylase Genes Differ by Evolutionary Patterns and Selection Pressure Schemes Acting before and after Whole-Genome Duplications
    Article Snippet: BESs were aligned using BLASTn algorithm [ ] in Geneious 8.1 [ ] to the draft assembly of the L. angustifolius genome [ ] and overlapping BAC clones were identified. .. Nucleic acid fragmentation was performed in E210× (Covaris, Woburn, MA, USA).

    Amplification:

    Article Title: Legume Cytosolic and Plastid Acetyl-Coenzyme—A Carboxylase Genes Differ by Evolutionary Patterns and Selection Pressure Schemes Acting before and after Whole-Genome Duplications
    Article Snippet: The contigs were verified by PCR amplification using BAC DNA and primers designed on the templates of appropriate BESs. .. Nucleic acid fragmentation was performed in E210× (Covaris, Woburn, MA, USA).

    Article Title: SETDB1 Links the Meiotic DNA Damage Response to Sex Chromosome Silencing in Mice
    Article Snippet: Total RNA was extracted from 500 pachytene cells using RNAqueous-Micro Total RNA Isolation Kit (ThermoFisher, AM1931) and eluted in 10 μl of elution solution. cDNA was amplified from 1 μl of total RNA by using Smart-seq2 protocol ( , ) (15 amplification cycles). .. 10 ng of cDNA was sheared using Covaris E220.

    Article Title: Hybrid selection for sequencing pathogen genomes from clinical samples
    Article Snippet: For input, 3 μg of P. falciparum 3D7 DNA was sheared for 4 minutes on a Covaris E210 instrument set to duty cycle 5, intensity 5 and 200 cycles per burst. .. End repair, addition of a 3'-A, adaptor ligation and reaction clean-up followed the Illumina's genomic DNA sample preparation kit protocol except that adapter consisted of oligonucleotides 5'-TGTAACATCACAGCATCACCGCCATCAGTCxT-3' ('x' refers to an exonuclease I-resistant phosphorothioate linkage) and 5'-[PHOS]GACTGATGGCGCACTACGACACTACAATGT-3'.

    Article Title: Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers
    Article Snippet: Following RNA isolation, 100 ng of total RNA was converted to cDNA using the Ovation RNA-seq System V2 (Nugen Technologies, San Carlos, CA). .. 2 μg of the amplified cDNA was sheared to 150–200 bp size distribution by Adaptive Focused Acoustics using a Covaris E220 instrument (Covaris, Woburn, MA) under the following conditions: 50 μl total volume, 20% duty cycle, 175 intensity, 200 cycles per burst, 165 sec in frequency sweeping mode. .. The remainder of the library preparation followed manufacturer’s protocol as described in Encore Rapid IL Multiplex System (Nugen Technologies).

    Construct:

    Article Title: Molecular Epidemiology of Community-Associated Methicillin-resistant Staphylococcus aureus in the genomic era: a Cross-Sectional Study
    Article Snippet: After confirmation of quality and determination of quantity, 5 μg of each isolate gDNA was sequenced on the Illumina HiSeq 2000 sequencing system. .. Libraries were constructed for each isolate using the Covaris E220 and the SPRIworks Fragment Library System (Beckman Coulter), and accurate quality control was performed using the Agilent Bioanalyzer and qPCR, ensuring library quality before sequencing and ideal cluster density during sequencing. .. Isolates were uniquely tagged and combined in one of eight lanes of the flow cell for a paired-end 75 base pair read.

    Article Title: A deep insight into the sialotranscriptome of the mosquito, Psorophora albipes
    Article Snippet: The SG library was constructed using the TruSeq RNA sample prep kit, v2 (Illumina Inc., San Diego, CA). .. The resulting cDNA was fragmented using a Covaris E210™ focused ultrasonicator (Covaris, Woburn, MA).

    Article Title: Whole Genome Analyses of a Well-Differentiated Liposarcoma Reveals Novel SYT1 and DDR2 Rearrangements
    Article Snippet: Briefly, DNA was fragmented using the Covaris E210 sonicator to generate double-stranded DNA fragments with a fragment size of 400–500 bp. .. Briefly, DNA was fragmented using the Covaris E210 sonicator to generate double-stranded DNA fragments with a fragment size of 400–500 bp.

    Article Title: Whole Genome Sequence-Based Analysis of a Model Complex Trait, High Density Lipoprotein Cholesterol
    Article Snippet: DNA concentration was determined by pico green assays while DNA integrity was determined through Agilent Bioanalyzer traces and agarose gels. .. Libraries were constructed using 1ug of genomic DNA in 100ul volume and sheared into fragments of approximately 300 base pairs in a Covaris plate with E210 system (Covaris, Inc. Woburn, MA). .. The setting was 10% Duty cycle, Intensity of 4, 200 Cycles per Burst, for 120 seconds.

    Article Title: Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh)
    Article Snippet: Sequencing libraries were constructed according to the TruSeq DNA sample preparation protocol (Illumina) with minor modifications, in particular employing double size selection steps. .. Two micrograms of genomic DNA were fragmented with a Covaris E210 and size selected to 300–600 bps.

    Article Title: A Deep Insight into the Sialome of Male and Female Aedes aegypti Mosquitoes
    Article Snippet: The SG library was constructed using the TruSeq RNA sample prep kit, v2 (Illumina Inc., San Diego, CA) following the manufacturer recommendations. .. The resulting cDNA was fragmented using a Covaris E210 system (Covaris, Woburn, MA).

    Real-time Polymerase Chain Reaction:

    Article Title: Molecular Epidemiology of Community-Associated Methicillin-resistant Staphylococcus aureus in the genomic era: a Cross-Sectional Study
    Article Snippet: After confirmation of quality and determination of quantity, 5 μg of each isolate gDNA was sequenced on the Illumina HiSeq 2000 sequencing system. .. Libraries were constructed for each isolate using the Covaris E220 and the SPRIworks Fragment Library System (Beckman Coulter), and accurate quality control was performed using the Agilent Bioanalyzer and qPCR, ensuring library quality before sequencing and ideal cluster density during sequencing. .. Isolates were uniquely tagged and combined in one of eight lanes of the flow cell for a paired-end 75 base pair read.

    Article Title: Vitamin C induces Tet-dependent DNA demethylation in ESCs to promote a blastocyst-like state
    Article Snippet: For each sample, 12 µg of genomic DNA was isolated, split into 3 replicates of 4 µg each and sonicated to ~100–500 bp on a Covaris E210 platform (75 s, 10% duty cycle). .. Ligated genomic DNA was size selected (100–300 bp) by 8% PAGE (Nuvex, Invitrogen) to remove unligated adapters.

    Article Title: Genomics and Transcriptomics Analyses of the Oil-Accumulating Basidiomycete Yeast Trichosporon oleaginosus: Insights into Substrate Utilization and Alternative Evolutionary Trajectories of Fungal Mating Systems
    Article Snippet: One hundred nanograms of genomic DNA was sheared to 270 bp by using the Covaris E210 apparatus and size selected by using SPRI beads (Beckman Coulter). .. The fragments were treated with end repair, A-tailing, and ligation of Illumina compatible adapters (IDT, Inc.) by using the KAPA Illumina library creation kit (KAPA Biosystems).

    cDNA Library Assay:

    Article Title: A Deep Insight into the Sialome of Male and Female Aedes aegypti Mosquitoes
    Article Snippet: Paragraph title: cDNA library constructions and next generation sequencing ... The resulting cDNA was fragmented using a Covaris E210 system (Covaris, Woburn, MA).

    Incubation:

    Article Title: Whole Genome Sequence-Based Analysis of a Model Complex Trait, High Density Lipoprotein Cholesterol
    Article Snippet: Libraries were constructed using 1ug of genomic DNA in 100ul volume and sheared into fragments of approximately 300 base pairs in a Covaris plate with E210 system (Covaris, Inc. Woburn, MA). .. Libraries were constructed using 1ug of genomic DNA in 100ul volume and sheared into fragments of approximately 300 base pairs in a Covaris plate with E210 system (Covaris, Inc. Woburn, MA).

    Article Title: The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion
    Article Snippet: Briefly, DNA was fragmented to 400 to 550 bp using Adaptive Focused Acoustics technology with the E210 instrument (Covaris, Woburn, MA, USA) (duty cycle 20; intensity 5; cycles/bursts 200; seconds 30; temperature 4°C). .. To ligate sequencing adaptors, a 50 μl reaction mixture containing the sample was set with addition of 25 μl of 2× DNA T4 ligase buffer (New England Biolabs, Inc.), 4 μl 4 μM Illumina paired-end duplex adaptors (Integrated DNA Technologies, Coralville, IA, USA) and 2 μl T4 DNA ligase.

    Derivative Assay:

    Article Title: Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms
    Article Snippet: The NuGen Ovation RNA-Seq kit produces non-stranded cDNA (3–5 microgram, measured with Qubit (Life Technologies, Foster City, CA)). .. The double-stranded cDNA derived from long RNAs was sheared to 150–200 bp fragments with a Covaris focused-ultrasonicator (Covaris, Inc. Woburn, MA) and recovered by centrifuging over an YM-30 spin filter (Amicon EMD Millipore Billerica, MA). .. We generated barcoded sequencing libraries from 100 ng of sheared cDNA using the NEBNext Fast DNA Library Prep Set for Ion Torrent sequencing (New England Biolabs, NEB, Ipswich, MA), as described [ , ].

    Electron Microscopy:

    Article Title: Complete Genome Sequences of Erwinia amylovora Phages vB_EamP-S2 and vB_EamM-Bue1
    Article Snippet: Transmission electron microscopy identified S2 as a podovirus , with an average capsid size of 64 nm (±4.6 nm), and Bue1 as a myovirus, with an average capsid size of 79 nm (±2.4 nm) and a 126-nm-long (±7.4 nm) contractile tail. .. Phage DNA was extracted as described previously ( ) and sheared into 550-bp fragments on an E220 ultrasonicator (Covaris, Woburn, MA).

    Flow Cytometry:

    Article Title: A deep insight into the sialotranscriptome of the mosquito, Psorophora albipes
    Article Snippet: The resulting cDNA was fragmented using a Covaris E210™ focused ultrasonicator (Covaris, Woburn, MA). .. Library amplification was performed using eight cycles to minimize the risk of over-amplification.

    Article Title: A Deep Insight into the Sialome of Male and Female Aedes aegypti Mosquitoes
    Article Snippet: The resulting cDNA was fragmented using a Covaris E210 system (Covaris, Woburn, MA). .. Library amplification was performed using eight cycles to minimize the risk of over-amplification.

    DNA Immunoprecipitation Sequencing:

    Article Title: Vitamin C induces Tet-dependent DNA demethylation in ESCs to promote a blastocyst-like state
    Article Snippet: Paragraph title: hmC and mC DIP-seq ... For each sample, 12 µg of genomic DNA was isolated, split into 3 replicates of 4 µg each and sonicated to ~100–500 bp on a Covaris E210 platform (75 s, 10% duty cycle).

    Ligation:

    Article Title: Vitamin C induces Tet-dependent DNA demethylation in ESCs to promote a blastocyst-like state
    Article Snippet: For each sample, 12 µg of genomic DNA was isolated, split into 3 replicates of 4 µg each and sonicated to ~100–500 bp on a Covaris E210 platform (75 s, 10% duty cycle). .. Ligated genomic DNA was size selected (100–300 bp) by 8% PAGE (Nuvex, Invitrogen) to remove unligated adapters.

    Article Title: Hybrid selection for sequencing pathogen genomes from clinical samples
    Article Snippet: For input, 3 μg of P. falciparum 3D7 DNA was sheared for 4 minutes on a Covaris E210 instrument set to duty cycle 5, intensity 5 and 200 cycles per burst. .. For input, 3 μg of P. falciparum 3D7 DNA was sheared for 4 minutes on a Covaris E210 instrument set to duty cycle 5, intensity 5 and 200 cycles per burst.

    Article Title: Novel Compound Heterozygous Mutations in MYO7A Associated with Usher Syndrome 1 in a Chinese Family
    Article Snippet: High-molecular-weight gDNA (∼3 µg) was fragmented ultrasonically using an E210 DNA-shearing instrument (Covaris; Woburn, MA, USA) to an average size of 300 base pairs (bps). .. Fragmented gDNA libraries for Illumina GAII sequencing were prepared with the NEBNext™ DNA Sample Prep Master Mix set (E6040, New England BioLabs; Ipswich, MA).

    Article Title: The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion
    Article Snippet: Briefly, DNA was fragmented to 400 to 550 bp using Adaptive Focused Acoustics technology with the E210 instrument (Covaris, Woburn, MA, USA) (duty cycle 20; intensity 5; cycles/bursts 200; seconds 30; temperature 4°C). .. To ligate sequencing adaptors, a 50 μl reaction mixture containing the sample was set with addition of 25 μl of 2× DNA T4 ligase buffer (New England Biolabs, Inc.), 4 μl 4 μM Illumina paired-end duplex adaptors (Integrated DNA Technologies, Coralville, IA, USA) and 2 μl T4 DNA ligase.

    Generated:

    Article Title: Complete Genome Sequences of Erwinia amylovora Phages vB_EamP-S2 and vB_EamM-Bue1
    Article Snippet: Phage DNA was extracted as described previously ( ) and sheared into 550-bp fragments on an E220 ultrasonicator (Covaris, Woburn, MA). .. Paired-end sequencing of 300 bp was performed on a MiSeq instrument (Illumina) using a 600-cycle MiSeq reagent kit version 3 (Illumina), according to the manufacturer’s instructions.

    Article Title: Hybrid selection for sequencing pathogen genomes from clinical samples
    Article Snippet: WGB was generated at the Broad Institute. .. For input, 3 μg of P. falciparum 3D7 DNA was sheared for 4 minutes on a Covaris E210 instrument set to duty cycle 5, intensity 5 and 200 cycles per burst.

    Article Title: EasyCloneMulti: A Set of Vectors for Simultaneous and Multiple Genomic Integrations in Saccharomyces cerevisiae
    Article Snippet: The genomic libraries were generated using the TruSeq Nano DNA LT Library Prep Kit (Illumina Inc., San Diego CA). .. Briefly, 100 ng of genomic DNA diluted in 52.5 μL TE buffer was fragmented in Covaris Crimp Cap microtubes on a Covaris E220 ultrasonicator (Woburn, MA) with 5% duty factor, 175 W peak incident power, 200 cycles/burst, and 50-s duration under frequency sweeping mode at 5.5 to 6°C (Illumina recommendations for a 350-bp average fragment size).

    Imaging:

    Article Title: Novel Compound Heterozygous Mutations in MYO7A Associated with Usher Syndrome 1 in a Chinese Family
    Article Snippet: Then, we sequenced all of the coding exons plus ∼100 bp of the flanking intronic sequences for 131 deafness genes and ∼5 kilobases of GJB2 regulatory sequences ( ) in three affected members (II:1, II:2, II:4) and three unaffected members (II:3, I:1, I:2) of family 7162. gDNA quality was evaluated using the optical density ratio (260/280 ratio) and gel electrophoresis imaging. .. High-molecular-weight gDNA (∼3 µg) was fragmented ultrasonically using an E210 DNA-shearing instrument (Covaris; Woburn, MA, USA) to an average size of 300 base pairs (bps).

    Transmission Assay:

    Article Title: Complete Genome Sequences of Erwinia amylovora Phages vB_EamP-S2 and vB_EamM-Bue1
    Article Snippet: Transmission electron microscopy identified S2 as a podovirus , with an average capsid size of 64 nm (±4.6 nm), and Bue1 as a myovirus, with an average capsid size of 79 nm (±2.4 nm) and a 126-nm-long (±7.4 nm) contractile tail. .. Phage DNA was extracted as described previously ( ) and sheared into 550-bp fragments on an E220 ultrasonicator (Covaris, Woburn, MA).

    Polymerase Chain Reaction:

    Article Title: Legume Cytosolic and Plastid Acetyl-Coenzyme—A Carboxylase Genes Differ by Evolutionary Patterns and Selection Pressure Schemes Acting before and after Whole-Genome Duplications
    Article Snippet: The contigs were verified by PCR amplification using BAC DNA and primers designed on the templates of appropriate BESs. .. Nucleic acid fragmentation was performed in E210× (Covaris, Woburn, MA, USA).

    Article Title: Whole Genome Analyses of a Well-Differentiated Liposarcoma Reveals Novel SYT1 and DDR2 Rearrangements
    Article Snippet: Briefly, DNA was fragmented using the Covaris E210 sonicator to generate double-stranded DNA fragments with a fragment size of 400–500 bp. .. The excised gel band was purified following manufacturer's protocol utilizing Qiagen Gel Extraction Kits.

    Article Title: Vitamin C induces Tet-dependent DNA demethylation in ESCs to promote a blastocyst-like state
    Article Snippet: For each sample, 12 µg of genomic DNA was isolated, split into 3 replicates of 4 µg each and sonicated to ~100–500 bp on a Covaris E210 platform (75 s, 10% duty cycle). .. Ligated genomic DNA was size selected (100–300 bp) by 8% PAGE (Nuvex, Invitrogen) to remove unligated adapters.

    Article Title: Hybrid selection for sequencing pathogen genomes from clinical samples
    Article Snippet: For input, 3 μg of P. falciparum 3D7 DNA was sheared for 4 minutes on a Covaris E210 instrument set to duty cycle 5, intensity 5 and 200 cycles per burst. .. End repair, addition of a 3'-A, adaptor ligation and reaction clean-up followed the Illumina's genomic DNA sample preparation kit protocol except that adapter consisted of oligonucleotides 5'-TGTAACATCACAGCATCACCGCCATCAGTCxT-3' ('x' refers to an exonuclease I-resistant phosphorothioate linkage) and 5'-[PHOS]GACTGATGGCGCACTACGACACTACAATGT-3'.

    Article Title: EasyCloneMulti: A Set of Vectors for Simultaneous and Multiple Genomic Integrations in Saccharomyces cerevisiae
    Article Snippet: Briefly, 100 ng of genomic DNA diluted in 52.5 μL TE buffer was fragmented in Covaris Crimp Cap microtubes on a Covaris E220 ultrasonicator (Woburn, MA) with 5% duty factor, 175 W peak incident power, 200 cycles/burst, and 50-s duration under frequency sweeping mode at 5.5 to 6°C (Illumina recommendations for a 350-bp average fragment size). .. The adapters were ligated to the ends of the DNA fragments, and the DNA fragments ranging from 300–400 bp were recovered by beads purification.

    Article Title: A somatic reference standard for cancer genome sequencing
    Article Snippet: 1.1 μg of DNA from each line was used to generate whole genome libraries using the Illumina TruSeq DNA PCR-free LT Sample Prep Kit (Set A; cat#FC-121-3001) following the manufacturer’s protocol. .. Following sonication on the Covaris E210, 100 ng of each sample was electrophoretically separated on a 1% TAE gel to verify fragmentation.

    Sonication:

    Article Title: Vitamin C induces Tet-dependent DNA demethylation in ESCs to promote a blastocyst-like state
    Article Snippet: Oct4 -GiP ESCs were treated with VitC (100 µg/ml) for 12 and 72 hrs. .. For each sample, 12 µg of genomic DNA was isolated, split into 3 replicates of 4 µg each and sonicated to ~100–500 bp on a Covaris E210 platform (75 s, 10% duty cycle). .. Sheared DNA was end-repaired, A-tailed, and ligated to custom paired-end adapters as described .

    Article Title: Next generation sequencing analysis of platinum refractory advanced germ cell tumor sensitive to Sunitinib (Sutent®) a VEGFR2/PDGFRβ/c-kit/ FLT3/RET/CSF1R inhibitor in a phase II trial
    Article Snippet: The trial was an investigator initiated single institutional trial supported by Pfizer inc. (New York, NY) which provided Sunitinib (Sutent®) to the patients enrolled on the trial was closed early due to slow accrual. .. Next generation targeted exomic sequencing was performed for genomic profling.200-500ug of genomic DNA from each sample was sheared by sonication using the Covaris E220 instrument (Covaris). .. Library preparation utilized the KAPA kit following the “with beads” manufacturer protocol using KAPA HiFi polymerase (6 cycles).

    Article Title: A somatic reference standard for cancer genome sequencing
    Article Snippet: 1.1 μg of DNA from each line was used to generate whole genome libraries using the Illumina TruSeq DNA PCR-free LT Sample Prep Kit (Set A; cat#FC-121-3001) following the manufacturer’s protocol. .. Following sonication on the Covaris E210, 100 ng of each sample was electrophoretically separated on a 1% TAE gel to verify fragmentation. .. Final libraries were evaluated on the Agilent Bioanalyzer and quantitated by Qubit.

    Multiplexing:

    Article Title: Whole Genome Sequence-Based Analysis of a Model Complex Trait, High Density Lipoprotein Cholesterol
    Article Snippet: To date, over 15,000 libraries have been completed using these automated methods for capture and WGS applications with up to 96 sample barcodes now employed for multiplexing. .. Libraries were constructed using 1ug of genomic DNA in 100ul volume and sheared into fragments of approximately 300 base pairs in a Covaris plate with E210 system (Covaris, Inc. Woburn, MA).

    Nucleic Acid Electrophoresis:

    Article Title: Novel Compound Heterozygous Mutations in MYO7A Associated with Usher Syndrome 1 in a Chinese Family
    Article Snippet: Then, we sequenced all of the coding exons plus ∼100 bp of the flanking intronic sequences for 131 deafness genes and ∼5 kilobases of GJB2 regulatory sequences ( ) in three affected members (II:1, II:2, II:4) and three unaffected members (II:3, I:1, I:2) of family 7162. gDNA quality was evaluated using the optical density ratio (260/280 ratio) and gel electrophoresis imaging. .. High-molecular-weight gDNA (∼3 µg) was fragmented ultrasonically using an E210 DNA-shearing instrument (Covaris; Woburn, MA, USA) to an average size of 300 base pairs (bps).

    RNA Sequencing Assay:

    Article Title: SETDB1 Links the Meiotic DNA Damage Response to Sex Chromosome Silencing in Mice
    Article Snippet: Paragraph title: RNA Sequencing (RNA-Seq) ... 10 ng of cDNA was sheared using Covaris E220.

    Article Title: Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms
    Article Snippet: The NuGen Ovation RNA-Seq kit produces non-stranded cDNA (3–5 microgram, measured with Qubit (Life Technologies, Foster City, CA)). .. The double-stranded cDNA derived from long RNAs was sheared to 150–200 bp fragments with a Covaris focused-ultrasonicator (Covaris, Inc. Woburn, MA) and recovered by centrifuging over an YM-30 spin filter (Amicon EMD Millipore Billerica, MA).

    Article Title: Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers
    Article Snippet: Paragraph title: Next generation RNA sequencing ... 2 μg of the amplified cDNA was sheared to 150–200 bp size distribution by Adaptive Focused Acoustics using a Covaris E220 instrument (Covaris, Woburn, MA) under the following conditions: 50 μl total volume, 20% duty cycle, 175 intensity, 200 cycles per burst, 165 sec in frequency sweeping mode.

    BAC Assay:

    Article Title: Legume Cytosolic and Plastid Acetyl-Coenzyme—A Carboxylase Genes Differ by Evolutionary Patterns and Selection Pressure Schemes Acting before and after Whole-Genome Duplications
    Article Snippet: The contigs were verified by PCR amplification using BAC DNA and primers designed on the templates of appropriate BESs. .. Nucleic acid fragmentation was performed in E210× (Covaris, Woburn, MA, USA).

    Magnetic Beads:

    Article Title: The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion
    Article Snippet: Briefly, DNA was fragmented to 400 to 550 bp using Adaptive Focused Acoustics technology with the E210 instrument (Covaris, Woburn, MA, USA) (duty cycle 20; intensity 5; cycles/bursts 200; seconds 30; temperature 4°C). .. Briefly, DNA was fragmented to 400 to 550 bp using Adaptive Focused Acoustics technology with the E210 instrument (Covaris, Woburn, MA, USA) (duty cycle 20; intensity 5; cycles/bursts 200; seconds 30; temperature 4°C).

    Isolation:

    Article Title: SETDB1 Links the Meiotic DNA Damage Response to Sex Chromosome Silencing in Mice
    Article Snippet: Total RNA was extracted from 500 pachytene cells using RNAqueous-Micro Total RNA Isolation Kit (ThermoFisher, AM1931) and eluted in 10 μl of elution solution. cDNA was amplified from 1 μl of total RNA by using Smart-seq2 protocol ( , ) (15 amplification cycles). .. 10 ng of cDNA was sheared using Covaris E220.

    Article Title: Complete Genome Sequences of Erwinia amylovora Phages vB_EamP-S2 and vB_EamM-Bue1
    Article Snippet: E. amylovora -specific phages vB_EamP-S2 (S2) and vB_EamM-Bue1 (Bue1) were isolated from soil samples (Swiss apple orchards). .. Phage DNA was extracted as described previously ( ) and sheared into 550-bp fragments on an E220 ultrasonicator (Covaris, Woburn, MA).

    Article Title: Vitamin C induces Tet-dependent DNA demethylation in ESCs to promote a blastocyst-like state
    Article Snippet: Oct4 -GiP ESCs were treated with VitC (100 µg/ml) for 12 and 72 hrs. .. For each sample, 12 µg of genomic DNA was isolated, split into 3 replicates of 4 µg each and sonicated to ~100–500 bp on a Covaris E210 platform (75 s, 10% duty cycle). .. Sheared DNA was end-repaired, A-tailed, and ligated to custom paired-end adapters as described .

    Article Title: Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers
    Article Snippet: Following RNA isolation, 100 ng of total RNA was converted to cDNA using the Ovation RNA-seq System V2 (Nugen Technologies, San Carlos, CA). .. 2 μg of the amplified cDNA was sheared to 150–200 bp size distribution by Adaptive Focused Acoustics using a Covaris E220 instrument (Covaris, Woburn, MA) under the following conditions: 50 μl total volume, 20% duty cycle, 175 intensity, 200 cycles per burst, 165 sec in frequency sweeping mode.

    Size-exclusion Chromatography:

    Article Title: Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers
    Article Snippet: Following RNA isolation, 100 ng of total RNA was converted to cDNA using the Ovation RNA-seq System V2 (Nugen Technologies, San Carlos, CA). .. 2 μg of the amplified cDNA was sheared to 150–200 bp size distribution by Adaptive Focused Acoustics using a Covaris E220 instrument (Covaris, Woburn, MA) under the following conditions: 50 μl total volume, 20% duty cycle, 175 intensity, 200 cycles per burst, 165 sec in frequency sweeping mode. .. The remainder of the library preparation followed manufacturer’s protocol as described in Encore Rapid IL Multiplex System (Nugen Technologies).

    Labeling:

    Article Title: Next generation sequencing analysis of platinum refractory advanced germ cell tumor sensitive to Sunitinib (Sutent®) a VEGFR2/PDGFRβ/c-kit/ FLT3/RET/CSF1R inhibitor in a phase II trial
    Article Snippet: Next generation targeted exomic sequencing was performed for genomic profling.200-500ug of genomic DNA from each sample was sheared by sonication using the Covaris E220 instrument (Covaris). .. Next generation targeted exomic sequencing was performed for genomic profling.200-500ug of genomic DNA from each sample was sheared by sonication using the Covaris E220 instrument (Covaris).

    Purification:

    Article Title: Whole Genome Analyses of a Well-Differentiated Liposarcoma Reveals Novel SYT1 and DDR2 Rearrangements
    Article Snippet: Briefly, DNA was fragmented using the Covaris E210 sonicator to generate double-stranded DNA fragments with a fragment size of 400–500 bp. .. Paired end DNA adaptors were ligated and the resulting constructs size selected for ∼500 bp fragments.

    Article Title: Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms
    Article Snippet: First, long RNA ( > 200 bases) was separated using SpinSmart RNA Purification column (Denville), and the flowthrough ( < 200 bases) was placed on a second column for small RNA (microRNA) separation with mirPremier microRNA isolation kit (Sigma-Aldrich, St. Louis, MO). .. The double-stranded cDNA derived from long RNAs was sheared to 150–200 bp fragments with a Covaris focused-ultrasonicator (Covaris, Inc. Woburn, MA) and recovered by centrifuging over an YM-30 spin filter (Amicon EMD Millipore Billerica, MA).

    Article Title: Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers
    Article Snippet: 2 μg of the amplified cDNA was sheared to 150–200 bp size distribution by Adaptive Focused Acoustics using a Covaris E220 instrument (Covaris, Woburn, MA) under the following conditions: 50 μl total volume, 20% duty cycle, 175 intensity, 200 cycles per burst, 165 sec in frequency sweeping mode. .. The remainder of the library preparation followed manufacturer’s protocol as described in Encore Rapid IL Multiplex System (Nugen Technologies).

    Article Title: EasyCloneMulti: A Set of Vectors for Simultaneous and Multiple Genomic Integrations in Saccharomyces cerevisiae
    Article Snippet: Briefly, 100 ng of genomic DNA diluted in 52.5 μL TE buffer was fragmented in Covaris Crimp Cap microtubes on a Covaris E220 ultrasonicator (Woburn, MA) with 5% duty factor, 175 W peak incident power, 200 cycles/burst, and 50-s duration under frequency sweeping mode at 5.5 to 6°C (Illumina recommendations for a 350-bp average fragment size). .. Briefly, 100 ng of genomic DNA diluted in 52.5 μL TE buffer was fragmented in Covaris Crimp Cap microtubes on a Covaris E220 ultrasonicator (Woburn, MA) with 5% duty factor, 175 W peak incident power, 200 cycles/burst, and 50-s duration under frequency sweeping mode at 5.5 to 6°C (Illumina recommendations for a 350-bp average fragment size).

    Sequencing:

    Article Title: Legume Cytosolic and Plastid Acetyl-Coenzyme—A Carboxylase Genes Differ by Evolutionary Patterns and Selection Pressure Schemes Acting before and after Whole-Genome Duplications
    Article Snippet: Paragraph title: 2.4. Contig Assembly and Bacterial Artificial Chromosome Clone Sequencing ... Nucleic acid fragmentation was performed in E210× (Covaris, Woburn, MA, USA).

    Article Title: SETDB1 Links the Meiotic DNA Damage Response to Sex Chromosome Silencing in Mice
    Article Snippet: 10 ng of cDNA was sheared using Covaris E220. .. Libraries of ∼300 bp were generated using Ovation Ultralow DR kit (NuGEN, 0330) with 14 PCR cycles.

    Article Title: Complete Genome Sequences of Erwinia amylovora Phages vB_EamP-S2 and vB_EamM-Bue1
    Article Snippet: Phage DNA was extracted as described previously ( ) and sheared into 550-bp fragments on an E220 ultrasonicator (Covaris, Woburn, MA). .. Libraries were prepared on a NeoPrep system (Illumina, San Diego, CA) using a TruSeq Nano DNA kit (Illumina) with six PCR cycles, according to the manufacturer’s instructions.

    Article Title: Molecular Epidemiology of Community-Associated Methicillin-resistant Staphylococcus aureus in the genomic era: a Cross-Sectional Study
    Article Snippet: After confirmation of quality and determination of quantity, 5 μg of each isolate gDNA was sequenced on the Illumina HiSeq 2000 sequencing system. .. Libraries were constructed for each isolate using the Covaris E220 and the SPRIworks Fragment Library System (Beckman Coulter), and accurate quality control was performed using the Agilent Bioanalyzer and qPCR, ensuring library quality before sequencing and ideal cluster density during sequencing. .. Isolates were uniquely tagged and combined in one of eight lanes of the flow cell for a paired-end 75 base pair read.

    Article Title: A deep insight into the sialotranscriptome of the mosquito, Psorophora albipes
    Article Snippet: The resulting cDNA was fragmented using a Covaris E210™ focused ultrasonicator (Covaris, Woburn, MA). .. Library amplification was performed using eight cycles to minimize the risk of over-amplification.

    Article Title: Whole Genome Sequence-Based Analysis of a Model Complex Trait, High Density Lipoprotein Cholesterol
    Article Snippet: Paragraph title: Description of whole genome sequencing and calling ... Libraries were constructed using 1ug of genomic DNA in 100ul volume and sheared into fragments of approximately 300 base pairs in a Covaris plate with E210 system (Covaris, Inc. Woburn, MA).

    Article Title: Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh)
    Article Snippet: Sequencing libraries were constructed according to the TruSeq DNA sample preparation protocol (Illumina) with minor modifications, in particular employing double size selection steps. .. Two micrograms of genomic DNA were fragmented with a Covaris E210 and size selected to 300–600 bps.

    Article Title: Novel Compound Heterozygous Mutations in MYO7A Associated with Usher Syndrome 1 in a Chinese Family
    Article Snippet: High-molecular-weight gDNA (∼3 µg) was fragmented ultrasonically using an E210 DNA-shearing instrument (Covaris; Woburn, MA, USA) to an average size of 300 base pairs (bps). .. High-molecular-weight gDNA (∼3 µg) was fragmented ultrasonically using an E210 DNA-shearing instrument (Covaris; Woburn, MA, USA) to an average size of 300 base pairs (bps).

    Article Title: Next generation sequencing analysis of platinum refractory advanced germ cell tumor sensitive to Sunitinib (Sutent®) a VEGFR2/PDGFRβ/c-kit/ FLT3/RET/CSF1R inhibitor in a phase II trial
    Article Snippet: The trial was an investigator initiated single institutional trial supported by Pfizer inc. (New York, NY) which provided Sunitinib (Sutent®) to the patients enrolled on the trial was closed early due to slow accrual. .. Next generation targeted exomic sequencing was performed for genomic profling.200-500ug of genomic DNA from each sample was sheared by sonication using the Covaris E220 instrument (Covaris). .. Library preparation utilized the KAPA kit following the “with beads” manufacturer protocol using KAPA HiFi polymerase (6 cycles).

    Article Title: The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion
    Article Snippet: Paragraph title: Paired-end illumina sequencing ... Briefly, DNA was fragmented to 400 to 550 bp using Adaptive Focused Acoustics technology with the E210 instrument (Covaris, Woburn, MA, USA) (duty cycle 20; intensity 5; cycles/bursts 200; seconds 30; temperature 4°C).

    Article Title: Point Mutations in Centromeric Histone Induce Post-zygotic Incompatibility and Uniparental Inheritance
    Article Snippet: Paragraph title: Whole genome sequencing ... DNA was sheared to 300–400 bp fragments using Covaris E220 sonicator under following settings: Peak incident power 175, duty factor 5%, cycle per burst 200, treatment time 60s at 7°C.

    Article Title: Genomics and Transcriptomics Analyses of the Oil-Accumulating Basidiomycete Yeast Trichosporon oleaginosus: Insights into Substrate Utilization and Alternative Evolutionary Trajectories of Fungal Mating Systems
    Article Snippet: Paragraph title: Genome sequencing and assembly. ... One hundred nanograms of genomic DNA was sheared to 270 bp by using the Covaris E210 apparatus and size selected by using SPRI beads (Beckman Coulter).

    Article Title: Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers
    Article Snippet: 2 μg of the amplified cDNA was sheared to 150–200 bp size distribution by Adaptive Focused Acoustics using a Covaris E220 instrument (Covaris, Woburn, MA) under the following conditions: 50 μl total volume, 20% duty cycle, 175 intensity, 200 cycles per burst, 165 sec in frequency sweeping mode. .. The final NGS libraries were quantified using Agilent Bioanalyzer DNA Chip 1000 then pooled; 11 libraries per pool.

    Article Title: A Deep Insight into the Sialome of Male and Female Aedes aegypti Mosquitoes
    Article Snippet: The salivary gland mRNA library construction and sequencing were done by the NIH Intramural Sequencing Center. .. The resulting cDNA was fragmented using a Covaris E210 system (Covaris, Woburn, MA).

    Article Title: EasyCloneMulti: A Set of Vectors for Simultaneous and Multiple Genomic Integrations in Saccharomyces cerevisiae
    Article Snippet: Paragraph title: Genomic DNA extraction and library sequencing ... Briefly, 100 ng of genomic DNA diluted in 52.5 μL TE buffer was fragmented in Covaris Crimp Cap microtubes on a Covaris E220 ultrasonicator (Woburn, MA) with 5% duty factor, 175 W peak incident power, 200 cycles/burst, and 50-s duration under frequency sweeping mode at 5.5 to 6°C (Illumina recommendations for a 350-bp average fragment size).

    Article Title: A somatic reference standard for cancer genome sequencing
    Article Snippet: Paragraph title: Library preparation and sequencing ... Following sonication on the Covaris E210, 100 ng of each sample was electrophoretically separated on a 1% TAE gel to verify fragmentation.

    Immunoprecipitation:

    Article Title: Vitamin C induces Tet-dependent DNA demethylation in ESCs to promote a blastocyst-like state
    Article Snippet: For each sample, 12 µg of genomic DNA was isolated, split into 3 replicates of 4 µg each and sonicated to ~100–500 bp on a Covaris E210 platform (75 s, 10% duty cycle). .. For each sample, 12 µg of genomic DNA was isolated, split into 3 replicates of 4 µg each and sonicated to ~100–500 bp on a Covaris E210 platform (75 s, 10% duty cycle).

    Polyacrylamide Gel Electrophoresis:

    Article Title: Vitamin C induces Tet-dependent DNA demethylation in ESCs to promote a blastocyst-like state
    Article Snippet: For each sample, 12 µg of genomic DNA was isolated, split into 3 replicates of 4 µg each and sonicated to ~100–500 bp on a Covaris E210 platform (75 s, 10% duty cycle). .. For each sample, 12 µg of genomic DNA was isolated, split into 3 replicates of 4 µg each and sonicated to ~100–500 bp on a Covaris E210 platform (75 s, 10% duty cycle).

    IA:

    Article Title: The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion
    Article Snippet: Briefly, DNA was fragmented to 400 to 550 bp using Adaptive Focused Acoustics technology with the E210 instrument (Covaris, Woburn, MA, USA) (duty cycle 20; intensity 5; cycles/bursts 200; seconds 30; temperature 4°C). .. This was repeated after subsequent end repair and DA-tailing reactions with the respective modules supplied by New England Biolabs (Ipswich, MA, USA) (NEBNext™ DNA Sample Prep Reagent Set 1: E6000), following the manufacturer’s instructions.

    Sample Prep:

    Article Title: A deep insight into the sialotranscriptome of the mosquito, Psorophora albipes
    Article Snippet: The SG library was constructed using the TruSeq RNA sample prep kit, v2 (Illumina Inc., San Diego, CA). .. The resulting cDNA was fragmented using a Covaris E210™ focused ultrasonicator (Covaris, Woburn, MA).

    Article Title: Whole Genome Analyses of a Well-Differentiated Liposarcoma Reveals Novel SYT1 and DDR2 Rearrangements
    Article Snippet: Paired-end libraries were prepared using NEBNext DNA sample preparation kit following the manufacturer's protocol (New England Biolab). .. Briefly, DNA was fragmented using the Covaris E210 sonicator to generate double-stranded DNA fragments with a fragment size of 400–500 bp.

    Article Title: Hybrid selection for sequencing pathogen genomes from clinical samples
    Article Snippet: For input, 3 μg of P. falciparum 3D7 DNA was sheared for 4 minutes on a Covaris E210 instrument set to duty cycle 5, intensity 5 and 200 cycles per burst. .. For input, 3 μg of P. falciparum 3D7 DNA was sheared for 4 minutes on a Covaris E210 instrument set to duty cycle 5, intensity 5 and 200 cycles per burst.

    Article Title: Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh)
    Article Snippet: Sequencing libraries were constructed according to the TruSeq DNA sample preparation protocol (Illumina) with minor modifications, in particular employing double size selection steps. .. Two micrograms of genomic DNA were fragmented with a Covaris E210 and size selected to 300–600 bps.

    Article Title: Novel Compound Heterozygous Mutations in MYO7A Associated with Usher Syndrome 1 in a Chinese Family
    Article Snippet: High-molecular-weight gDNA (∼3 µg) was fragmented ultrasonically using an E210 DNA-shearing instrument (Covaris; Woburn, MA, USA) to an average size of 300 base pairs (bps). .. High-molecular-weight gDNA (∼3 µg) was fragmented ultrasonically using an E210 DNA-shearing instrument (Covaris; Woburn, MA, USA) to an average size of 300 base pairs (bps).

    Article Title: The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion
    Article Snippet: Briefly, DNA was fragmented to 400 to 550 bp using Adaptive Focused Acoustics technology with the E210 instrument (Covaris, Woburn, MA, USA) (duty cycle 20; intensity 5; cycles/bursts 200; seconds 30; temperature 4°C). .. After the DNA was fragmented it was cleaned and concentrated with a 1:1 ratio of Ampure XP magnetic beads.

    Article Title: A Deep Insight into the Sialome of Male and Female Aedes aegypti Mosquitoes
    Article Snippet: The SG library was constructed using the TruSeq RNA sample prep kit, v2 (Illumina Inc., San Diego, CA) following the manufacturer recommendations. .. The resulting cDNA was fragmented using a Covaris E210 system (Covaris, Woburn, MA).

    Article Title: A somatic reference standard for cancer genome sequencing
    Article Snippet: 1.1 μg of DNA from each line was used to generate whole genome libraries using the Illumina TruSeq DNA PCR-free LT Sample Prep Kit (Set A; cat#FC-121-3001) following the manufacturer’s protocol. .. Following sonication on the Covaris E210, 100 ng of each sample was electrophoretically separated on a 1% TAE gel to verify fragmentation.

    Chloramphenicol Acetyltransferase Assay:

    Article Title: A somatic reference standard for cancer genome sequencing
    Article Snippet: 1.1 μg of DNA from each line was used to generate whole genome libraries using the Illumina TruSeq DNA PCR-free LT Sample Prep Kit (Set A; catFC-121-3001) following the manufacturer’s protocol. .. Following sonication on the Covaris E210, 100 ng of each sample was electrophoretically separated on a 1% TAE gel to verify fragmentation.

    Chromatin Immunoprecipitation:

    Article Title: Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers
    Article Snippet: 2 μg of the amplified cDNA was sheared to 150–200 bp size distribution by Adaptive Focused Acoustics using a Covaris E220 instrument (Covaris, Woburn, MA) under the following conditions: 50 μl total volume, 20% duty cycle, 175 intensity, 200 cycles per burst, 165 sec in frequency sweeping mode. .. Briefly, the sheared cDNA was end-repaired to generate blunt ends then ligated to Illumina compatible adaptors with indexing tags, followed by 1× AMPure XP beads purification.

    Software:

    Article Title: Legume Cytosolic and Plastid Acetyl-Coenzyme—A Carboxylase Genes Differ by Evolutionary Patterns and Selection Pressure Schemes Acting before and after Whole-Genome Duplications
    Article Snippet: BAC-end sequences (BESs) were analyzed and manually edited with Chromas Lite software (Technylesium, South Brisbane, Australia). .. Nucleic acid fragmentation was performed in E210× (Covaris, Woburn, MA, USA).

    Article Title: Molecular Epidemiology of Community-Associated Methicillin-resistant Staphylococcus aureus in the genomic era: a Cross-Sectional Study
    Article Snippet: Libraries were constructed for each isolate using the Covaris E220 and the SPRIworks Fragment Library System (Beckman Coulter), and accurate quality control was performed using the Agilent Bioanalyzer and qPCR, ensuring library quality before sequencing and ideal cluster density during sequencing. .. A S. aureus reference strain was identified by querying available WGS in GenBank and utilizing the species tree to select the most appropriate sequence for assembly.

    Multiplex Assay:

    Article Title: Whole Genome Sequence-Based Analysis of a Model Complex Trait, High Density Lipoprotein Cholesterol
    Article Snippet: For this project, Illumina PE libraries were barcoded with standard Illumina multiplex adaptors and pooled for sequencing in sets of three samples to generate an average of 6-fold sequence coverage per sample. .. Libraries were constructed using 1ug of genomic DNA in 100ul volume and sheared into fragments of approximately 300 base pairs in a Covaris plate with E210 system (Covaris, Inc. Woburn, MA).

    Selection:

    Article Title: Development and Validation of a 20K Single Nucleotide Polymorphism (SNP) Whole Genome Genotyping Array for Apple (Malus × domestica Borkh)
    Article Snippet: Sequencing libraries were constructed according to the TruSeq DNA sample preparation protocol (Illumina) with minor modifications, in particular employing double size selection steps. .. Two micrograms of genomic DNA were fragmented with a Covaris E210 and size selected to 300–600 bps.

    Agarose Gel Electrophoresis:

    Article Title: Hybrid selection for sequencing pathogen genomes from clinical samples
    Article Snippet: For input, 3 μg of P. falciparum 3D7 DNA was sheared for 4 minutes on a Covaris E210 instrument set to duty cycle 5, intensity 5 and 200 cycles per burst. .. The ligation products were cleaned up (Qiagen), amplified by 8 to 12 cycles of PCR on an ABI GeneAmp 9700 thermocycler in Phusion High-Fidelity PCR master mix with HF buffer (NEB Ipswich, Massachusetts, United States) using PCR forward primer 5'-CGCTCAGCGGCCGCAGCATCACCGCCATCAGT-3' and reverse primer 5'-CGCTCAGCGGCCGCGTCGTAGTGCGCCATCAGT-3' (ABI Carlsbad, California, United States).

    In Vitro:

    Article Title: Hybrid selection for sequencing pathogen genomes from clinical samples
    Article Snippet: To generate synthetic single-stranded biotinylated RNA bait, in vitro transcription was performed with biotin-labeled UTP using the MEGAshortscript T7 kit (Ambion Austin, Texas, United States) as described previously [ ]. .. For input, 3 μg of P. falciparum 3D7 DNA was sheared for 4 minutes on a Covaris E210 instrument set to duty cycle 5, intensity 5 and 200 cycles per burst.

    Next-Generation Sequencing:

    Article Title: Molecular Epidemiology of Community-Associated Methicillin-resistant Staphylococcus aureus in the genomic era: a Cross-Sectional Study
    Article Snippet: Paragraph title: Next-generation sequencing and data analysis ... Libraries were constructed for each isolate using the Covaris E220 and the SPRIworks Fragment Library System (Beckman Coulter), and accurate quality control was performed using the Agilent Bioanalyzer and qPCR, ensuring library quality before sequencing and ideal cluster density during sequencing.

    Article Title: A deep insight into the sialotranscriptome of the mosquito, Psorophora albipes
    Article Snippet: Paragraph title: Next-Generation Sequencing (NGS) and bioinformatic analysis ... The resulting cDNA was fragmented using a Covaris E210™ focused ultrasonicator (Covaris, Woburn, MA).

    Article Title: Next generation sequencing analysis of platinum refractory advanced germ cell tumor sensitive to Sunitinib (Sutent®) a VEGFR2/PDGFRβ/c-kit/ FLT3/RET/CSF1R inhibitor in a phase II trial
    Article Snippet: Paragraph title: Next generation sequencing (T200 platform) ... Next generation targeted exomic sequencing was performed for genomic profling.200-500ug of genomic DNA from each sample was sheared by sonication using the Covaris E220 instrument (Covaris).

    Article Title: Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers
    Article Snippet: 2 μg of the amplified cDNA was sheared to 150–200 bp size distribution by Adaptive Focused Acoustics using a Covaris E220 instrument (Covaris, Woburn, MA) under the following conditions: 50 μl total volume, 20% duty cycle, 175 intensity, 200 cycles per burst, 165 sec in frequency sweeping mode. .. Briefly, the sheared cDNA was end-repaired to generate blunt ends then ligated to Illumina compatible adaptors with indexing tags, followed by 1× AMPure XP beads purification.

    Article Title: A Deep Insight into the Sialome of Male and Female Aedes aegypti Mosquitoes
    Article Snippet: Paragraph title: cDNA library constructions and next generation sequencing ... The resulting cDNA was fragmented using a Covaris E210 system (Covaris, Woburn, MA).

    DNA Extraction:

    Article Title: Novel Compound Heterozygous Mutations in MYO7A Associated with Usher Syndrome 1 in a Chinese Family
    Article Snippet: Genomic DNA (gDNA) was extracted from peripheral blood using a blood DNA extraction kit, according to the manufacturer’s protocol (Tiangen, Beijing, China). .. High-molecular-weight gDNA (∼3 µg) was fragmented ultrasonically using an E210 DNA-shearing instrument (Covaris; Woburn, MA, USA) to an average size of 300 base pairs (bps).

    Article Title: Point Mutations in Centromeric Histone Induce Post-zygotic Incompatibility and Uniparental Inheritance
    Article Snippet: DNA extraction was performed using Nucleon PhytoPure DNA extraction kit (GE Healthcare Life Sciences Inc.). .. DNA was sheared to 300–400 bp fragments using Covaris E220 sonicator under following settings: Peak incident power 175, duty factor 5%, cycle per burst 200, treatment time 60s at 7°C.

    Article Title: EasyCloneMulti: A Set of Vectors for Simultaneous and Multiple Genomic Integrations in Saccharomyces cerevisiae
    Article Snippet: Paragraph title: Genomic DNA extraction and library sequencing ... Briefly, 100 ng of genomic DNA diluted in 52.5 μL TE buffer was fragmented in Covaris Crimp Cap microtubes on a Covaris E220 ultrasonicator (Woburn, MA) with 5% duty factor, 175 W peak incident power, 200 cycles/burst, and 50-s duration under frequency sweeping mode at 5.5 to 6°C (Illumina recommendations for a 350-bp average fragment size).

    Concentration Assay:

    Article Title: Whole Genome Sequence-Based Analysis of a Model Complex Trait, High Density Lipoprotein Cholesterol
    Article Snippet: DNA concentration was determined by pico green assays while DNA integrity was determined through Agilent Bioanalyzer traces and agarose gels. .. Libraries were constructed using 1ug of genomic DNA in 100ul volume and sheared into fragments of approximately 300 base pairs in a Covaris plate with E210 system (Covaris, Inc. Woburn, MA).

    DNA Purification:

    Article Title: Novel Compound Heterozygous Mutations in MYO7A Associated with Usher Syndrome 1 in a Chinese Family
    Article Snippet: High-molecular-weight gDNA (∼3 µg) was fragmented ultrasonically using an E210 DNA-shearing instrument (Covaris; Woburn, MA, USA) to an average size of 300 base pairs (bps). .. End repair of DNA fragments, the addition of a 3′ adenine (A), adaptor ligation, and reaction cleanup were performed following the manufacturer’s protocol.

    Gel Extraction:

    Article Title: Whole Genome Analyses of a Well-Differentiated Liposarcoma Reveals Novel SYT1 and DDR2 Rearrangements
    Article Snippet: Briefly, DNA was fragmented using the Covaris E210 sonicator to generate double-stranded DNA fragments with a fragment size of 400–500 bp. .. Paired end DNA adaptors were ligated and the resulting constructs size selected for ∼500 bp fragments.

    Article Title: Hybrid selection for sequencing pathogen genomes from clinical samples
    Article Snippet: For input, 3 μg of P. falciparum 3D7 DNA was sheared for 4 minutes on a Covaris E210 instrument set to duty cycle 5, intensity 5 and 200 cycles per burst. .. The ligation products were cleaned up (Qiagen), amplified by 8 to 12 cycles of PCR on an ABI GeneAmp 9700 thermocycler in Phusion High-Fidelity PCR master mix with HF buffer (NEB Ipswich, Massachusetts, United States) using PCR forward primer 5'-CGCTCAGCGGCCGCAGCATCACCGCCATCAGT-3' and reverse primer 5'-CGCTCAGCGGCCGCGTCGTAGTGCGCCATCAGT-3' (ABI Carlsbad, California, United States).

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    Covaris e210 sonicator
    A low adapter concentration magnifies the base composition bias for AT libraries. Aliquots of E. coli DNA extracts were sheared using the Covaris <t>E210</t> sonicator, size selected, and built into AT libraries using a low (“low”, 0.012 µM) or a standard (“std”, 0.6 µM) adapter concentration. We report the base composition observed at the start (position +1) and the end (position N) of sequences for reads mapping with high quality a unique position of the E. coli NC_010473 genome. The base compositions of the first nucleotide located upstream (position –1) and downstream (position N+1) read alignments are also provided. The average base composition is reported with dashed lines and is calculated using base counts within the reference genome.
    E210 Sonicator, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    A low adapter concentration magnifies the base composition bias for AT libraries. Aliquots of E. coli DNA extracts were sheared using the Covaris E210 sonicator, size selected, and built into AT libraries using a low (“low”, 0.012 µM) or a standard (“std”, 0.6 µM) adapter concentration. We report the base composition observed at the start (position +1) and the end (position N) of sequences for reads mapping with high quality a unique position of the E. coli NC_010473 genome. The base compositions of the first nucleotide located upstream (position –1) and downstream (position N+1) read alignments are also provided. The average base composition is reported with dashed lines and is calculated using base counts within the reference genome.

    Journal: PLoS ONE

    Article Title: Ligation Bias in Illumina Next-Generation DNA Libraries: Implications for Sequencing Ancient Genomes

    doi: 10.1371/journal.pone.0078575

    Figure Lengend Snippet: A low adapter concentration magnifies the base composition bias for AT libraries. Aliquots of E. coli DNA extracts were sheared using the Covaris E210 sonicator, size selected, and built into AT libraries using a low (“low”, 0.012 µM) or a standard (“std”, 0.6 µM) adapter concentration. We report the base composition observed at the start (position +1) and the end (position N) of sequences for reads mapping with high quality a unique position of the E. coli NC_010473 genome. The base compositions of the first nucleotide located upstream (position –1) and downstream (position N+1) read alignments are also provided. The average base composition is reported with dashed lines and is calculated using base counts within the reference genome.

    Article Snippet: Fresh aliquots of E. h. onager DNA extracts were sheared using the Covaris E210 sonicator, size selected, and built into AT libraries (adapter concentration = 0.012 µM) or BE libraries (adapter concentration = 0.6 µM).

    Techniques: Concentration Assay

    Base composition bias: AT versus BE libraries. Fresh aliquots of E. coli DNA extracts were sheared using the Covaris E210 sonicator, size selected, and built into AT and BE libraries (adapter concentration = 0.6 µM). We report the base composition observed at the first 10 (positions 1 to 10) and last 10 (positions N-9 to N) nucleotide positions within sequence reads mapping with high quality a unique position of the E. coli NC_010473 genome. The genomic composition of the 10 nucleotides located upstream (positions –10 to –1) and downstream (positions N+1 to N+10) DNA inserts are also provided.

    Journal: PLoS ONE

    Article Title: Ligation Bias in Illumina Next-Generation DNA Libraries: Implications for Sequencing Ancient Genomes

    doi: 10.1371/journal.pone.0078575

    Figure Lengend Snippet: Base composition bias: AT versus BE libraries. Fresh aliquots of E. coli DNA extracts were sheared using the Covaris E210 sonicator, size selected, and built into AT and BE libraries (adapter concentration = 0.6 µM). We report the base composition observed at the first 10 (positions 1 to 10) and last 10 (positions N-9 to N) nucleotide positions within sequence reads mapping with high quality a unique position of the E. coli NC_010473 genome. The genomic composition of the 10 nucleotides located upstream (positions –10 to –1) and downstream (positions N+1 to N+10) DNA inserts are also provided.

    Article Snippet: Fresh aliquots of E. h. onager DNA extracts were sheared using the Covaris E210 sonicator, size selected, and built into AT libraries (adapter concentration = 0.012 µM) or BE libraries (adapter concentration = 0.6 µM).

    Techniques: Concentration Assay, Sequencing