e210  (Covaris)


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    Structured Review

    Covaris e210
    E210, supplied by Covaris, used in various techniques. Bioz Stars score: 88/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/e210/product/Covaris
    Average 88 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    e210 - by Bioz Stars, 2020-05
    88/100 stars

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    Purification:

    Article Title: SC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expression
    Article Snippet: .. The purified cDNAs were diluted to 130 μl by DDW and fragmented by shearing with Covaris S2 or E210 (duty cycle: 20%; intensity: 5; cycles per burst: 200; duration: 50 s; an intensifier was installed in the case of E210) [Covaris, Woburn, MA, USA] and then end-polished in the End-polish buffer [1 × NEBnext End Repair Reaction buffer [NEB (B6052S), Ipswich, MA, USA], 0.01 U/μl of T4 DNA polymerase [NEB (M0203)] and 0.033 U/μl of T4 polynucleotide kinase [NEB (M0201)]] for 30 min at 20ºC. .. After incubation, a 0.8 × volume of the AMPureXP was immediately added, the solution was mixed for more than 20 min and then the supernatant was transferred to a 1.2 × volume of the AMPureXP reagent and the cDNAs were purified.

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    Covaris covaris e210
    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 <t>Covaris™</t> <t>E210</t> 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).
    Covaris E210, supplied by Covaris, used in various techniques. Bioz Stars score: 93/100, based on 22 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/covaris e210/product/Covaris
    Average 93 stars, based on 22 article reviews
    Price from $9.99 to $1999.99
    covaris e210 - by Bioz Stars, 2020-05
    93/100 stars
      Buy from Supplier

    89
    Covaris 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 <t>Covaris</t> <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.
    Covaris E210 Sonicator, supplied by Covaris, used in various techniques. Bioz Stars score: 89/100, based on 32 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/covaris e210 sonicator/product/Covaris
    Average 89 stars, based on 32 article reviews
    Price from $9.99 to $1999.99
    covaris e210 sonicator - by Bioz Stars, 2020-05
    89/100 stars
      Buy from Supplier

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    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).

    Journal: Genome Biology

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

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

    Figure Lengend 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).

    Article Snippet: Adaptive focused acoustic shearing of DNA We use the Covaris E210 from Covaris Inc. (Woburn, MA, USA) and 96-well Optical Reaction Plates (ABI Cat. #4306737) for our plate-based shearing protocols.

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

    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

    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+/−

    Journal: Nature protocols

    Article Title: Genome wide copy number analysis of single cells

    doi: 10.1038/nprot.2012.039

    Figure Lengend 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+/−

    Article Snippet: Sonicator Covaris E210 (Covaris, cat. no: 500008) .

    Techniques: Sonication, Whole Genome Amplification