s2 adaptive acoustic instrument  (Covaris)


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    Structured Review

    Covaris s2 adaptive acoustic instrument
    S2 Adaptive Acoustic Instrument, supplied by Covaris, used in various techniques. Bioz Stars score: 77/100, based on 28 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/s2 adaptive acoustic instrument/product/Covaris
    Average 77 stars, based on 28 article reviews
    Price from $9.99 to $1999.99
    s2 adaptive acoustic instrument - by Bioz Stars, 2020-02
    77/100 stars

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    Related Articles

    Centrifugation:

    Article Title: Lupus Risk Variant Increases pSTAT1 Binding and Decreases ETS1 Expression
    Article Snippet: Nuclei were harvested after centrifugation at 5,000 rpm for 10 min, resuspended in lysis buffer L2 (10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 200 mM NaCl, and 0.5 mM EGTA), and incubated at room temperature for 10 min. .. A S220 focused ultrasonicator (COVARIS) was used to shear genomic DNA (150- to 500-bp fragments) with 10% duty cycle, 175 peak power, and 200 bursts per cycle for 7 min. Sheared chromatin was precleared with 10 μl Dynabeads Protein G (Life Technologies) at 4°C for 1 hr.

    Article Title: CDK9-dependent RNA polymerase II pausing controls transcription initiation
    Article Snippet: Cells were harvested by centrifugation at 3000 x g for 2 min. Total RNA was extracted using QIAzol according to the manufacturer’s instructions. .. RNAs were sonicated to generate fragments of < 1.5 kbp using AFAmicro tubes in a S220 Focused-ultrasonicator (Covaris Inc., Woburn, MA USA).

    Article Title: C/EBPβ Is a Transcriptional Regulator of Wee1 at the G2/M Phase of the Cell Cycle
    Article Snippet: Fixation proceeded at RT for 10 min and was stopped by the addition of glycine to a final concentration of 0.125 M. The cells were collected by centrifugation and rinsed in cold phosphate-buffered saline (PBS). .. The samples were sonicated to an average length of 300–500 bp with a S220 Focused-ultrasonicator (Covaris, Woburn, MA, USA).

    Amplification:

    Article Title: Autosomal recessive limb-girdle muscular dystrophies in the Czech Republic
    Article Snippet: We replaced nebulization by shearing using the S220 Focused Ultrasonicator (Covaris) (3 μg DNA, peak incident power 140 W, duty factor 10%, 200 cycles per burst, and treatment time 80 s) and replaced hybridization for three days by hybridization according to the NimbleGen technical note “Double Capture High Efficiency Sequence Capture of Small Targets for use in SeqCap EZ Library, Applications on 454 Sequencing Systems”. .. Emulsion PCR and sequencing on the GS Junior System (Roche) were performed according to the “emPCR Amplification Method Manual - Lib-L” and the “Sequencing Method Manual”.

    Article Title: Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses
    Article Snippet: .. The thermocycler protocol was: 42°C for 60 min then 94°C for 2 min then 5 cycles of 94°C for 30 sec, 44°C for 30 sec, 68°C for 3 min, then 28 cycles of 94°C for 30 sec, 57°C for 30 sec, 68°C for 3 min. Amplification of all 8 segments was confirmed by gel electrophoresis, and 750ng of each cDNA mixture were sheared to an average size of 300 to 400bp using a Covaris S220 focused ultrasonicator. .. Sequencing libraries were prepared using the NEBNext Ultra DNA library prep kit (NEB E7370L), Agencourt AMPure XP beads (Beckman Coulter A63881), and NEBNext multiplex oligonucleotides for Illumina (NEB E7600S).

    Article Title: Mutation of a serine near the catalytic site of the choline acetyltransferase a gene almost completely abolishes motility of the zebrafish embryo
    Article Snippet: The amount equivalent to 1 μg DNA was processed with the S220 Focused-ultrasonicator (Covaris Ltd, Brighton UK) in a glass vial (microTUBE AFA Fiber Pre-Slit Snap-Cap 6x16mm, Covaris Ltd) to generate 350 bp DNA fragments which were used for indexed DNA library preparation using the TruSeq Nano DNA LT Library Preparation Kit following the protocol from Illumina. .. Purified adapter-ligated DNA fragments were amplified by PCR (polymerase chain reaction; 12–14 cycles) to enrich genomic DNA fragments.

    Article Title: Oncogenic BRAF disrupts thyroid morphogenesis and function via twist expression
    Article Snippet: .. Amplified ds cDNA was purified using QIAquick PCR purification kit (Qiagen, Hilden, Germany) and 200 ng of amplified cDNA was fragmented in a final volume of 50 µl using S220 Focused-ultrasonicator (Covaris, Woburn, MA), to obtain 150 bp DNA fragment size (peak incident power: 175W, duty factor: 10%, cycles per burst: 200, time: 280s). .. Fragmented DNA samples were used to prepare the library using TruSeq RNA sample preparation kit v2 (Illumina, San Diego, CA).

    Scaffolding:

    Article Title: Large-scale diversification without genetic isolation in nematode symbionts of figs
    Article Snippet: The DNA was sheared using a S220 focused ultrasonicator (Covaris) under the following operation conditions: 10 dc, 4 i, 200 cpb, and 80 s. Genomic paired-end libraries were prepared using Low Input Library Preparation Kit (Clontech Laboratories). .. Paired-end libraries were sequenced using a HiSeq 2000 system (Illumina). mRNA libraries that were used for scaffolding (see below) were prepared from TRIzol-lysed individuals.

    Quantitative RT-PCR:

    Article Title: C/EBPβ Is a Transcriptional Regulator of Wee1 at the G2/M Phase of the Cell Cycle
    Article Snippet: The samples were sonicated to an average length of 300–500 bp with a S220 Focused-ultrasonicator (Covaris, Woburn, MA, USA). .. C/EBPβ binding to specific sites on the Wee1 promoter was analyzed by quantitative real-time PCR (qRT-PCR).

    SYBR Green Assay:

    Article Title: Oncogenic BRAF disrupts thyroid morphogenesis and function via twist expression
    Article Snippet: Amplified ds cDNA was purified using QIAquick PCR purification kit (Qiagen, Hilden, Germany) and 200 ng of amplified cDNA was fragmented in a final volume of 50 µl using S220 Focused-ultrasonicator (Covaris, Woburn, MA), to obtain 150 bp DNA fragment size (peak incident power: 175W, duty factor: 10%, cycles per burst: 200, time: 280s). .. For qPCR validation cDNA was diluted 1:7 and 2 µl were used in a 10 µl reaction using the PerfeCTa SYBR Green FastMix (Quanta Biosciences, Gaithersburg, MD).

    Incubation:

    Article Title: Lupus Risk Variant Increases pSTAT1 Binding and Decreases ETS1 Expression
    Article Snippet: Nuclei were harvested after centrifugation at 5,000 rpm for 10 min, resuspended in lysis buffer L2 (10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 200 mM NaCl, and 0.5 mM EGTA), and incubated at room temperature for 10 min. .. A S220 focused ultrasonicator (COVARIS) was used to shear genomic DNA (150- to 500-bp fragments) with 10% duty cycle, 175 peak power, and 200 bursts per cycle for 7 min. Sheared chromatin was precleared with 10 μl Dynabeads Protein G (Life Technologies) at 4°C for 1 hr.

    Article Title: C/EBPβ Is a Transcriptional Regulator of Wee1 at the G2/M Phase of the Cell Cycle
    Article Snippet: The cell pellets were resuspended in hypotonic buffer containing 0.5 mM PMSF, protease inhibitor cocktail, and incubated on ice for 15 min. .. The samples were sonicated to an average length of 300–500 bp with a S220 Focused-ultrasonicator (Covaris, Woburn, MA, USA).

    Modification:

    Article Title: Aging-dependent demethylation of regulatory elements correlates with chromatin state and improved β-cell function
    Article Snippet: WGSBS was performed as previously published (Lister et al. 2009) with some modifications; Genomic DNA isolated from pure β cell populations obtained from 10 young and 10 old mice, was fragmented into ≈300bp pieces using the S220 Focused-ultrasonicator (Covaris). .. Libraries were bisulfite converted using Imprint DNA Modification Kit (Sigma).

    Real-time Polymerase Chain Reaction:

    Article Title: A Novel G-Quadruplex Binding Protein in Yeast—Slx9
    Article Snippet: Paragraph title: 4.5. ChIP-Seq -and ChIP Plus qPCR Analysis ... For ChIP-Seq, chromatin was sheared to an average length of 200 bp using a S220 focused ultrasonicator (Covaris, Brighton, UK).

    Article Title: Lupus Risk Variant Increases pSTAT1 Binding and Decreases ETS1 Expression
    Article Snippet: Paragraph title: Chromatin Immunoprecipitation qPCR ... A S220 focused ultrasonicator (COVARIS) was used to shear genomic DNA (150- to 500-bp fragments) with 10% duty cycle, 175 peak power, and 200 bursts per cycle for 7 min. Sheared chromatin was precleared with 10 μl Dynabeads Protein G (Life Technologies) at 4°C for 1 hr.

    Article Title: Oncogenic BRAF disrupts thyroid morphogenesis and function via twist expression
    Article Snippet: Amplified ds cDNA was purified using QIAquick PCR purification kit (Qiagen, Hilden, Germany) and 200 ng of amplified cDNA was fragmented in a final volume of 50 µl using S220 Focused-ultrasonicator (Covaris, Woburn, MA), to obtain 150 bp DNA fragment size (peak incident power: 175W, duty factor: 10%, cycles per burst: 200, time: 280s). .. For qPCR validation cDNA was diluted 1:7 and 2 µl were used in a 10 µl reaction using the PerfeCTa SYBR Green FastMix (Quanta Biosciences, Gaithersburg, MD).

    Article Title: C/EBPβ Is a Transcriptional Regulator of Wee1 at the G2/M Phase of the Cell Cycle
    Article Snippet: The samples were sonicated to an average length of 300–500 bp with a S220 Focused-ultrasonicator (Covaris, Woburn, MA, USA). .. C/EBPβ binding to specific sites on the Wee1 promoter was analyzed by quantitative real-time PCR (qRT-PCR).

    Hybridization:

    Article Title: Autosomal recessive limb-girdle muscular dystrophies in the Czech Republic
    Article Snippet: .. We replaced nebulization by shearing using the S220 Focused Ultrasonicator (Covaris) (3 μg DNA, peak incident power 140 W, duty factor 10%, 200 cycles per burst, and treatment time 80 s) and replaced hybridization for three days by hybridization according to the NimbleGen technical note “Double Capture High Efficiency Sequence Capture of Small Targets for use in SeqCap EZ Library, Applications on 454 Sequencing Systems”. .. Emulsion PCR and sequencing on the GS Junior System (Roche) were performed according to the “emPCR Amplification Method Manual - Lib-L” and the “Sequencing Method Manual”.

    Ligation:

    Article Title: Mutation of a serine near the catalytic site of the choline acetyltransferase a gene almost completely abolishes motility of the zebrafish embryo
    Article Snippet: The amount equivalent to 1 μg DNA was processed with the S220 Focused-ultrasonicator (Covaris Ltd, Brighton UK) in a glass vial (microTUBE AFA Fiber Pre-Slit Snap-Cap 6x16mm, Covaris Ltd) to generate 350 bp DNA fragments which were used for indexed DNA library preparation using the TruSeq Nano DNA LT Library Preparation Kit following the protocol from Illumina. .. Briefly, after the sonication the overhangs of DNA fragments were converted to blunt ends and a single adenine nucleotide was added to the 3’ ends for optimal adapter ligation.

    Protease Inhibitor:

    Article Title: C/EBPβ Is a Transcriptional Regulator of Wee1 at the G2/M Phase of the Cell Cycle
    Article Snippet: The nuclei were collected by micro-centrifugation and then resuspended in SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl (pH 8.1), 0.5 mM PMSF, and protease inhibitor cocktail). .. The samples were sonicated to an average length of 300–500 bp with a S220 Focused-ultrasonicator (Covaris, Woburn, MA, USA).

    Genomic Sequencing:

    Article Title: Aging-dependent demethylation of regulatory elements correlates with chromatin state and improved β-cell function
    Article Snippet: WGSBS was performed as previously published (Lister et al. 2009) with some modifications; Genomic DNA isolated from pure β cell populations obtained from 10 young and 10 old mice, was fragmented into ≈300bp pieces using the S220 Focused-ultrasonicator (Covaris). .. Sequencing libraries were generated with ≥500ng genomic DNA using the NEBNext genomic sequencing kit (NEB) and Illumina adaptors (PE-102-1001.

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus
    Article Snippet: RNA was harvested from either cell-free supernatants or tissues as above and was reverse-transcribed using the SuperScript III First Strand Synthesis System for RT-PCR (Invitrogen 18080) and a mixture of random hexamers and oligo dT primer. .. Seven hundred and fifty nanograms of each cDNA mixture were sheared to an average size of 300 to 400 bp using a Covaris S220 focused ultrasonicator.

    Article Title: Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses
    Article Snippet: Illumina library preparation and sequencing We amplified cDNA corresponding to all 8 genomic segments from 3μl of the viral RNA using the SuperScript III One-Step RT-PCR Platinum Taq HiFi Kit (Invitrogen 12574). .. The thermocycler protocol was: 42°C for 60 min then 94°C for 2 min then 5 cycles of 94°C for 30 sec, 44°C for 30 sec, 68°C for 3 min, then 28 cycles of 94°C for 30 sec, 57°C for 30 sec, 68°C for 3 min. Amplification of all 8 segments was confirmed by gel electrophoresis, and 750ng of each cDNA mixture were sheared to an average size of 300 to 400bp using a Covaris S220 focused ultrasonicator.

    Article Title: Measurements of Intrahost Viral Diversity Are Extremely Sensitive to Systematic Errors in Variant Calling
    Article Snippet: Seven hundred and fifty nanograms of each mixture was sheared to an average size of 300 to 400 bp using a Covaris S220 focused ultrasonicator with the following settings: intensity, 4; duty cycle, 10%; bursts per second, 200; duration, 80 s. Sequencing libraries were prepared from these fragmented products using the NEBNext Ultra DNA library prep kit (NEB), Agencourt AMPure XP beads (Beckman Coulter), and NEBNext multiplex oligonucleotides for Illumina (NEB). .. The plasmids were mixed to equal molarity, and cDNA was generated using a multiplex one-step RT-PCR with the primers Uni12/Inf1 (5′-GGGGGGAGCAAAAGCAGG-3′), Uni12/Inf3 (5′-GGGGGAGCGAAAGCAGG-3′), and Uni13/Inf1 (5′-5CGGGTTATTAGTAGAAACAAGG-3′) as described previously ( , ).

    Generated:

    Article Title: Our love-hate relationship with DNA barcodes, the Y2K problem, and the search for next generation barcodes
    Article Snippet: The DNA sample was sheared by sonication with an S220 Focused-Ultrasonicator (Covaris, Woburn, Massachusetts, USA). .. The sequences for each of the species included in this study represents about 10% of the data generated from a run of the MiSeq instrument.

    Article Title: Mutation of a serine near the catalytic site of the choline acetyltransferase a gene almost completely abolishes motility of the zebrafish embryo
    Article Snippet: Library preparation Whole genome DNA sequencing was performed with a HiSeq 1500 machine (Illumina) and a compatible indexed library was generated as follows. .. The amount equivalent to 1 μg DNA was processed with the S220 Focused-ultrasonicator (Covaris Ltd, Brighton UK) in a glass vial (microTUBE AFA Fiber Pre-Slit Snap-Cap 6x16mm, Covaris Ltd) to generate 350 bp DNA fragments which were used for indexed DNA library preparation using the TruSeq Nano DNA LT Library Preparation Kit following the protocol from Illumina.

    Article Title: Measurements of Intrahost Viral Diversity Are Extremely Sensitive to Systematic Errors in Variant Calling
    Article Snippet: Seven hundred and fifty nanograms of each mixture was sheared to an average size of 300 to 400 bp using a Covaris S220 focused ultrasonicator with the following settings: intensity, 4; duty cycle, 10%; bursts per second, 200; duration, 80 s. Sequencing libraries were prepared from these fragmented products using the NEBNext Ultra DNA library prep kit (NEB), Agencourt AMPure XP beads (Beckman Coulter), and NEBNext multiplex oligonucleotides for Illumina (NEB). .. The plasmids were mixed to equal molarity, and cDNA was generated using a multiplex one-step RT-PCR with the primers Uni12/Inf1 (5′-GGGGGGAGCAAAAGCAGG-3′), Uni12/Inf3 (5′-GGGGGAGCGAAAGCAGG-3′), and Uni13/Inf1 (5′-5CGGGTTATTAGTAGAAACAAGG-3′) as described previously ( , ).

    Article Title: Aging-dependent demethylation of regulatory elements correlates with chromatin state and improved β-cell function
    Article Snippet: WGSBS was performed as previously published (Lister et al. 2009) with some modifications; Genomic DNA isolated from pure β cell populations obtained from 10 young and 10 old mice, was fragmented into ≈300bp pieces using the S220 Focused-ultrasonicator (Covaris). .. Sequencing libraries were generated with ≥500ng genomic DNA using the NEBNext genomic sequencing kit (NEB) and Illumina adaptors (PE-102-1001.

    other:

    Article Title: Genome-wide identification of transcript start and end sites by Transcript Isoform Sequencing, TIF-Seq
    Article Snippet: Themocycler DNA engine tetrad 2 (Bio-Rad) Thermomixer Confort (Eppendorf) 2100 Bioanalyzer (Agilent, cat. no. G2939AA) Qubit 2.0 fluorometer (Life technologies) S220 Focused-ultrasonicator (Covaris) CRITICAL: It should be switched on in advance to ensure it has reached 4°C before its use.

    DNA Sequencing:

    Article Title: Mutation of a serine near the catalytic site of the choline acetyltransferase a gene almost completely abolishes motility of the zebrafish embryo
    Article Snippet: Library preparation Whole genome DNA sequencing was performed with a HiSeq 1500 machine (Illumina) and a compatible indexed library was generated as follows. .. The amount equivalent to 1 μg DNA was processed with the S220 Focused-ultrasonicator (Covaris Ltd, Brighton UK) in a glass vial (microTUBE AFA Fiber Pre-Slit Snap-Cap 6x16mm, Covaris Ltd) to generate 350 bp DNA fragments which were used for indexed DNA library preparation using the TruSeq Nano DNA LT Library Preparation Kit following the protocol from Illumina.

    Polymerase Chain Reaction:

    Article Title: Autosomal recessive limb-girdle muscular dystrophies in the Czech Republic
    Article Snippet: We replaced nebulization by shearing using the S220 Focused Ultrasonicator (Covaris) (3 μg DNA, peak incident power 140 W, duty factor 10%, 200 cycles per burst, and treatment time 80 s) and replaced hybridization for three days by hybridization according to the NimbleGen technical note “Double Capture High Efficiency Sequence Capture of Small Targets for use in SeqCap EZ Library, Applications on 454 Sequencing Systems”. .. Emulsion PCR and sequencing on the GS Junior System (Roche) were performed according to the “emPCR Amplification Method Manual - Lib-L” and the “Sequencing Method Manual”.

    Article Title: Mutation of a serine near the catalytic site of the choline acetyltransferase a gene almost completely abolishes motility of the zebrafish embryo
    Article Snippet: The amount equivalent to 1 μg DNA was processed with the S220 Focused-ultrasonicator (Covaris Ltd, Brighton UK) in a glass vial (microTUBE AFA Fiber Pre-Slit Snap-Cap 6x16mm, Covaris Ltd) to generate 350 bp DNA fragments which were used for indexed DNA library preparation using the TruSeq Nano DNA LT Library Preparation Kit following the protocol from Illumina. .. Purified adapter-ligated DNA fragments were amplified by PCR (polymerase chain reaction; 12–14 cycles) to enrich genomic DNA fragments.

    Article Title: Id2 and Id3 maintain the regulatory T cell pool to suppress inflammatory disease
    Article Snippet: The double-stranded cDNA was sonicated using S220 Focused-ultrasonicator (Covaris). .. The size-selected cDNA was treated with uracil-N-glycosylase and then multiplex-amplified by PCR. cDNA libraries were sequenced with a HiSeq 2000 sequencer (Illumina).

    Article Title: Oncogenic BRAF disrupts thyroid morphogenesis and function via twist expression
    Article Snippet: .. Amplified ds cDNA was purified using QIAquick PCR purification kit (Qiagen, Hilden, Germany) and 200 ng of amplified cDNA was fragmented in a final volume of 50 µl using S220 Focused-ultrasonicator (Covaris, Woburn, MA), to obtain 150 bp DNA fragment size (peak incident power: 175W, duty factor: 10%, cycles per burst: 200, time: 280s). .. Fragmented DNA samples were used to prepare the library using TruSeq RNA sample preparation kit v2 (Illumina, San Diego, CA).

    Article Title: Measurements of Intrahost Viral Diversity Are Extremely Sensitive to Systematic Errors in Variant Calling
    Article Snippet: Molar equivalents of each PCR product were pooled to generate reconstituted cDNA genomes of both WSN33 and PR8. .. Seven hundred and fifty nanograms of each mixture was sheared to an average size of 300 to 400 bp using a Covaris S220 focused ultrasonicator with the following settings: intensity, 4; duty cycle, 10%; bursts per second, 200; duration, 80 s. Sequencing libraries were prepared from these fragmented products using the NEBNext Ultra DNA library prep kit (NEB), Agencourt AMPure XP beads (Beckman Coulter), and NEBNext multiplex oligonucleotides for Illumina (NEB).

    Sonication:

    Article Title: Lupus Risk Variant Increases pSTAT1 Binding and Decreases ETS1 Expression
    Article Snippet: Nuclei were resuspended in sonication buffer (10 mM Tris [pH 8.0], 1 mM EDTA, and 0.1% SDS) after centrifuging. .. A S220 focused ultrasonicator (COVARIS) was used to shear genomic DNA (150- to 500-bp fragments) with 10% duty cycle, 175 peak power, and 200 bursts per cycle for 7 min. Sheared chromatin was precleared with 10 μl Dynabeads Protein G (Life Technologies) at 4°C for 1 hr.

    Article Title: Our love-hate relationship with DNA barcodes, the Y2K problem, and the search for next generation barcodes
    Article Snippet: .. The DNA sample was sheared by sonication with an S220 Focused-Ultrasonicator (Covaris, Woburn, Massachusetts, USA). .. Fragment sizes were evaluated using a High Sensitivity DNA chip for the Bioanalyzer 2100 electrophoresis system (Agilent, Santa Clara, California, USA) using the standard manufacturer protocol.

    Article Title: CDK9-dependent RNA polymerase II pausing controls transcription initiation
    Article Snippet: .. RNAs were sonicated to generate fragments of < 1.5 kbp using AFAmicro tubes in a S220 Focused-ultrasonicator (Covaris Inc., Woburn, MA USA). .. 4sU-labeled RNA was purified from 150 µg total fragmented RNA.

    Article Title: Mutation of a serine near the catalytic site of the choline acetyltransferase a gene almost completely abolishes motility of the zebrafish embryo
    Article Snippet: The amount equivalent to 1 μg DNA was processed with the S220 Focused-ultrasonicator (Covaris Ltd, Brighton UK) in a glass vial (microTUBE AFA Fiber Pre-Slit Snap-Cap 6x16mm, Covaris Ltd) to generate 350 bp DNA fragments which were used for indexed DNA library preparation using the TruSeq Nano DNA LT Library Preparation Kit following the protocol from Illumina. .. Briefly, after the sonication the overhangs of DNA fragments were converted to blunt ends and a single adenine nucleotide was added to the 3’ ends for optimal adapter ligation.

    Article Title: Id2 and Id3 maintain the regulatory T cell pool to suppress inflammatory disease
    Article Snippet: .. The double-stranded cDNA was sonicated using S220 Focused-ultrasonicator (Covaris). .. Sonicated cDNA was next ligated to adaptors and size-selected.

    Article Title: C/EBPβ Is a Transcriptional Regulator of Wee1 at the G2/M Phase of the Cell Cycle
    Article Snippet: .. The samples were sonicated to an average length of 300–500 bp with a S220 Focused-ultrasonicator (Covaris, Woburn, MA, USA). .. Chromatin immunoprecipitation was performed with anti-C/EBPβ (sc-150X, Santacruz Biotechnology, Santa Cruz, CA, USA) or HDAC2 (sc-9959X, Santacruz Biotechnology, Santa Cruz, CA, USA) and protein G agarose.

    Binding Assay:

    Article Title: C/EBPβ Is a Transcriptional Regulator of Wee1 at the G2/M Phase of the Cell Cycle
    Article Snippet: The samples were sonicated to an average length of 300–500 bp with a S220 Focused-ultrasonicator (Covaris, Woburn, MA, USA). .. C/EBPβ binding to specific sites on the Wee1 promoter was analyzed by quantitative real-time PCR (qRT-PCR).

    ChIP-sequencing:

    Article Title: A Novel G-Quadruplex Binding Protein in Yeast—Slx9
    Article Snippet: .. For ChIP-Seq, chromatin was sheared to an average length of 200 bp using a S220 focused ultrasonicator (Covaris, Brighton, UK). .. For conventional ChIP, the DNA was sheared to an average length of 250 bp using a Branson sonifier W250-D (50% amplitude, 50% duty cycle, 5 × 5 pulses).

    DNA Extraction:

    Article Title: Large-scale diversification without genetic isolation in nematode symbionts of figs
    Article Snippet: Living nematode individuals were kept in a sterile buffer for 10 to 15 min to minimize possible surface contamination, after which the nematodes were individually transferred into a lysis solution and thereafter frozen until DNA extraction. .. The DNA was sheared using a S220 focused ultrasonicator (Covaris) under the following operation conditions: 10 dc, 4 i, 200 cpb, and 80 s. Genomic paired-end libraries were prepared using Low Input Library Preparation Kit (Clontech Laboratories).

    Nucleic Acid Electrophoresis:

    Article Title: Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses
    Article Snippet: .. The thermocycler protocol was: 42°C for 60 min then 94°C for 2 min then 5 cycles of 94°C for 30 sec, 44°C for 30 sec, 68°C for 3 min, then 28 cycles of 94°C for 30 sec, 57°C for 30 sec, 68°C for 3 min. Amplification of all 8 segments was confirmed by gel electrophoresis, and 750ng of each cDNA mixture were sheared to an average size of 300 to 400bp using a Covaris S220 focused ultrasonicator. .. Sequencing libraries were prepared using the NEBNext Ultra DNA library prep kit (NEB E7370L), Agencourt AMPure XP beads (Beckman Coulter A63881), and NEBNext multiplex oligonucleotides for Illumina (NEB E7600S).

    RNA Sequencing Assay:

    Article Title: Id2 and Id3 maintain the regulatory T cell pool to suppress inflammatory disease
    Article Snippet: Paragraph title: RNA sequencing ... The double-stranded cDNA was sonicated using S220 Focused-ultrasonicator (Covaris).

    Article Title: Oncogenic BRAF disrupts thyroid morphogenesis and function via twist expression
    Article Snippet: Paragraph title: Amplification-library preparation and RNA-seq ... Amplified ds cDNA was purified using QIAquick PCR purification kit (Qiagen, Hilden, Germany) and 200 ng of amplified cDNA was fragmented in a final volume of 50 µl using S220 Focused-ultrasonicator (Covaris, Woburn, MA), to obtain 150 bp DNA fragment size (peak incident power: 175W, duty factor: 10%, cycles per burst: 200, time: 280s).

    Isolation:

    Article Title: A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus
    Article Snippet: Seven hundred and fifty nanograms of each cDNA mixture were sheared to an average size of 300 to 400 bp using a Covaris S220 focused ultrasonicator. .. Residual primer dimers were removed by gel isolation of a 300 to 500 bp band, which was purified using a GeneJet Gel Extraction Kit (ThermoFisher Scientific).

    Article Title: Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses
    Article Snippet: The thermocycler protocol was: 42°C for 60 min then 94°C for 2 min then 5 cycles of 94°C for 30 sec, 44°C for 30 sec, 68°C for 3 min, then 28 cycles of 94°C for 30 sec, 57°C for 30 sec, 68°C for 3 min. Amplification of all 8 segments was confirmed by gel electrophoresis, and 750ng of each cDNA mixture were sheared to an average size of 300 to 400bp using a Covaris S220 focused ultrasonicator. .. Residual primer dimers were removed by gel isolation of a 300-500bp band, which was purified using a GeneJet Gel Extraction Kit (ThermoFisher Scientific).

    Article Title: Id2 and Id3 maintain the regulatory T cell pool to suppress inflammatory disease
    Article Snippet: Total RNA was isolated using the RNeasy-Mini Kit (Qiagen) and was processed for deep sequencing as described previously with slight modifications. .. The double-stranded cDNA was sonicated using S220 Focused-ultrasonicator (Covaris).

    Article Title: Large-scale diversification without genetic isolation in nematode symbionts of figs
    Article Snippet: The DNA of individual nematodes was isolated using the MasterPure DNA Purification Kit (Epicentre), following the manufacturer’s protocol for DNA purification from tissue samples. .. The DNA was sheared using a S220 focused ultrasonicator (Covaris) under the following operation conditions: 10 dc, 4 i, 200 cpb, and 80 s. Genomic paired-end libraries were prepared using Low Input Library Preparation Kit (Clontech Laboratories).

    Article Title: Aging-dependent demethylation of regulatory elements correlates with chromatin state and improved β-cell function
    Article Snippet: .. WGSBS was performed as previously published (Lister et al. 2009) with some modifications; Genomic DNA isolated from pure β cell populations obtained from 10 young and 10 old mice, was fragmented into ≈300bp pieces using the S220 Focused-ultrasonicator (Covaris). .. Sequencing libraries were generated with ≥500ng genomic DNA using the NEBNext genomic sequencing kit (NEB) and Illumina adaptors (PE-102-1001.

    Size-exclusion Chromatography:

    Article Title: Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses
    Article Snippet: .. The thermocycler protocol was: 42°C for 60 min then 94°C for 2 min then 5 cycles of 94°C for 30 sec, 44°C for 30 sec, 68°C for 3 min, then 28 cycles of 94°C for 30 sec, 57°C for 30 sec, 68°C for 3 min. Amplification of all 8 segments was confirmed by gel electrophoresis, and 750ng of each cDNA mixture were sheared to an average size of 300 to 400bp using a Covaris S220 focused ultrasonicator. .. Sequencing libraries were prepared using the NEBNext Ultra DNA library prep kit (NEB E7370L), Agencourt AMPure XP beads (Beckman Coulter A63881), and NEBNext multiplex oligonucleotides for Illumina (NEB E7600S).

    Labeling:

    Article Title: CDK9-dependent RNA polymerase II pausing controls transcription initiation
    Article Snippet: After 10 min of treatment, labeling was performed by adding 500 µM of 4-thiouracil (4sU) (Sigma-Aldrich, St. Louis, MO, USA) for 5 min at 37°C and 5% CO2 . .. RNAs were sonicated to generate fragments of < 1.5 kbp using AFAmicro tubes in a S220 Focused-ultrasonicator (Covaris Inc., Woburn, MA USA).

    Purification:

    Article Title: A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus
    Article Snippet: Seven hundred and fifty nanograms of each cDNA mixture were sheared to an average size of 300 to 400 bp using a Covaris S220 focused ultrasonicator. .. Residual primer dimers were removed by gel isolation of a 300 to 500 bp band, which was purified using a GeneJet Gel Extraction Kit (ThermoFisher Scientific).

    Article Title: Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses
    Article Snippet: The thermocycler protocol was: 42°C for 60 min then 94°C for 2 min then 5 cycles of 94°C for 30 sec, 44°C for 30 sec, 68°C for 3 min, then 28 cycles of 94°C for 30 sec, 57°C for 30 sec, 68°C for 3 min. Amplification of all 8 segments was confirmed by gel electrophoresis, and 750ng of each cDNA mixture were sheared to an average size of 300 to 400bp using a Covaris S220 focused ultrasonicator. .. Residual primer dimers were removed by gel isolation of a 300-500bp band, which was purified using a GeneJet Gel Extraction Kit (ThermoFisher Scientific).

    Article Title: CDK9-dependent RNA polymerase II pausing controls transcription initiation
    Article Snippet: RNAs were sonicated to generate fragments of < 1.5 kbp using AFAmicro tubes in a S220 Focused-ultrasonicator (Covaris Inc., Woburn, MA USA). .. 4sU-labeled RNA was purified from 150 µg total fragmented RNA.

    Article Title: Mutation of a serine near the catalytic site of the choline acetyltransferase a gene almost completely abolishes motility of the zebrafish embryo
    Article Snippet: The amount equivalent to 1 μg DNA was processed with the S220 Focused-ultrasonicator (Covaris Ltd, Brighton UK) in a glass vial (microTUBE AFA Fiber Pre-Slit Snap-Cap 6x16mm, Covaris Ltd) to generate 350 bp DNA fragments which were used for indexed DNA library preparation using the TruSeq Nano DNA LT Library Preparation Kit following the protocol from Illumina. .. Purified adapter-ligated DNA fragments were amplified by PCR (polymerase chain reaction; 12–14 cycles) to enrich genomic DNA fragments.

    Article Title: Id2 and Id3 maintain the regulatory T cell pool to suppress inflammatory disease
    Article Snippet: Briefly, mRNA was purified from total RNA using Dynabeads mRNA purification kit (Invitrogen). .. The double-stranded cDNA was sonicated using S220 Focused-ultrasonicator (Covaris).

    Article Title: Oncogenic BRAF disrupts thyroid morphogenesis and function via twist expression
    Article Snippet: .. Amplified ds cDNA was purified using QIAquick PCR purification kit (Qiagen, Hilden, Germany) and 200 ng of amplified cDNA was fragmented in a final volume of 50 µl using S220 Focused-ultrasonicator (Covaris, Woburn, MA), to obtain 150 bp DNA fragment size (peak incident power: 175W, duty factor: 10%, cycles per burst: 200, time: 280s). .. Fragmented DNA samples were used to prepare the library using TruSeq RNA sample preparation kit v2 (Illumina, San Diego, CA).

    Article Title: C/EBPβ Is a Transcriptional Regulator of Wee1 at the G2/M Phase of the Cell Cycle
    Article Snippet: The samples were sonicated to an average length of 300–500 bp with a S220 Focused-ultrasonicator (Covaris, Woburn, MA, USA). .. ChIP products were eluted and DNA was recovered from reverse crosslinking and purification.

    Article Title: Measurements of Intrahost Viral Diversity Are Extremely Sensitive to Systematic Errors in Variant Calling
    Article Snippet: For the experiment on the accuracy of DeepSNV (see ), WSN33 and PR8 viruses were plaque purified and passaged three times in MDCK cells. .. Seven hundred and fifty nanograms of each mixture was sheared to an average size of 300 to 400 bp using a Covaris S220 focused ultrasonicator with the following settings: intensity, 4; duty cycle, 10%; bursts per second, 200; duration, 80 s. Sequencing libraries were prepared from these fragmented products using the NEBNext Ultra DNA library prep kit (NEB), Agencourt AMPure XP beads (Beckman Coulter), and NEBNext multiplex oligonucleotides for Illumina (NEB).

    Sequencing:

    Article Title: Autosomal recessive limb-girdle muscular dystrophies in the Czech Republic
    Article Snippet: .. We replaced nebulization by shearing using the S220 Focused Ultrasonicator (Covaris) (3 μg DNA, peak incident power 140 W, duty factor 10%, 200 cycles per burst, and treatment time 80 s) and replaced hybridization for three days by hybridization according to the NimbleGen technical note “Double Capture High Efficiency Sequence Capture of Small Targets for use in SeqCap EZ Library, Applications on 454 Sequencing Systems”. .. Emulsion PCR and sequencing on the GS Junior System (Roche) were performed according to the “emPCR Amplification Method Manual - Lib-L” and the “Sequencing Method Manual”.

    Article Title: A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus
    Article Snippet: Seven hundred and fifty nanograms of each cDNA mixture were sheared to an average size of 300 to 400 bp using a Covaris S220 focused ultrasonicator. .. Sequencing libraries were prepared using the NEBNext Ultra DNA library prep kit (NEB E7370L), Agencourt AMPure XP beads (Beckman Coulter A63881), and NEBNext multiplex oligonucleotides for Illumina (NEB E7600S).

    Article Title: Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses
    Article Snippet: Paragraph title: Illumina library preparation and sequencing ... The thermocycler protocol was: 42°C for 60 min then 94°C for 2 min then 5 cycles of 94°C for 30 sec, 44°C for 30 sec, 68°C for 3 min, then 28 cycles of 94°C for 30 sec, 57°C for 30 sec, 68°C for 3 min. Amplification of all 8 segments was confirmed by gel electrophoresis, and 750ng of each cDNA mixture were sheared to an average size of 300 to 400bp using a Covaris S220 focused ultrasonicator.

    Article Title: Our love-hate relationship with DNA barcodes, the Y2K problem, and the search for next generation barcodes
    Article Snippet: Paragraph title: Sequence preparation, assembly, and annotation ... The DNA sample was sheared by sonication with an S220 Focused-Ultrasonicator (Covaris, Woburn, Massachusetts, USA).

    Article Title: Id2 and Id3 maintain the regulatory T cell pool to suppress inflammatory disease
    Article Snippet: Total RNA was isolated using the RNeasy-Mini Kit (Qiagen) and was processed for deep sequencing as described previously with slight modifications. .. The double-stranded cDNA was sonicated using S220 Focused-ultrasonicator (Covaris).

    Article Title: Large-scale diversification without genetic isolation in nematode symbionts of figs
    Article Snippet: Paragraph title: Genome sequencing of individuals of P. borbonicus ... The DNA was sheared using a S220 focused ultrasonicator (Covaris) under the following operation conditions: 10 dc, 4 i, 200 cpb, and 80 s. Genomic paired-end libraries were prepared using Low Input Library Preparation Kit (Clontech Laboratories).

    Article Title: Measurements of Intrahost Viral Diversity Are Extremely Sensitive to Systematic Errors in Variant Calling
    Article Snippet: .. Seven hundred and fifty nanograms of each mixture was sheared to an average size of 300 to 400 bp using a Covaris S220 focused ultrasonicator with the following settings: intensity, 4; duty cycle, 10%; bursts per second, 200; duration, 80 s. Sequencing libraries were prepared from these fragmented products using the NEBNext Ultra DNA library prep kit (NEB), Agencourt AMPure XP beads (Beckman Coulter), and NEBNext multiplex oligonucleotides for Illumina (NEB). .. The pooled libraries were sequenced on an Illumina MiSeq machine with 2 × 250 paired-end reads.

    Article Title: Aging-dependent demethylation of regulatory elements correlates with chromatin state and improved β-cell function
    Article Snippet: WGSBS was performed as previously published (Lister et al. 2009) with some modifications; Genomic DNA isolated from pure β cell populations obtained from 10 young and 10 old mice, was fragmented into ≈300bp pieces using the S220 Focused-ultrasonicator (Covaris). .. Sequencing libraries were generated with ≥500ng genomic DNA using the NEBNext genomic sequencing kit (NEB) and Illumina adaptors (PE-102-1001.

    Gel Extraction:

    Article Title: A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus
    Article Snippet: Seven hundred and fifty nanograms of each cDNA mixture were sheared to an average size of 300 to 400 bp using a Covaris S220 focused ultrasonicator. .. Residual primer dimers were removed by gel isolation of a 300 to 500 bp band, which was purified using a GeneJet Gel Extraction Kit (ThermoFisher Scientific).

    Article Title: Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses
    Article Snippet: The thermocycler protocol was: 42°C for 60 min then 94°C for 2 min then 5 cycles of 94°C for 30 sec, 44°C for 30 sec, 68°C for 3 min, then 28 cycles of 94°C for 30 sec, 57°C for 30 sec, 68°C for 3 min. Amplification of all 8 segments was confirmed by gel electrophoresis, and 750ng of each cDNA mixture were sheared to an average size of 300 to 400bp using a Covaris S220 focused ultrasonicator. .. Residual primer dimers were removed by gel isolation of a 300-500bp band, which was purified using a GeneJet Gel Extraction Kit (ThermoFisher Scientific).

    Agarose Gel Electrophoresis:

    Article Title: Large-scale diversification without genetic isolation in nematode symbionts of figs
    Article Snippet: The DNA was sheared using a S220 focused ultrasonicator (Covaris) under the following operation conditions: 10 dc, 4 i, 200 cpb, and 80 s. Genomic paired-end libraries were prepared using Low Input Library Preparation Kit (Clontech Laboratories). .. Size selection was performed on final libraries using BluePippin and 1.5% agarose gel cassettes (Sage Science).

    Mouse Assay:

    Article Title: Aging-dependent demethylation of regulatory elements correlates with chromatin state and improved β-cell function
    Article Snippet: .. WGSBS was performed as previously published (Lister et al. 2009) with some modifications; Genomic DNA isolated from pure β cell populations obtained from 10 young and 10 old mice, was fragmented into ≈300bp pieces using the S220 Focused-ultrasonicator (Covaris). .. Sequencing libraries were generated with ≥500ng genomic DNA using the NEBNext genomic sequencing kit (NEB) and Illumina adaptors (PE-102-1001.

    Chromatin Immunoprecipitation:

    Article Title: A Novel G-Quadruplex Binding Protein in Yeast—Slx9
    Article Snippet: Paragraph title: 4.5. ChIP-Seq -and ChIP Plus qPCR Analysis ... For ChIP-Seq, chromatin was sheared to an average length of 200 bp using a S220 focused ultrasonicator (Covaris, Brighton, UK).

    Article Title: Lupus Risk Variant Increases pSTAT1 Binding and Decreases ETS1 Expression
    Article Snippet: Paragraph title: Chromatin Immunoprecipitation qPCR ... A S220 focused ultrasonicator (COVARIS) was used to shear genomic DNA (150- to 500-bp fragments) with 10% duty cycle, 175 peak power, and 200 bursts per cycle for 7 min. Sheared chromatin was precleared with 10 μl Dynabeads Protein G (Life Technologies) at 4°C for 1 hr.

    Article Title: Our love-hate relationship with DNA barcodes, the Y2K problem, and the search for next generation barcodes
    Article Snippet: The DNA sample was sheared by sonication with an S220 Focused-Ultrasonicator (Covaris, Woburn, Massachusetts, USA). .. Fragment sizes were evaluated using a High Sensitivity DNA chip for the Bioanalyzer 2100 electrophoresis system (Agilent, Santa Clara, California, USA) using the standard manufacturer protocol.

    Article Title: Mutation of a serine near the catalytic site of the choline acetyltransferase a gene almost completely abolishes motility of the zebrafish embryo
    Article Snippet: The amount equivalent to 1 μg DNA was processed with the S220 Focused-ultrasonicator (Covaris Ltd, Brighton UK) in a glass vial (microTUBE AFA Fiber Pre-Slit Snap-Cap 6x16mm, Covaris Ltd) to generate 350 bp DNA fragments which were used for indexed DNA library preparation using the TruSeq Nano DNA LT Library Preparation Kit following the protocol from Illumina. .. Quantity and quality of DNA library was assessed with an Agilent 2100 Bioanalyzer using either a High Sensitivity DNA chip or DNA 1000 chip.

    Article Title: C/EBPβ Is a Transcriptional Regulator of Wee1 at the G2/M Phase of the Cell Cycle
    Article Snippet: Paragraph title: 2.9. Chromatin Immunoprecipitation ... The samples were sonicated to an average length of 300–500 bp with a S220 Focused-ultrasonicator (Covaris, Woburn, MA, USA).

    Plasmid Preparation:

    Article Title: Measurements of Intrahost Viral Diversity Are Extremely Sensitive to Systematic Errors in Variant Calling
    Article Snippet: Seven hundred and fifty nanograms of each mixture was sheared to an average size of 300 to 400 bp using a Covaris S220 focused ultrasonicator with the following settings: intensity, 4; duty cycle, 10%; bursts per second, 200; duration, 80 s. Sequencing libraries were prepared from these fragmented products using the NEBNext Ultra DNA library prep kit (NEB), Agencourt AMPure XP beads (Beckman Coulter), and NEBNext multiplex oligonucleotides for Illumina (NEB). .. A clonal plasmid control library was prepared from 8 plasmids containing PR8 genomic segments.

    Electrophoresis:

    Article Title: Our love-hate relationship with DNA barcodes, the Y2K problem, and the search for next generation barcodes
    Article Snippet: The DNA sample was sheared by sonication with an S220 Focused-Ultrasonicator (Covaris, Woburn, Massachusetts, USA). .. Fragment sizes were evaluated using a High Sensitivity DNA chip for the Bioanalyzer 2100 electrophoresis system (Agilent, Santa Clara, California, USA) using the standard manufacturer protocol.

    Multiplex Assay:

    Article Title: A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus
    Article Snippet: Seven hundred and fifty nanograms of each cDNA mixture were sheared to an average size of 300 to 400 bp using a Covaris S220 focused ultrasonicator. .. Sequencing libraries were prepared using the NEBNext Ultra DNA library prep kit (NEB E7370L), Agencourt AMPure XP beads (Beckman Coulter A63881), and NEBNext multiplex oligonucleotides for Illumina (NEB E7600S).

    Article Title: Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses
    Article Snippet: The thermocycler protocol was: 42°C for 60 min then 94°C for 2 min then 5 cycles of 94°C for 30 sec, 44°C for 30 sec, 68°C for 3 min, then 28 cycles of 94°C for 30 sec, 57°C for 30 sec, 68°C for 3 min. Amplification of all 8 segments was confirmed by gel electrophoresis, and 750ng of each cDNA mixture were sheared to an average size of 300 to 400bp using a Covaris S220 focused ultrasonicator. .. Sequencing libraries were prepared using the NEBNext Ultra DNA library prep kit (NEB E7370L), Agencourt AMPure XP beads (Beckman Coulter A63881), and NEBNext multiplex oligonucleotides for Illumina (NEB E7600S).

    Article Title: Id2 and Id3 maintain the regulatory T cell pool to suppress inflammatory disease
    Article Snippet: The double-stranded cDNA was sonicated using S220 Focused-ultrasonicator (Covaris). .. The size-selected cDNA was treated with uracil-N-glycosylase and then multiplex-amplified by PCR. cDNA libraries were sequenced with a HiSeq 2000 sequencer (Illumina).

    Article Title: Measurements of Intrahost Viral Diversity Are Extremely Sensitive to Systematic Errors in Variant Calling
    Article Snippet: .. Seven hundred and fifty nanograms of each mixture was sheared to an average size of 300 to 400 bp using a Covaris S220 focused ultrasonicator with the following settings: intensity, 4; duty cycle, 10%; bursts per second, 200; duration, 80 s. Sequencing libraries were prepared from these fragmented products using the NEBNext Ultra DNA library prep kit (NEB), Agencourt AMPure XP beads (Beckman Coulter), and NEBNext multiplex oligonucleotides for Illumina (NEB). .. The pooled libraries were sequenced on an Illumina MiSeq machine with 2 × 250 paired-end reads.

    Selection:

    Article Title: Large-scale diversification without genetic isolation in nematode symbionts of figs
    Article Snippet: The DNA was sheared using a S220 focused ultrasonicator (Covaris) under the following operation conditions: 10 dc, 4 i, 200 cpb, and 80 s. Genomic paired-end libraries were prepared using Low Input Library Preparation Kit (Clontech Laboratories). .. Size selection was performed on final libraries using BluePippin and 1.5% agarose gel cassettes (Sage Science).

    Sample Prep:

    Article Title: Oncogenic BRAF disrupts thyroid morphogenesis and function via twist expression
    Article Snippet: Amplified ds cDNA was purified using QIAquick PCR purification kit (Qiagen, Hilden, Germany) and 200 ng of amplified cDNA was fragmented in a final volume of 50 µl using S220 Focused-ultrasonicator (Covaris, Woburn, MA), to obtain 150 bp DNA fragment size (peak incident power: 175W, duty factor: 10%, cycles per burst: 200, time: 280s). .. Fragmented DNA samples were used to prepare the library using TruSeq RNA sample preparation kit v2 (Illumina, San Diego, CA).

    Transgenic Assay:

    Article Title: Oncogenic BRAF disrupts thyroid morphogenesis and function via twist expression
    Article Snippet: Amplification-library preparation and RNA-seq One ng of RNA from three biological replicates of sorted cells for each transgenic line tg-TOM and tg-BRAFV600E -TOM was used to prepare amplified ds cDNA using Ovation RNA-Seq System V2 (Nugen, San Carlos, CA). .. Amplified ds cDNA was purified using QIAquick PCR purification kit (Qiagen, Hilden, Germany) and 200 ng of amplified cDNA was fragmented in a final volume of 50 µl using S220 Focused-ultrasonicator (Covaris, Woburn, MA), to obtain 150 bp DNA fragment size (peak incident power: 175W, duty factor: 10%, cycles per burst: 200, time: 280s).

    Next-Generation Sequencing:

    Article Title: A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus
    Article Snippet: Paragraph title: Next-generation sequencing ... Seven hundred and fifty nanograms of each cDNA mixture were sheared to an average size of 300 to 400 bp using a Covaris S220 focused ultrasonicator.

    Article Title: Our love-hate relationship with DNA barcodes, the Y2K problem, and the search for next generation barcodes
    Article Snippet: Sequence preparation, assembly, and annotation DNA libraries were prepared and samples were sequenced at the Next Generation Sequencing (NGS) Platform facility at the Children's Hospital Research Institute of Manitoba (Winnipeg, Manitoba, Canada). .. The DNA sample was sheared by sonication with an S220 Focused-Ultrasonicator (Covaris, Woburn, Massachusetts, USA).

    Concentration Assay:

    Article Title: Lupus Risk Variant Increases pSTAT1 Binding and Decreases ETS1 Expression
    Article Snippet: Crosslinking of protein-chromatin complexes was achieved by incubation of Epstein-Barr-virus-transformed B cells in crosslinking solution (1% formaldehyde, 5 mM HEPES [pH 8.0], 10 mM sodium chloride [NaCl], 0.1 mM EDTA, and 0.05 mM EGTA) and shaking at room temperature for 10 min. Glycine was added to a final concentration of 0.125 M to quench the crosslinking. .. A S220 focused ultrasonicator (COVARIS) was used to shear genomic DNA (150- to 500-bp fragments) with 10% duty cycle, 175 peak power, and 200 bursts per cycle for 7 min. Sheared chromatin was precleared with 10 μl Dynabeads Protein G (Life Technologies) at 4°C for 1 hr.

    Article Title: A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus
    Article Snippet: Seven hundred and fifty nanograms of each cDNA mixture were sheared to an average size of 300 to 400 bp using a Covaris S220 focused ultrasonicator. .. The final concentration of each barcoded library was determined by Quanti PicoGreen dsDNA quantification (ThermoFisher Scientific), and equal nanomolar concentrations were pooled.

    Article Title: Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses
    Article Snippet: The thermocycler protocol was: 42°C for 60 min then 94°C for 2 min then 5 cycles of 94°C for 30 sec, 44°C for 30 sec, 68°C for 3 min, then 28 cycles of 94°C for 30 sec, 57°C for 30 sec, 68°C for 3 min. Amplification of all 8 segments was confirmed by gel electrophoresis, and 750ng of each cDNA mixture were sheared to an average size of 300 to 400bp using a Covaris S220 focused ultrasonicator. .. The final concentration of each barcoded library was determined by Quanti PicoGreen dsDNA quantification (ThermoFisher Scientific), and equal nanomolar concentrations were pooled.

    Article Title: Mutation of a serine near the catalytic site of the choline acetyltransferase a gene almost completely abolishes motility of the zebrafish embryo
    Article Snippet: The concentration of genomic DNA (ng/μl) was quantified by the fluorometric method using Qubit (Thermo Fisher Scientific Inc.). .. The amount equivalent to 1 μg DNA was processed with the S220 Focused-ultrasonicator (Covaris Ltd, Brighton UK) in a glass vial (microTUBE AFA Fiber Pre-Slit Snap-Cap 6x16mm, Covaris Ltd) to generate 350 bp DNA fragments which were used for indexed DNA library preparation using the TruSeq Nano DNA LT Library Preparation Kit following the protocol from Illumina.

    Article Title: C/EBPβ Is a Transcriptional Regulator of Wee1 at the G2/M Phase of the Cell Cycle
    Article Snippet: Fixation proceeded at RT for 10 min and was stopped by the addition of glycine to a final concentration of 0.125 M. The cells were collected by centrifugation and rinsed in cold phosphate-buffered saline (PBS). .. The samples were sonicated to an average length of 300–500 bp with a S220 Focused-ultrasonicator (Covaris, Woburn, MA, USA).

    DNA Purification:

    Article Title: Large-scale diversification without genetic isolation in nematode symbionts of figs
    Article Snippet: The DNA of individual nematodes was isolated using the MasterPure DNA Purification Kit (Epicentre), following the manufacturer’s protocol for DNA purification from tissue samples. .. The DNA was sheared using a S220 focused ultrasonicator (Covaris) under the following operation conditions: 10 dc, 4 i, 200 cpb, and 80 s. Genomic paired-end libraries were prepared using Low Input Library Preparation Kit (Clontech Laboratories).

    Lysis:

    Article Title: Lupus Risk Variant Increases pSTAT1 Binding and Decreases ETS1 Expression
    Article Snippet: Nuclei were harvested after centrifugation at 5,000 rpm for 10 min, resuspended in lysis buffer L2 (10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 200 mM NaCl, and 0.5 mM EGTA), and incubated at room temperature for 10 min. .. A S220 focused ultrasonicator (COVARIS) was used to shear genomic DNA (150- to 500-bp fragments) with 10% duty cycle, 175 peak power, and 200 bursts per cycle for 7 min. Sheared chromatin was precleared with 10 μl Dynabeads Protein G (Life Technologies) at 4°C for 1 hr.

    Article Title: Large-scale diversification without genetic isolation in nematode symbionts of figs
    Article Snippet: Living nematode individuals were kept in a sterile buffer for 10 to 15 min to minimize possible surface contamination, after which the nematodes were individually transferred into a lysis solution and thereafter frozen until DNA extraction. .. The DNA was sheared using a S220 focused ultrasonicator (Covaris) under the following operation conditions: 10 dc, 4 i, 200 cpb, and 80 s. Genomic paired-end libraries were prepared using Low Input Library Preparation Kit (Clontech Laboratories).

    Article Title: C/EBPβ Is a Transcriptional Regulator of Wee1 at the G2/M Phase of the Cell Cycle
    Article Snippet: The nuclei were collected by micro-centrifugation and then resuspended in SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl (pH 8.1), 0.5 mM PMSF, and protease inhibitor cocktail). .. The samples were sonicated to an average length of 300–500 bp with a S220 Focused-ultrasonicator (Covaris, Woburn, MA, USA).

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    Covaris s2 adaptive acoustic instrument
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