m220  (Covaris)


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    Name:
    M220 Focused ultrasonicator
    Description:
    designed for Next Gen Sequencing applications requiring fragment sizes between 150bp and 5kb Compact size and ease of use make the M220 Focused ultrasonicator the ideal DNA shearing solution for MiSeq and PGM users
    Catalog Number:
    500295PGD
    Product Aliases:
    M220, Ultrasonicator
    Price:
    None
    Size:
    33cm W 38 7cm D 27 3cm H
    Category:
    Instrument
    Quantity:
    1
    Buy from Supplier


    Structured Review

    Covaris m220
    M220 Focused ultrasonicator
    designed for Next Gen Sequencing applications requiring fragment sizes between 150bp and 5kb Compact size and ease of use make the M220 Focused ultrasonicator the ideal DNA shearing solution for MiSeq and PGM users
    https://www.bioz.com/result/m220/product/Covaris
    Average 99 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    m220 - by Bioz Stars, 2019-09
    99/100 stars

    Images

    1) Product Images from "Impact of Three Illumina Library Construction Methods on GC Bias and HLA Genotype Calling"

    Article Title: Impact of Three Illumina Library Construction Methods on GC Bias and HLA Genotype Calling

    Journal: Human immunology

    doi: 10.1016/j.humimm.2014.12.016

    Comparison of three Illumina library construction protocols. Covaris M220 was used to fragment DNA in TruSeq Nano.
    Figure Legend Snippet: Comparison of three Illumina library construction protocols. Covaris M220 was used to fragment DNA in TruSeq Nano.

    Techniques Used:

    Related Articles

    Methylation Sequencing:

    Article Title: Transient reduction of DNA methylation at the onset of meiosis in male mice
    Article Snippet: Paragraph title: Whole-genome bisulfite sequencing (WGBS) ... Isolated mouse gDNA was spiked with approximately 0.1% unmethylated cl857 Sam7 Lambda DNA (Promega) and sheared to fragments with a range of 200–600 bp using a Covaris M220 Ultrasonicator.

    Amplification:

    Article Title: Transient reduction of DNA methylation at the onset of meiosis in male mice
    Article Snippet: Isolated mouse gDNA was spiked with approximately 0.1% unmethylated cl857 Sam7 Lambda DNA (Promega) and sheared to fragments with a range of 200–600 bp using a Covaris M220 Ultrasonicator. .. The adaptor-ligated DNA fragments were processed for bisulfite conversion according to the manufacturer’s protocol (EZ DNA methylation Gold kit, Zymo Research).

    Article Title: The utilization of next-generation sequencing to detect somatic mutations and predict clinical prognosis of Chinese non-small cell lung cancer patients
    Article Snippet: DNA shearing was performed using Covaris M220. .. End repair and A-tailing was followed by adaptor ligation.

    Article Title: Characterizing Phage Genomes for Therapeutic Applications
    Article Snippet: Briefly, 250 ng of genomic DNA was fragmented using the Covaris M220 (Covaris, Inc, Woburn, MA, USA). .. Briefly, 250 ng of genomic DNA was fragmented using the Covaris M220 (Covaris, Inc, Woburn, MA, USA).

    Article Title: Targeted next generation sequencing identified clinically actionable mutations in patients with esophageal sarcomatoid carcinoma
    Article Snippet: 500 ng~ 1 μg of extracted DNA for each sample was sheared into 350 bp fragments using Covaris M220 instrument (Covaris, Woburn, MA), followed by library preparation using KAPA Hyper DNA Library Prep Kit (KAPA Biosystems, Wilmington, MA). .. 500 ng~ 1 μg of extracted DNA for each sample was sheared into 350 bp fragments using Covaris M220 instrument (Covaris, Woburn, MA), followed by library preparation using KAPA Hyper DNA Library Prep Kit (KAPA Biosystems, Wilmington, MA).

    Article Title: No Evidence of Clonal Dominance after Transplant of HOXB4-Expanded Cord Blood Cells in a Nonhuman Primate Model
    Article Snippet: Paragraph title: Acoustic mediated-Modified Genomic Sequencing (MGS)-PCR for amplification of retroviral integrations sites ... Between 300ng to 3μg of gDNA samples were acoustically sheared to a mean fragment size of 1500bp using the M220 focused-ultrasonicator (Covaris Inc., Woburn, MA, USA).

    Lambda DNA Preparation:

    Article Title: Transient reduction of DNA methylation at the onset of meiosis in male mice
    Article Snippet: DNA was precipitated using ethanol and quantified with Quant-iT PicoGreen reagent (Molecular Probes) using SpectraMax microplate spectrophotometer. .. Isolated mouse gDNA was spiked with approximately 0.1% unmethylated cl857 Sam7 Lambda DNA (Promega) and sheared to fragments with a range of 200–600 bp using a Covaris M220 Ultrasonicator. .. WGBS library preparation was based on Illumina’s ‘WGBS for Methylation Analysis’ protocol.

    Construct:

    Article Title: Characterizing Phage Genomes for Therapeutic Applications
    Article Snippet: Sequencing libraries were constructed using the Accel-NGS® 2S Plus library kit (Swift Biosciences, Ann Arbor, MI, USA) with a slight modification. .. Briefly, 250 ng of genomic DNA was fragmented using the Covaris M220 (Covaris, Inc, Woburn, MA, USA).

    Article Title: Consolidated bioprocessing of butanol production from xylan by a thermophilic and butanologenic Thermoanaerobacterium sp. M5
    Article Snippet: The genomic DNA was extracted using G+ bacteria genomic DNA kit (ZOMANBIO, China). .. The large fragment of genomic DNA was firstly broken into small sequences with an average 300 bp by Covaris M220 (Covaris, USA), and the DNA libraries were constructed via NEBNext® UltraTM DNA Library Prep Kit for Illumina (NEB, USA). .. Then the draft genome was sequenced using Illumina HiSeq2500 system sequencing technology.

    Electrophoresis:

    Article Title: Shifts in rDNA levels act as a genome buffer promoting chromosome homeostasis
    Article Snippet: After 100 generations in the presence and absence of 5% ethanol, a 100 ng of the purified dsDNA from strain 4 was sheared to the average fragment sizes of 350 bp with Covaris M220 ultrasonicator. .. Briefly, the protocol involved DNA ends repair, magnetic beads-based size selection, 3′ end adenylation, ligation of indexed adapters and library enrichment by PCR.

    IA:

    Article Title: Targeted next generation sequencing identified clinically actionable mutations in patients with esophageal sarcomatoid carcinoma
    Article Snippet: 500 ng~ 1 μg of extracted DNA for each sample was sheared into 350 bp fragments using Covaris M220 instrument (Covaris, Woburn, MA), followed by library preparation using KAPA Hyper DNA Library Prep Kit (KAPA Biosystems, Wilmington, MA). .. A customized NGS panel targeting exons of 416 cancer-relevant genes and introns of 16 fusions genes was used for hybridization enrichment (Additional file : Table S1).

    Incubation:

    Article Title: Transient reduction of DNA methylation at the onset of meiosis in male mice
    Article Snippet: One microliter of RNase A (Thermo Scientific, #EN0531, 10 mg/ml) was added to the aqueous phase, and the samples were incubated at 37 °C for 30 min, transferred to a PLG tube and mixed with chloroform. .. Isolated mouse gDNA was spiked with approximately 0.1% unmethylated cl857 Sam7 Lambda DNA (Promega) and sheared to fragments with a range of 200–600 bp using a Covaris M220 Ultrasonicator.

    Article Title: Wnt/β-catenin signaling stimulates the expression and synaptic clustering of the autism-associated Neuroligin 3 gene
    Article Snippet: Briefly, 2.0 × 107 cells were incubated with cell-conditioned medium containing Wnt3a (Wnt3a-CM; Wnt3a-CM 50% plus 50% of fresh HT22 incubation media), LiCl or CHIR 98014 (Sigma-Aldrich), as Wnt/β-catenin pharmacological agonists., Cells were cross-linked with 1% formaldehyde (Sigma-Aldrich) for 10 min at room temperature and then the reaction was stopped with 0.125 M glycine. .. Samples were sonicated with the M220 Focused-ultrasonicator (Covaris, Woburn, MA, USA) using milliTube caps (Covaris), following the high cell chromatin shearing protocol suggested by the manufacturer.

    Article Title: Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages
    Article Snippet: Exponentially growing cultures were infected with S-EIV1 and incubated as above for 14–17 days until lysis occurred. .. The DNA was sheared into ∼300 bp fragments using a Covaris M220 ultrasonicator (Covaris, Woburn, MA, USA) and purified using Agencourt AMPure XP beads (Beckham Coulter).

    Article Title: Random shearing as an alternative to digestion for mitochondrial DNA processing in droplet digital PCR
    Article Snippet: 250 ng DNA in 10 μL 10 mM Tris-EDTA (TE) buffer was added to 10 μL 0.2× Bam HI Buffer containing 10 U Bam HI enzyme and incubated at 37 °C for 1 h. Sonication - Sonication was performed by adding 375 ng DNA in 30 μL TE buffer to a microtube. .. A range of sonication target lengths of 200 bp, 500 bp, 800 bp, 2 kb, and 5 kb were tested using a Covaris M220 Focused Ultrasonicator.

    Formalin-fixed Paraffin-Embedded:

    Article Title: Targeted next generation sequencing identified clinically actionable mutations in patients with esophageal sarcomatoid carcinoma
    Article Snippet: FFPE sections containing both carcinoma and sarcoma components of the tumor were collected for genomic DNA extraction using QIAamp FFPE DNA kit (Qiagen, Hilden, Germany) according to manufacturer’s protocol. .. 500 ng~ 1 μg of extracted DNA for each sample was sheared into 350 bp fragments using Covaris M220 instrument (Covaris, Woburn, MA), followed by library preparation using KAPA Hyper DNA Library Prep Kit (KAPA Biosystems, Wilmington, MA).

    Cell Culture:

    Article Title: Large-scale detection of in vivo transcription errors
    Article Snippet: C. elegans strains (wild-type N2, RB886, and VC1305) were cultured on Nematode growth media following standard protocols ( ) with E. coli OP50 except that plates were made using agarose. .. DNA libraries were generated from 1 μg of genomic DNA sheared to ∼300 base pair fragments on an M-series focused ultrasonicator (Covaris) following the standard TruSeq library protocol (Illumina).

    Mass Spectrometry:

    Article Title: Artificial selection increased body weight but induced increase of runs of homozygosity in Hanwoo cattle
    Article Snippet: In the second step, 4,500 cows were inseminated with the semen from the selected bulls and 30 bulls were selected based on selection index which used weighted breeding values for BF, MS, and EMA of 800 male calves [ , , ]. .. Briefly, 200 ng of gDNA was fragmented by Covaris M220 (Woburn, MA, USA) resulting in a median fragment size of ~500 bp followed by end repair, A-tailing, and indexed adapter ligation (~125bp adapter).

    Modification:

    Article Title: Characterizing Phage Genomes for Therapeutic Applications
    Article Snippet: Sequencing libraries were constructed using the Accel-NGS® 2S Plus library kit (Swift Biosciences, Ann Arbor, MI, USA) with a slight modification. .. Briefly, 250 ng of genomic DNA was fragmented using the Covaris M220 (Covaris, Inc, Woburn, MA, USA).

    Article Title: No Evidence of Clonal Dominance after Transplant of HOXB4-Expanded Cord Blood Cells in a Nonhuman Primate Model
    Article Snippet: Between 300ng to 3μg of gDNA samples were acoustically sheared to a mean fragment size of 1500bp using the M220 focused-ultrasonicator (Covaris Inc., Woburn, MA, USA). .. The sheared fragments were then isolated, polished to blunt-ended dsDNA, and ligated to modified linkers for PCR amplification.

    Hybridization:

    Article Title: Targeted next generation sequencing identified clinically actionable mutations in patients with esophageal sarcomatoid carcinoma
    Article Snippet: 500 ng~ 1 μg of extracted DNA for each sample was sheared into 350 bp fragments using Covaris M220 instrument (Covaris, Woburn, MA), followed by library preparation using KAPA Hyper DNA Library Prep Kit (KAPA Biosystems, Wilmington, MA). .. 500 ng~ 1 μg of extracted DNA for each sample was sheared into 350 bp fragments using Covaris M220 instrument (Covaris, Woburn, MA), followed by library preparation using KAPA Hyper DNA Library Prep Kit (KAPA Biosystems, Wilmington, MA).

    Flow Cytometry:

    Article Title: Shifts in rDNA levels act as a genome buffer promoting chromosome homeostasis
    Article Snippet: After 100 generations in the presence and absence of 5% ethanol, a 100 ng of the purified dsDNA from strain 4 was sheared to the average fragment sizes of 350 bp with Covaris M220 ultrasonicator. .. Purified libraries were quantified with the use of Qubit Fluorometer (Life Technologies) and quality was then controlled by the Agilent's 2200 TapeStation electrophoresis.

    Ligation:

    Article Title: Artificial selection increased body weight but induced increase of runs of homozygosity in Hanwoo cattle
    Article Snippet: Using DNA from the blood samples, we produced indexed shotgun paired-end (PE) libraries with approximately 500bp inserts using TruSeq Nano DNA Library Prep Kit (Illumina, USA) following standard Illumina sample-preparation protocol. .. Briefly, 200 ng of gDNA was fragmented by Covaris M220 (Woburn, MA, USA) resulting in a median fragment size of ~500 bp followed by end repair, A-tailing, and indexed adapter ligation (~125bp adapter). .. For the next step, the gel-based size selection was done in the range of 550 to 650 bp for the adapter ligated DNA and PCR amplification was performed for 8 cycles in the case of library.

    Article Title: Shifts in rDNA levels act as a genome buffer promoting chromosome homeostasis
    Article Snippet: After 100 generations in the presence and absence of 5% ethanol, a 100 ng of the purified dsDNA from strain 4 was sheared to the average fragment sizes of 350 bp with Covaris M220 ultrasonicator. .. The sequencing libraries were prepared with TruSeq Nano DNA Sample Prep kit (Illumina, San Diego, CA).

    Genomic Sequencing:

    Article Title: No Evidence of Clonal Dominance after Transplant of HOXB4-Expanded Cord Blood Cells in a Nonhuman Primate Model
    Article Snippet: Paragraph title: Acoustic mediated-Modified Genomic Sequencing (MGS)-PCR for amplification of retroviral integrations sites ... Between 300ng to 3μg of gDNA samples were acoustically sheared to a mean fragment size of 1500bp using the M220 focused-ultrasonicator (Covaris Inc., Woburn, MA, USA).

    Infection:

    Article Title: Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages
    Article Snippet: Exponentially growing cultures were infected with S-EIV1 and incubated as above for 14–17 days until lysis occurred. .. The DNA was sheared into ∼300 bp fragments using a Covaris M220 ultrasonicator (Covaris, Woburn, MA, USA) and purified using Agencourt AMPure XP beads (Beckham Coulter).

    Digital PCR:

    Article Title: HIV Protease-Generated Casp8p41, When Bound and Inactivated by Bcl2, Is Degraded by the Proteasome
    Article Snippet: DNA for analysis was extracted using a Qiagen DNA blood minikit (Qiagen, CA), linearized using a Covaris M220 focused ultrasonicator with 3.0 kb minitube blue (Covaris, MA), and quantified using a NanoDrop 2000 spectrophotometer. .. DNA for analysis was extracted using a Qiagen DNA blood minikit (Qiagen, CA), linearized using a Covaris M220 focused ultrasonicator with 3.0 kb minitube blue (Covaris, MA), and quantified using a NanoDrop 2000 spectrophotometer.

    Generated:

    Article Title: Postnatal DNA demethylation and its role in tissue maturation
    Article Snippet: RNA-Seq libraries were generated using the TruSeq RNA Sample Preparation Kit v2 (Illumina). .. For ChIP analysis, chromatin was fixed and sheared with the M220 Focused-ultrasonicator™ (Covaris® ) using the microTube snap-cap.

    Article Title: Large-scale detection of in vivo transcription errors
    Article Snippet: Total DNA was extracted using Qiagen Genomic-Tip protocol (Qiagen). .. DNA libraries were generated from 1 μg of genomic DNA sheared to ∼300 base pair fragments on an M-series focused ultrasonicator (Covaris) following the standard TruSeq library protocol (Illumina). .. Sequencing was conducted on a single lane of a HiSeq2000.

    DNA Sequencing:

    Article Title: The utilization of next-generation sequencing to detect somatic mutations and predict clinical prognosis of Chinese non-small cell lung cancer patients
    Article Snippet: Paragraph title: NGS library preparation and capture-based targeted DNA sequencing ... DNA shearing was performed using Covaris M220.

    Polymerase Chain Reaction:

    Article Title: Transient reduction of DNA methylation at the onset of meiosis in male mice
    Article Snippet: Isolated mouse gDNA was spiked with approximately 0.1% unmethylated cl857 Sam7 Lambda DNA (Promega) and sheared to fragments with a range of 200–600 bp using a Covaris M220 Ultrasonicator. .. The adaptor-ligated DNA fragments were processed for bisulfite conversion according to the manufacturer’s protocol (EZ DNA methylation Gold kit, Zymo Research).

    Article Title: The utilization of next-generation sequencing to detect somatic mutations and predict clinical prognosis of Chinese non-small cell lung cancer patients
    Article Snippet: DNA shearing was performed using Covaris M220. .. End repair and A-tailing was followed by adaptor ligation.

    Article Title: Characterizing Phage Genomes for Therapeutic Applications
    Article Snippet: Briefly, 250 ng of genomic DNA was fragmented using the Covaris M220 (Covaris, Inc, Woburn, MA, USA). .. Briefly, 250 ng of genomic DNA was fragmented using the Covaris M220 (Covaris, Inc, Woburn, MA, USA).

    Article Title: HIV Protease-Generated Casp8p41, When Bound and Inactivated by Bcl2, Is Degraded by the Proteasome
    Article Snippet: Paragraph title: Total cell-associated HIV DNA measurement and integrated HIV DNA measurement. (i) Quantification of HIV-1 DNA using Raindance digital droplet PCR. ... DNA for analysis was extracted using a Qiagen DNA blood minikit (Qiagen, CA), linearized using a Covaris M220 focused ultrasonicator with 3.0 kb minitube blue (Covaris, MA), and quantified using a NanoDrop 2000 spectrophotometer.

    Article Title: Shifts in rDNA levels act as a genome buffer promoting chromosome homeostasis
    Article Snippet: After 100 generations in the presence and absence of 5% ethanol, a 100 ng of the purified dsDNA from strain 4 was sheared to the average fragment sizes of 350 bp with Covaris M220 ultrasonicator. .. The sequencing libraries were prepared with TruSeq Nano DNA Sample Prep kit (Illumina, San Diego, CA).

    Article Title: ACK1 Regulates Histone H4 Tyr88-phosphorylation and AR Gene Expression in Castration Resistant Prostate Cancer
    Article Snippet: ChIP DNA was purified using PCR DNA purification columns (Qiagen). .. Fifty nanograms of immunoprecipitated DNA was fragmented to 300 base pairs using a Covaris M220 Focused-ultrasonicator (Covaris, Inc., Woburn, MA) and then used to generate sequencing libraries using the Kapa Hyper Prep Kit (Kapa Biosystems, Wilmington, MA).

    Article Title: No Evidence of Clonal Dominance after Transplant of HOXB4-Expanded Cord Blood Cells in a Nonhuman Primate Model
    Article Snippet: Between 300ng to 3μg of gDNA samples were acoustically sheared to a mean fragment size of 1500bp using the M220 focused-ultrasonicator (Covaris Inc., Woburn, MA, USA). .. Between 300ng to 3μg of gDNA samples were acoustically sheared to a mean fragment size of 1500bp using the M220 focused-ultrasonicator (Covaris Inc., Woburn, MA, USA).

    Article Title: A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis
    Article Snippet: Chromatin was sheared using Covaris M220 Focused-ultrasonicator (Covaris, Woburn, MA) to obtain DNA fragments of about 400–600 bp. .. Chromatin was sheared using Covaris M220 Focused-ultrasonicator (Covaris, Woburn, MA) to obtain DNA fragments of about 400–600 bp.

    Sonication:

    Article Title: Phylogenomic reclassification of the world’s most venomous spiders (Mygalomorphae, Atracinae), with implications for venom evolution
    Article Snippet: Sequence capture data were collected in multiple library preparation and sequencing experiments that differed mainly in sequencing platform. .. Up to 500 ng of genomic DNA was used in sonication, using either a Bioruptor for 7 cycles at 30 s on and 90 s off, or using a Covaris M220 Focused-ultrasonicator with treatment time of 65 s, Peak Incident Power of 50, 10% Duty Factor, and 200 cycles per burst. .. Samples were run out on agarose gels to verify sonication success.

    Article Title: Wnt/β-catenin signaling stimulates the expression and synaptic clustering of the autism-associated Neuroligin 3 gene
    Article Snippet: Briefly, 2.0 × 107 cells were incubated with cell-conditioned medium containing Wnt3a (Wnt3a-CM; Wnt3a-CM 50% plus 50% of fresh HT22 incubation media), LiCl or CHIR 98014 (Sigma-Aldrich), as Wnt/β-catenin pharmacological agonists., Cells were cross-linked with 1% formaldehyde (Sigma-Aldrich) for 10 min at room temperature and then the reaction was stopped with 0.125 M glycine. .. Samples were sonicated with the M220 Focused-ultrasonicator (Covaris, Woburn, MA, USA) using milliTube caps (Covaris), following the high cell chromatin shearing protocol suggested by the manufacturer. .. In total 25 µg of chromatin was used in each ChIP assay.

    Article Title: A stable phylogenomic classification of Travunioidea ( Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements
    Article Snippet: Extractions were quantified using a Qubit Fluorometer (Life Technologies, Inc.) Broad Range kit, and quality was assessed via gel electrophoresis on a 0.8% agarose gel. .. Up to 500 ng of genomic DNA was used in sonication procedures, using a Bioruptor for 7 cycles at 30 seconds on and 90 seconds off, or a Covaris M220 Ultrasonicator for 60 seconds with a Peak Incidence Power of 50, Duty Factor of 10%, and 200 cycles per burst. .. Samples were run out on a gel to verify sonication success.

    Article Title: HIV Protease-Generated Casp8p41, When Bound and Inactivated by Bcl2, Is Degraded by the Proteasome
    Article Snippet: DNA for analysis was extracted using a Qiagen DNA blood minikit (Qiagen, CA), linearized using a Covaris M220 focused ultrasonicator with 3.0 kb minitube blue (Covaris, MA), and quantified using a NanoDrop 2000 spectrophotometer. .. Raindance digital PCR was performed using HIV primers and probes specific for HIV Pol (Hxb2 positions 2536 to 2662) and an RPP30 (RNase P) primer-probe set as previously reported ( ).

    Article Title: Random shearing as an alternative to digestion for mitochondrial DNA processing in droplet digital PCR
    Article Snippet: 250 ng DNA in 10 μL 10 mM Tris-EDTA (TE) buffer was added to 10 μL 0.2× Bam HI Buffer containing 10 U Bam HI enzyme and incubated at 37 °C for 1 h. Sonication - Sonication was performed by adding 375 ng DNA in 30 μL TE buffer to a microtube. .. A range of sonication target lengths of 200 bp, 500 bp, 800 bp, 2 kb, and 5 kb were tested using a Covaris M220 Focused Ultrasonicator. .. Quantification of target sequences using ddPCR was used to determine which sonication length was optimal.

    ChIP-sequencing:

    Article Title: Postnatal DNA demethylation and its role in tissue maturation
    Article Snippet: Paragraph title: RNA-Seq, ChIP-Seq and 5hmeDIP-Seq ... For ChIP analysis, chromatin was fixed and sheared with the M220 Focused-ultrasonicator™ (Covaris® ) using the microTube snap-cap.

    Article Title: ACK1 Regulates Histone H4 Tyr88-phosphorylation and AR Gene Expression in Castration Resistant Prostate Cancer
    Article Snippet: Paragraph title: Chromatin immunoprecipitation (ChIP) and ChIP-sequencing ... Fifty nanograms of immunoprecipitated DNA was fragmented to 300 base pairs using a Covaris M220 Focused-ultrasonicator (Covaris, Inc., Woburn, MA) and then used to generate sequencing libraries using the Kapa Hyper Prep Kit (Kapa Biosystems, Wilmington, MA).

    Article Title: A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis
    Article Snippet: Paragraph title: ChIP-Seq Analysis ... Chromatin was sheared using Covaris M220 Focused-ultrasonicator (Covaris, Woburn, MA) to obtain DNA fragments of about 400–600 bp.

    DNA Extraction:

    Article Title: Targeted next generation sequencing identified clinically actionable mutations in patients with esophageal sarcomatoid carcinoma
    Article Snippet: FFPE sections containing both carcinoma and sarcoma components of the tumor were collected for genomic DNA extraction using QIAamp FFPE DNA kit (Qiagen, Hilden, Germany) according to manufacturer’s protocol. .. 500 ng~ 1 μg of extracted DNA for each sample was sheared into 350 bp fragments using Covaris M220 instrument (Covaris, Woburn, MA), followed by library preparation using KAPA Hyper DNA Library Prep Kit (KAPA Biosystems, Wilmington, MA).

    Article Title: Assembly and comparative analysis of the complete mitochondrial genome sequence of Sophora japonica ‘JinhuaiJ2’
    Article Snippet: Paragraph title: DNA extraction and sequencing ... For Illumina HiSeq 2000 platform, 1μg high quality genomic DNA was sheared into 300–500 bp fragments using Covaris M220, and subsequently used to generate the sequenced library using TruSeqTM DNA Sample Prep Kit following the manufacturer’s instructions.

    Article Title: Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages
    Article Snippet: Paragraph title: DNA extraction, sequencing and assembly ... The DNA was sheared into ∼300 bp fragments using a Covaris M220 ultrasonicator (Covaris, Woburn, MA, USA) and purified using Agencourt AMPure XP beads (Beckham Coulter).

    Article Title: Large-scale detection of in vivo transcription errors
    Article Snippet: Paragraph title: RNA and DNA isolation. ... DNA libraries were generated from 1 μg of genomic DNA sheared to ∼300 base pair fragments on an M-series focused ultrasonicator (Covaris) following the standard TruSeq library protocol (Illumina).

    Article Title: Protracted Regional Dissemination of GIM-1-Producing Serratia marcescens in Western Germany
    Article Snippet: Paragraph title: Whole-genome sequencing analysis. (i) Genomic DNA extraction, library preparation, and whole-genome sequencing. ... Genomic DNA from 13 GIM-1-positive S. marcescens strains was extracted using a QIAamp DNA minikit (Qiagen, Hilden, Germany) and sheared by use of a M220 focused ultrasonicator (Covaris, Woburn, MA, USA) to obtain 550-bp fragments.

    Nucleic Acid Electrophoresis:

    Article Title: A stable phylogenomic classification of Travunioidea ( Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements
    Article Snippet: Extractions were quantified using a Qubit Fluorometer (Life Technologies, Inc.) Broad Range kit, and quality was assessed via gel electrophoresis on a 0.8% agarose gel. .. Up to 500 ng of genomic DNA was used in sonication procedures, using a Bioruptor for 7 cycles at 30 seconds on and 90 seconds off, or a Covaris M220 Ultrasonicator for 60 seconds with a Peak Incidence Power of 50, Duty Factor of 10%, and 200 cycles per burst.

    RNA Sequencing Assay:

    Article Title: Postnatal DNA demethylation and its role in tissue maturation
    Article Snippet: Paragraph title: RNA-Seq, ChIP-Seq and 5hmeDIP-Seq ... For ChIP analysis, chromatin was fixed and sheared with the M220 Focused-ultrasonicator™ (Covaris® ) using the microTube snap-cap.

    Magnetic Beads:

    Article Title: The utilization of next-generation sequencing to detect somatic mutations and predict clinical prognosis of Chinese non-small cell lung cancer patients
    Article Snippet: DNA shearing was performed using Covaris M220. .. End repair and A-tailing was followed by adaptor ligation.

    Isolation:

    Article Title: Transient reduction of DNA methylation at the onset of meiosis in male mice
    Article Snippet: DNA was precipitated using ethanol and quantified with Quant-iT PicoGreen reagent (Molecular Probes) using SpectraMax microplate spectrophotometer. .. Isolated mouse gDNA was spiked with approximately 0.1% unmethylated cl857 Sam7 Lambda DNA (Promega) and sheared to fragments with a range of 200–600 bp using a Covaris M220 Ultrasonicator. .. WGBS library preparation was based on Illumina’s ‘WGBS for Methylation Analysis’ protocol.

    Article Title: Postnatal DNA demethylation and its role in tissue maturation
    Article Snippet: RNA was isolated from mouse hepatocytes using the miRNeasy Kit according to the manufacturer’s instructions (Qiagen). .. For ChIP analysis, chromatin was fixed and sheared with the M220 Focused-ultrasonicator™ (Covaris® ) using the microTube snap-cap.

    Article Title: Assembly and comparative analysis of the complete mitochondrial genome sequence of Sophora japonica ‘JinhuaiJ2’
    Article Snippet: For Illumina HiSeq 2000 platform, 1μg high quality genomic DNA was sheared into 300–500 bp fragments using Covaris M220, and subsequently used to generate the sequenced library using TruSeqTM DNA Sample Prep Kit following the manufacturer’s instructions. .. The library was amplified using TruSeq PE Cluster Kit v3-cBot-HS and sequenced using TruSeq SBS Kit v3-HS for 200 cycles, and yielded 5,066 Mb sequencing data of 150 bp paired-end (PE) reads.

    Article Title: Large-scale detection of in vivo transcription errors
    Article Snippet: Total RNA was isolated using the the Ambion RiboPure Kit (Life Tech). .. DNA libraries were generated from 1 μg of genomic DNA sheared to ∼300 base pair fragments on an M-series focused ultrasonicator (Covaris) following the standard TruSeq library protocol (Illumina).

    Purification:

    Article Title: Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages
    Article Snippet: The pellet was treated with DNase 1 and RNase A to remove free nucleic acids, and the nucleic acids extracted using a QiAamp MinElute Virus Spin Kit (Qiagen, Mississauga, ON, Canada). .. The DNA was sheared into ∼300 bp fragments using a Covaris M220 ultrasonicator (Covaris, Woburn, MA, USA) and purified using Agencourt AMPure XP beads (Beckham Coulter). .. The sequencing library was constructed using NxSeq DNA Sample Prep Kits (Lucigen, Middleton, WI, USA) and sequenced on an Illumina MiSeq at the Génome Québec Innovation Centre at McGill University (Montréal, QC, Canada).

    Article Title: Shifts in rDNA levels act as a genome buffer promoting chromosome homeostasis
    Article Snippet: After standard PFGE separation, Y’ sequences within particular yeast chromosomes were detected using digoxigenin labeling, anti-digoxigenin antibody and phosphate alkaline-based chemiluminescence.15 Y’ sequence length was estimated after DNA digestion with Pst I. .. After 100 generations in the presence and absence of 5% ethanol, a 100 ng of the purified dsDNA from strain 4 was sheared to the average fragment sizes of 350 bp with Covaris M220 ultrasonicator. .. The sequencing libraries were prepared with TruSeq Nano DNA Sample Prep kit (Illumina, San Diego, CA).

    Article Title: ACK1 Regulates Histone H4 Tyr88-phosphorylation and AR Gene Expression in Castration Resistant Prostate Cancer
    Article Snippet: ChIP DNA was purified using PCR DNA purification columns (Qiagen). .. Fifty nanograms of immunoprecipitated DNA was fragmented to 300 base pairs using a Covaris M220 Focused-ultrasonicator (Covaris, Inc., Woburn, MA) and then used to generate sequencing libraries using the Kapa Hyper Prep Kit (Kapa Biosystems, Wilmington, MA).

    Article Title: A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis
    Article Snippet: Chromatin was sheared using Covaris M220 Focused-ultrasonicator (Covaris, Woburn, MA) to obtain DNA fragments of about 400–600 bp. .. Chromatin was sheared using Covaris M220 Focused-ultrasonicator (Covaris, Woburn, MA) to obtain DNA fragments of about 400–600 bp.

    Sequencing:

    Article Title: Phylogenomic reclassification of the world’s most venomous spiders (Mygalomorphae, Atracinae), with implications for venom evolution
    Article Snippet: Up to 500 ng of genomic DNA was used in sonication, using either a Bioruptor for 7 cycles at 30 s on and 90 s off, or using a Covaris M220 Focused-ultrasonicator with treatment time of 65 s, Peak Incident Power of 50, 10% Duty Factor, and 200 cycles per burst. .. Up to 500 ng of genomic DNA was used in sonication, using either a Bioruptor for 7 cycles at 30 s on and 90 s off, or using a Covaris M220 Focused-ultrasonicator with treatment time of 65 s, Peak Incident Power of 50, 10% Duty Factor, and 200 cycles per burst.

    Article Title: Characterizing Phage Genomes for Therapeutic Applications
    Article Snippet: Paragraph title: 2.2. Library Preparation and Sequencing ... Briefly, 250 ng of genomic DNA was fragmented using the Covaris M220 (Covaris, Inc, Woburn, MA, USA).

    Article Title: Artificial selection increased body weight but induced increase of runs of homozygosity in Hanwoo cattle
    Article Snippet: Paragraph title: Sample information and whole genome sequencing ... Briefly, 200 ng of gDNA was fragmented by Covaris M220 (Woburn, MA, USA) resulting in a median fragment size of ~500 bp followed by end repair, A-tailing, and indexed adapter ligation (~125bp adapter).

    Article Title: Consolidated bioprocessing of butanol production from xylan by a thermophilic and butanologenic Thermoanaerobacterium sp. M5
    Article Snippet: Paragraph title: The draft complete genome sequencing and analysis of strain M5 ... The large fragment of genomic DNA was firstly broken into small sequences with an average 300 bp by Covaris M220 (Covaris, USA), and the DNA libraries were constructed via NEBNext® UltraTM DNA Library Prep Kit for Illumina (NEB, USA).

    Article Title: Targeted next generation sequencing identified clinically actionable mutations in patients with esophageal sarcomatoid carcinoma
    Article Snippet: Paragraph title: Sample collection and sequencing library preparation ... 500 ng~ 1 μg of extracted DNA for each sample was sheared into 350 bp fragments using Covaris M220 instrument (Covaris, Woburn, MA), followed by library preparation using KAPA Hyper DNA Library Prep Kit (KAPA Biosystems, Wilmington, MA).

    Article Title: Assembly and comparative analysis of the complete mitochondrial genome sequence of Sophora japonica ‘JinhuaiJ2’
    Article Snippet: Paragraph title: DNA extraction and sequencing ... For Illumina HiSeq 2000 platform, 1μg high quality genomic DNA was sheared into 300–500 bp fragments using Covaris M220, and subsequently used to generate the sequenced library using TruSeqTM DNA Sample Prep Kit following the manufacturer’s instructions.

    Article Title: Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages
    Article Snippet: Paragraph title: DNA extraction, sequencing and assembly ... The DNA was sheared into ∼300 bp fragments using a Covaris M220 ultrasonicator (Covaris, Woburn, MA, USA) and purified using Agencourt AMPure XP beads (Beckham Coulter).

    Article Title: ACK1 Regulates Histone H4 Tyr88-phosphorylation and AR Gene Expression in Castration Resistant Prostate Cancer
    Article Snippet: Chromatin immunoprecipitation sequencing (ChIP-seq) was performed by the Molecular Genomics Core Facility at the Moffitt Cancer Center. .. Fifty nanograms of immunoprecipitated DNA was fragmented to 300 base pairs using a Covaris M220 Focused-ultrasonicator (Covaris, Inc., Woburn, MA) and then used to generate sequencing libraries using the Kapa Hyper Prep Kit (Kapa Biosystems, Wilmington, MA). .. The size and quality of the library was evaluated using the Agilent BioAnalzyer, and the library was quantitated with the Kapa Library Quantification Kit.

    Article Title: Protracted Regional Dissemination of GIM-1-Producing Serratia marcescens in Western Germany
    Article Snippet: Paragraph title: Whole-genome sequencing analysis. (i) Genomic DNA extraction, library preparation, and whole-genome sequencing. ... Genomic DNA from 13 GIM-1-positive S. marcescens strains was extracted using a QIAamp DNA minikit (Qiagen, Hilden, Germany) and sheared by use of a M220 focused ultrasonicator (Covaris, Woburn, MA, USA) to obtain 550-bp fragments.

    Article Title: A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis
    Article Snippet: Chromatin was sheared using Covaris M220 Focused-ultrasonicator (Covaris, Woburn, MA) to obtain DNA fragments of about 400–600 bp. .. Chromatin was sheared using Covaris M220 Focused-ultrasonicator (Covaris, Woburn, MA) to obtain DNA fragments of about 400–600 bp.

    Immunoprecipitation:

    Article Title: Wnt/β-catenin signaling stimulates the expression and synaptic clustering of the autism-associated Neuroligin 3 gene
    Article Snippet: Samples were sonicated with the M220 Focused-ultrasonicator (Covaris, Woburn, MA, USA) using milliTube caps (Covaris), following the high cell chromatin shearing protocol suggested by the manufacturer. .. In total 25 µg of chromatin was used in each ChIP assay.

    Article Title: ACK1 Regulates Histone H4 Tyr88-phosphorylation and AR Gene Expression in Castration Resistant Prostate Cancer
    Article Snippet: Chromatin immunoprecipitation sequencing (ChIP-seq) was performed by the Molecular Genomics Core Facility at the Moffitt Cancer Center. .. Fifty nanograms of immunoprecipitated DNA was fragmented to 300 base pairs using a Covaris M220 Focused-ultrasonicator (Covaris, Inc., Woburn, MA) and then used to generate sequencing libraries using the Kapa Hyper Prep Kit (Kapa Biosystems, Wilmington, MA). .. The size and quality of the library was evaluated using the Agilent BioAnalzyer, and the library was quantitated with the Kapa Library Quantification Kit.

    Nested PCR:

    Article Title: No Evidence of Clonal Dominance after Transplant of HOXB4-Expanded Cord Blood Cells in a Nonhuman Primate Model
    Article Snippet: Between 300ng to 3μg of gDNA samples were acoustically sheared to a mean fragment size of 1500bp using the M220 focused-ultrasonicator (Covaris Inc., Woburn, MA, USA). .. Between 300ng to 3μg of gDNA samples were acoustically sheared to a mean fragment size of 1500bp using the M220 focused-ultrasonicator (Covaris Inc., Woburn, MA, USA).

    Sample Prep:

    Article Title: Transient reduction of DNA methylation at the onset of meiosis in male mice
    Article Snippet: Isolated mouse gDNA was spiked with approximately 0.1% unmethylated cl857 Sam7 Lambda DNA (Promega) and sheared to fragments with a range of 200–600 bp using a Covaris M220 Ultrasonicator. .. The adaptor-ligated DNA fragments were processed for bisulfite conversion according to the manufacturer’s protocol (EZ DNA methylation Gold kit, Zymo Research).

    Article Title: Postnatal DNA demethylation and its role in tissue maturation
    Article Snippet: RNA-Seq libraries were generated using the TruSeq RNA Sample Preparation Kit v2 (Illumina). .. For ChIP analysis, chromatin was fixed and sheared with the M220 Focused-ultrasonicator™ (Covaris® ) using the microTube snap-cap.

    Article Title: Artificial selection increased body weight but induced increase of runs of homozygosity in Hanwoo cattle
    Article Snippet: Using DNA from the blood samples, we produced indexed shotgun paired-end (PE) libraries with approximately 500bp inserts using TruSeq Nano DNA Library Prep Kit (Illumina, USA) following standard Illumina sample-preparation protocol. .. Briefly, 200 ng of gDNA was fragmented by Covaris M220 (Woburn, MA, USA) resulting in a median fragment size of ~500 bp followed by end repair, A-tailing, and indexed adapter ligation (~125bp adapter).

    Article Title: Assembly and comparative analysis of the complete mitochondrial genome sequence of Sophora japonica ‘JinhuaiJ2’
    Article Snippet: PacBio SMRT sequencing and Illumina Next Generation Sequencing (NGS) were carried-out at the Benagen Ltd. (Wuhan, China). .. For Illumina HiSeq 2000 platform, 1μg high quality genomic DNA was sheared into 300–500 bp fragments using Covaris M220, and subsequently used to generate the sequenced library using TruSeqTM DNA Sample Prep Kit following the manufacturer’s instructions. .. The library was amplified using TruSeq PE Cluster Kit v3-cBot-HS and sequenced using TruSeq SBS Kit v3-HS for 200 cycles, and yielded 5,066 Mb sequencing data of 150 bp paired-end (PE) reads.

    Chromatin Immunoprecipitation:

    Article Title: Postnatal DNA demethylation and its role in tissue maturation
    Article Snippet: RNA-Seq libraries were generated using the TruSeq RNA Sample Preparation Kit v2 (Illumina). .. For ChIP analysis, chromatin was fixed and sheared with the M220 Focused-ultrasonicator™ (Covaris® ) using the microTube snap-cap. .. Five micrograms of chromatin was then immunoprecipitated with 2 μg of H3K4me1, H3K27ac (Abcam), or HNF6 (Santa Cruz, sc-13050) antibodies.

    Article Title: Wnt/β-catenin signaling stimulates the expression and synaptic clustering of the autism-associated Neuroligin 3 gene
    Article Snippet: Paragraph title: Chromatin immunoprecipitation (ChIP) assays ... Samples were sonicated with the M220 Focused-ultrasonicator (Covaris, Woburn, MA, USA) using milliTube caps (Covaris), following the high cell chromatin shearing protocol suggested by the manufacturer.

    Article Title: ACK1 Regulates Histone H4 Tyr88-phosphorylation and AR Gene Expression in Castration Resistant Prostate Cancer
    Article Snippet: Paragraph title: Chromatin immunoprecipitation (ChIP) and ChIP-sequencing ... Fifty nanograms of immunoprecipitated DNA was fragmented to 300 base pairs using a Covaris M220 Focused-ultrasonicator (Covaris, Inc., Woburn, MA) and then used to generate sequencing libraries using the Kapa Hyper Prep Kit (Kapa Biosystems, Wilmington, MA).

    Software:

    Article Title: A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis
    Article Snippet: Chromatin was sheared using Covaris M220 Focused-ultrasonicator (Covaris, Woburn, MA) to obtain DNA fragments of about 400–600 bp. .. DNA was purified using MinElute PCR purification kit (Qiagen) and made to library for sequencing with Illumina Hiseq 2500 sequencer (Illumina, San Diego, CA).

    Selection:

    Article Title: Characterizing Phage Genomes for Therapeutic Applications
    Article Snippet: Briefly, 250 ng of genomic DNA was fragmented using the Covaris M220 (Covaris, Inc, Woburn, MA, USA). .. Briefly, 250 ng of genomic DNA was fragmented using the Covaris M220 (Covaris, Inc, Woburn, MA, USA).

    Article Title: Artificial selection increased body weight but induced increase of runs of homozygosity in Hanwoo cattle
    Article Snippet: In the second step, 4,500 cows were inseminated with the semen from the selected bulls and 30 bulls were selected based on selection index which used weighted breeding values for BF, MS, and EMA of 800 male calves [ , , ]. .. Briefly, 200 ng of gDNA was fragmented by Covaris M220 (Woburn, MA, USA) resulting in a median fragment size of ~500 bp followed by end repair, A-tailing, and indexed adapter ligation (~125bp adapter).

    Article Title: Shifts in rDNA levels act as a genome buffer promoting chromosome homeostasis
    Article Snippet: After 100 generations in the presence and absence of 5% ethanol, a 100 ng of the purified dsDNA from strain 4 was sheared to the average fragment sizes of 350 bp with Covaris M220 ultrasonicator. .. The sequencing libraries were prepared with TruSeq Nano DNA Sample Prep kit (Illumina, San Diego, CA).

    Agarose Gel Electrophoresis:

    Article Title: A stable phylogenomic classification of Travunioidea ( Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements
    Article Snippet: Extractions were quantified using a Qubit Fluorometer (Life Technologies, Inc.) Broad Range kit, and quality was assessed via gel electrophoresis on a 0.8% agarose gel. .. Up to 500 ng of genomic DNA was used in sonication procedures, using a Bioruptor for 7 cycles at 30 seconds on and 90 seconds off, or a Covaris M220 Ultrasonicator for 60 seconds with a Peak Incidence Power of 50, Duty Factor of 10%, and 200 cycles per burst.

    Next-Generation Sequencing:

    Article Title: The utilization of next-generation sequencing to detect somatic mutations and predict clinical prognosis of Chinese non-small cell lung cancer patients
    Article Snippet: Paragraph title: NGS library preparation and capture-based targeted DNA sequencing ... DNA shearing was performed using Covaris M220.

    Article Title: Targeted next generation sequencing identified clinically actionable mutations in patients with esophageal sarcomatoid carcinoma
    Article Snippet: 500 ng~ 1 μg of extracted DNA for each sample was sheared into 350 bp fragments using Covaris M220 instrument (Covaris, Woburn, MA), followed by library preparation using KAPA Hyper DNA Library Prep Kit (KAPA Biosystems, Wilmington, MA). .. In brief, fragmented DNA underwent sequential steps of end-repairing, A-tailing and ligation with indexed adapters, followed by size selection with Agencourt AMPure XP beads (Beckman Coulter, Mississauga, Canada) and PCR amplification.

    Article Title: Assembly and comparative analysis of the complete mitochondrial genome sequence of Sophora japonica ‘JinhuaiJ2’
    Article Snippet: PacBio SMRT sequencing and Illumina Next Generation Sequencing (NGS) were carried-out at the Benagen Ltd. (Wuhan, China). .. For Illumina HiSeq 2000 platform, 1μg high quality genomic DNA was sheared into 300–500 bp fragments using Covaris M220, and subsequently used to generate the sequenced library using TruSeqTM DNA Sample Prep Kit following the manufacturer’s instructions.

    Article Title: Shifts in rDNA levels act as a genome buffer promoting chromosome homeostasis
    Article Snippet: Paragraph title: Next-generation sequencing (NGS) ... After 100 generations in the presence and absence of 5% ethanol, a 100 ng of the purified dsDNA from strain 4 was sheared to the average fragment sizes of 350 bp with Covaris M220 ultrasonicator.

    Spectrophotometry:

    Article Title: Transient reduction of DNA methylation at the onset of meiosis in male mice
    Article Snippet: DNA was precipitated using ethanol and quantified with Quant-iT PicoGreen reagent (Molecular Probes) using SpectraMax microplate spectrophotometer. .. Isolated mouse gDNA was spiked with approximately 0.1% unmethylated cl857 Sam7 Lambda DNA (Promega) and sheared to fragments with a range of 200–600 bp using a Covaris M220 Ultrasonicator.

    Article Title: HIV Protease-Generated Casp8p41, When Bound and Inactivated by Bcl2, Is Degraded by the Proteasome
    Article Snippet: Viability was assessed using a CellTiter-Glo luminescent cell viability assay (Promega). .. DNA for analysis was extracted using a Qiagen DNA blood minikit (Qiagen, CA), linearized using a Covaris M220 focused ultrasonicator with 3.0 kb minitube blue (Covaris, MA), and quantified using a NanoDrop 2000 spectrophotometer. .. The fragmentation length was confirmed via gel electrophoresis.

    DNA Methylation Assay:

    Article Title: Transient reduction of DNA methylation at the onset of meiosis in male mice
    Article Snippet: Isolated mouse gDNA was spiked with approximately 0.1% unmethylated cl857 Sam7 Lambda DNA (Promega) and sheared to fragments with a range of 200–600 bp using a Covaris M220 Ultrasonicator. .. WGBS library preparation was based on Illumina’s ‘WGBS for Methylation Analysis’ protocol.

    Produced:

    Article Title: Artificial selection increased body weight but induced increase of runs of homozygosity in Hanwoo cattle
    Article Snippet: Using DNA from the blood samples, we produced indexed shotgun paired-end (PE) libraries with approximately 500bp inserts using TruSeq Nano DNA Library Prep Kit (Illumina, USA) following standard Illumina sample-preparation protocol. .. Briefly, 200 ng of gDNA was fragmented by Covaris M220 (Woburn, MA, USA) resulting in a median fragment size of ~500 bp followed by end repair, A-tailing, and indexed adapter ligation (~125bp adapter).

    Concentration Assay:

    Article Title: Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages
    Article Snippet: The DNA was sheared into ∼300 bp fragments using a Covaris M220 ultrasonicator (Covaris, Woburn, MA, USA) and purified using Agencourt AMPure XP beads (Beckham Coulter). .. The DNA was sheared into ∼300 bp fragments using a Covaris M220 ultrasonicator (Covaris, Woburn, MA, USA) and purified using Agencourt AMPure XP beads (Beckham Coulter).

    Article Title: Random shearing as an alternative to digestion for mitochondrial DNA processing in droplet digital PCR
    Article Snippet: A range of sonication target lengths of 200 bp, 500 bp, 800 bp, 2 kb, and 5 kb were tested using a Covaris M220 Focused Ultrasonicator. .. A range of sonication target lengths of 200 bp, 500 bp, 800 bp, 2 kb, and 5 kb were tested using a Covaris M220 Focused Ultrasonicator.

    DNA Purification:

    Article Title: ACK1 Regulates Histone H4 Tyr88-phosphorylation and AR Gene Expression in Castration Resistant Prostate Cancer
    Article Snippet: ChIP DNA was purified using PCR DNA purification columns (Qiagen). .. Fifty nanograms of immunoprecipitated DNA was fragmented to 300 base pairs using a Covaris M220 Focused-ultrasonicator (Covaris, Inc., Woburn, MA) and then used to generate sequencing libraries using the Kapa Hyper Prep Kit (Kapa Biosystems, Wilmington, MA).

    Lysis:

    Article Title: Transient reduction of DNA methylation at the onset of meiosis in male mice
    Article Snippet: Genomic DNA (gDNA) was prepared by incubating cells in tail lysis buffer with 5 µl of Proteinase K (Life Technologies, 20 mg/ml) at 55 °C for 2–3 h. At the end of lysis, 2 µl of linear acrylamide (Ambion, 5 mg/ml) was added to samples. .. Isolated mouse gDNA was spiked with approximately 0.1% unmethylated cl857 Sam7 Lambda DNA (Promega) and sheared to fragments with a range of 200–600 bp using a Covaris M220 Ultrasonicator.

    Article Title: Postnatal DNA demethylation and its role in tissue maturation
    Article Snippet: For ChIP analysis, chromatin was fixed and sheared with the M220 Focused-ultrasonicator™ (Covaris® ) using the microTube snap-cap. .. The ATAC-Seq protocol , was carried out on WT or Tet2/3 DKO hepatocytes with the following modifications.

    Article Title: Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages
    Article Snippet: Exponentially growing cultures were infected with S-EIV1 and incubated as above for 14–17 days until lysis occurred. .. The DNA was sheared into ∼300 bp fragments using a Covaris M220 ultrasonicator (Covaris, Woburn, MA, USA) and purified using Agencourt AMPure XP beads (Beckham Coulter).

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    Covaris m220 sonicator
    Comparison of three Illumina library construction protocols. Covaris <t>M220</t> was used to fragment DNA in TruSeq Nano.
    M220 Sonicator, supplied by Covaris, used in various techniques. Bioz Stars score: 99/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Comparison of three Illumina library construction protocols. Covaris M220 was used to fragment DNA in TruSeq Nano.

    Journal: Human immunology

    Article Title: Impact of Three Illumina Library Construction Methods on GC Bias and HLA Genotype Calling

    doi: 10.1016/j.humimm.2014.12.016

    Figure Lengend Snippet: Comparison of three Illumina library construction protocols. Covaris M220 was used to fragment DNA in TruSeq Nano.

    Article Snippet: Aiming for an insert size of 550 bp, 200 ng of pooled PCR products were sheared by sonication using Covaris M220 (Covaris, Woburn, MA) with duty factor 20%, peak incident power 50 W, and 200 cycles per burst for 60 sec. Amplicon fragments underwent further purification with Agencourt AMPure XP beads in 1.6× reaction volume.

    Techniques: