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  • Analysis of DNA fragments using the Agilent 2100 Bioanalyzer

    Application Notes
    DNA shearing protocols for Focused-ultrasonicators with the Agilent DNA 12000 kit was used to evaluate the average base pair size because of the large fragment size range, from 130 bp to 5 kb range.
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  • Cross-linked Yeast Chromatin shearing on the Covaris E210

    Application Notes
    Shearing cross-linked yeast samples on the Covaris E210.
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  • Active Extraction of Native Proteins from Yeast using Covaris Adaptive Focused Acoustics® (AFA®)

    Application Notes
    Native protein extraction reagents were tested for total protein yield and preservation of enzymatic activity using a “passive extraction” or an AFA-based “active extraction” method, both increased.
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  • Active paraffin removal from FFPE tissues with Adaptive Focused Acoustics

    Application Notes
    Covaris developed a method of active paraffin removal from FFPE tissues using AFA technology. AFA treatment is applied to a FFPE sample and paraffin is separated from the tissue by emulsification.
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  • A Streamlined Workflow to Perform ChIP from FFPE Samples

    Application Notes
    We demonstrate how AFA® technology combined with truXTRAC® and truChIP® effectively recovers chromatin suitable for studying histone modifications and transcription factor binding interaction events.
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  • High-Throughput, Low Volume gDNA Extraction from Whole Blood Enabled by Covaris Adaptive Focused Acoustics® (AFA®) and AFA-TUBE® TPX

    Application Notes
    Extraction of gDNA from whole blood is the first step in multiple translational research and molecular diagnostics applications, such as next-generation sequencing, multiplex PCR, qPCR, and ddPCR.
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  • Protein Extraction from Yeast: Comparison of the Covaris Adaptive Focused Acoustics®(AFA) Process to Conventional Bead Beating and Probe Sonication

    Application Notes
    The efficiency of several mechanical-based lysis and extraction techniques, such as Adaptive Focused Acoustics (AFA), probe sonication, and bead beating from yeast isolates was compared.
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  • Nucleic Acid Extraction from Laser-Capture Microdissected (LCM) FFPE Tissues

    Application Notes
    LCM
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  • DNA Shearing for Next Generation Sequencing (NGS) with the M220 Focused-ultrasonicator

    Application Notes
    DNA Shearing for NGS with the ME220 Focused-ultrasonicator.
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  • DNA Extraction from FFPE samples with Covaris Focused-ultrasonicators

    Application Notes
    When an Adaptive Focused Acoustics (AFA) treatment is applied to a FFPE sample to extract DNA, it simultaneously deparaffinizes the sample, emulsifies the paraffin, and rehydrates the tissue.
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  • Optimizing Sample Fixation and Chromatin Shearing for Improved Sensitivity and Reproducibility of Chromatin Immunoprecipitation

    Application Notes
    Adaptive Focused Acoustic (AFA) technology provides precise control over mechanical shearing and thermal control during processing to deliver high quality chromatin for sensitive results.
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  • AFA-based MALDI Biotyper Sample Preparation for Mycobacteria Colonies

    Application Notes
    AFA-based MALDI
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  • Release of Microbial Cells from a Solid Matrix, Cell Lysis, and Shearing of Released Nucleic Acids Performed in a One-Step Procedure

    Application Notes
    Release of Microbial Cells
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  • AFA-based MALDI Biotyper™ Sample Prep for MGIT™ Positive Mycobacteria Cultures

    Application Notes
    Positive Mycobacteria Cultures
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  • AFA-based Sputum Liquification to Enable Downstream Microbial Analysis

    Application Notes
    Sputim Liquification
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  • Microbiome Sample Preparation: Efficient DNA Extraction and Optional Mechanical Shearing

    Application Notes
    DNA Extraction
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  • Streamlined Ultra Low Sample Input and Processing Volume Chromatin Shearing Protocols for Fly Embryos and Mammalian Cell Lines

    Application Notes
    These protocols have been optimized for both mammalian cell lines and fly embryos and reliably fragment chromatin in low volumes from down to 10,000 mammalian cells and 5 stage-17 Drosophila embryos.
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  • Evaluation of Next Generation Library Preparation using DNA Extracted from Dried Blood Spots using truXTRAC® DBS DNA kit

    Application Notes
    The truXTRAC DBS DNA kit efficiently extracts NGS-grade DNA. AFA enables rehydration and provides cell lysis and mechanical DNA shearing, resulting in NGS library preparation ready DNA.
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  • Amplicon Shearing Using a Covaris® Focused-ultrasonicator

    Application Notes
    In this application note, we describe the use of Covaris AFA® technology for mechanical DNA shearing of amplicons ranging in size in preparation for massively parallel high-throughput sequencing.
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  • Preparation of whole body Caenorhabditis elegans extracts for chromatin immunoprecipitation using the Covaris® S220 Focused-ultrasonicator

    Application Notes
    This application note provides a sample preparation protocol using the Covaris S220 that can be used by investigators looking to process whole body C. elegans extracts for ChIP-based applications.
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  • Optimized Protocol for Robust Chromatin Shearing and Immunoprecipitation of Human Pancreatic Islets using the Covaris® Focused-ultrasonicator

    Application Notes
    We demonstrate how the Covaris S220 Focused-ultrasonicator provides highly reproducible chromatin shearing, resulting in improved signal-to-noise ratios and sensitivity for ChIP-seq or ChIP-qPCR.
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  • Optimized Covaris truXTRAC® FFPE RNA Protocol for Isolating RNA from Laser-Capture Microdissected (LCM) FFPE Tissue for Next Generation Sequencing

    Application Notes
    Covaris truXTRAC FFPE RNA kits and Focused-ultrasonicators enables NGS-grade nucleic acids for RNA sequencing, a feat previously challenging when using low input FFPE tissue such LCM-FFPE samples.
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  • Cross-linked Yeast Chromatin Shearing on the Covaris Focused-ultrasonicator

    Application Notes
    The Broad Institute developed a cross-linked chromatin shearing protocol for yeast samples that utilizes the Covaris E210 Focused-ultrasonicator, to be used prior to immunoprecipitation.
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  • Optimizing a Dual Fixation Protocol to Study Protein Complexes Binding to Chromatin in vivo

    Application Notes
    This application note provides shearing profiles, evaluates epitope integrity each shearing time and ChIP-qPCR results obtained using single step formaldehyde fixation and dual crosslinking protocol.
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  • Lysis and High Molecular Weight DNA Extraction from Eukaryotic and Prokaryotic Cells Powered by AFA-energetics®

    Application Notes
    This application note describes an automatable approach to cell lysis and extraction of high molecular weight DNA from microbial samples, which can be sequenced with long-read sequencing technology.
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  • Covaris Shearing Guide for 500 Base Pairs using the 96 AFA-TUBE TPX Plate

    Application Notes
    This application note provides additional support for the current AFA-TUBE TPX shearing protocol to achieve 500 base pair (bp) DNA fragments using AFA® on the LE220-plus Focused-ultrasonicator.
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  • AFA-energetics®-Mediated DNA Extraction from Yeast and Bacteria Using Scanning in a Labcyte 384-well Plate

    Application Notes
    This document describes the optimized AFA-energetics dose to lyse and extract DNA from S. cerevisiae, E. coli, & L. monocytogenes using a proprietary scanning method 384-well plates.
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  • Simplifying ChIP from Primary Cells and Clinical Samples for High-throughput Epigenetic Applications

    Application Notes
    Large-scale analysis of histone marks and transcription factor interactions uses high-quality chromatin, use of validated ChIP-grade antibodies, and optimized reagents to produce meaningful results.
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  • Variability in DNA Fragment Size and Distribution Analysis Across Various Fragment Analyzers

    Application Notes
    DNA Fragmentation
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  • Affinity-based Enrichment Analyses of DNA Methylation MCIp, MeDIP, hMeDIP

    Application Notes
    MeDIP
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  • Shallow Whole Genome Sequencing Workflow - sWGS

    Application Notes
    sWGS
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  • Chromosome Conformation Capture Using Biotinylated Oligos - Capture-C

    Application Notes
    Capture-C
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  • Covaris cryoPREP® with AFA: Enabling High-resolution Diagnostic Metagenomics

    Application Notes
    cryoPREP Applications
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  • A Comparison of Active and Passive FFPE DNA Extraction Methods and Effects on Downstream Analysis Metrics

    Application Notes
    Active and Passive FFPE DNA Extraction
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  • An Effect of a Shearing Process on the Re-Sequencing of the Arabidopsis thaliana Genome

    Application Notes
    Shearing Process of Arabedopis
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  • Combining Covaris 96 AFA-TUBE TPX Plate with Swift Biosciences Accel-NGS 2S Kit for an Optimized Single Tube Workflow for Robust, Low Input NGS Library Preparation

    Application Notes
    AFA-TUBE Case study
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  • Assessing FFPE DNA Quality: The “Illumina FFPE QC Kit” Enables Quantitation of Improvements in FFPE DNA Extraction Technologies

    Application Notes
    We used the Illumina FFPE QC kit (2) to assess the quality of DNA extracted from two different extraction technologies using four different types of FFPE samples.
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  • Covaris truSHEAR Mechanical DNA Shearing for NGS Applications

    Application Notes
    Mechanical DNA Shearing
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  • Automated NGS Library Preparation with Beckman Biomek FXP and Covaris E220

    Application Notes
    Key parameters for high quality library preparation are homogeneity of the library insert size and un-biased fragmentation profile, which is why Covaris AFA technology was chosen to fragment the DNA.
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  • Transitioning from custom amplicon-based parallel sequencing to hybrid capture-based sequencing in molecular pathology routine diagnostics

    Application Notes
    Molecular Pahology
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  • Covaris DNA shearing guide for the Agilent SureSelect Target Enrichment System©

    Application Notes
    DNA Shearing
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  • Automated NGS Library Construction with Eppendorf epMotion® 5075t/TMX and Covaris® Focused-ultrasonicators

    Application Notes
    This guide provides users with a complete set of protocols that encompass all Covaris AFA® instruments for DNA shearing to be readily compatible with the Agilent SureSelect Target Enrichment System.
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  • Pipetting Best Practices for Covaris 96 microTUBE Plate and 8 microTUBE Strip in Automated Liquid Handlers

    Application Notes
    Covaris labware has multi-well formats, like the 96 microTUBE Plate and 8 microTUBE Strip. The hardware and methods described here maximize the robustness of robot pipetting in Covaris consumables.
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  • Magnetic Bead-based Clean-up Using AFA-energetics®

    Application Notes
    When precisely tuned, this stream of Covaris Adaptive Focused Acoustic energy enables DNA shearing precisely and reliably to desired fragment sizes, in addition to gentle contact-free sample mixing.
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  • AFA-energetics®- Mediated RNA Extraction from Yeast

    Application Notes
    Mediated RNA Extraction from Yeast
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  • truXTRAC® FFPE RNA Extraction and Purification - Quality Metrics for Clinical Applications Powered by Adaptive Focused Acoustics® (AFA®)

    Application Notes
    FFPE RNA Extraction
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  • Chromatin Isolation by RNA Purification - ChIRP

    Application Notes
    ChIRP
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  • Chromatin Interaction Analysis by Paired-End Tag Sequencing - ChIA-PET

    Application Notes
    ChIA-PET
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  • Lysis and Extraction of Biomolecules from Eukaryotic and Prokaryotic Cells Powered by AFA-energetics®

    Application Notes
    Covaris developed a novel automatable approach for the extraction of biomolecules from microbial samples for analysis with mass spectrometry technologies using Adaptive Focused Acoustics® technology.
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  • High-resolution Chromosome Conformation Capture: Hi-C

    Application Notes
    Hi-C
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  • Nuclei EXtraction by SONication - NEXSON

    Application Notes
    NEXSON
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  • Formaldehyde-Assisted Isolation of Regulatory Elements - FAIRE

    Application Notes
    FAIRE
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  • HiC Chromatin Immunoprecipitation - Hi-ChIP

    Application Notes
    Hi-ChIP
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  • AFA-based RNA Extraction from Mycobacteria smegmatis

    Application Notes
    RNA Extraction
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  • AFA-based Efficient DNA Extraction and Optional Mechanical Shearing from Mycobacteria smegmatis

    Application Notes
    DNA Extraction from mycobacteria smegmatis.
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  • FA-sonication Followed by Modified Protein Aggregation Capture (APAC) Enables Direct, Reproducible and Non-toxic Sample Preparation of FFPE Tissue for Mass Spectrometry-based Proteomics

    Application Notes
    FA-sonication Followed by Modified Protein Aggregation Capture (APAC) Enables Direct, Reproducible and Non-toxic Sample Preparation of FFPE Tissue for Mass Spectrometry-based Proteomics  
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  • High Quality DNA and RNA Extraction and Purification from FFPE Samples with Covaris truXTRAC® FFPE tNA Ultra Kit – Magnetic Beads

    Application Notes
    Download PDF
  • Effective disruption of Pseudomonas aeruginosa biofilms using Adaptive Focused Acoustics® (AFA®)

    Application Notes
    Download PDF
  • Single Cell/Nuclei Isolation from Fresh Frozen Tissue

    Application Notes
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