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Variability in DNA Fragment Size and Distribution Analysis Across Various Fragment Analyzers
This application note addresses the observed bias of the determination of DNA fragment size and distribution among popular analytical instruments (Fragment Analyzer, Bioanalyzer, and TapeStation) when Tris-EDTA (TE) is used as shearing buffer.
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A Comparison of Active and Passive FFPE DNA Extraction Methods and Effects on Downstream Analysis Metrics
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Active and Passive FFPE DNA Extraction
Download PDFA Streamlined Workflow to Perform ChIP from FFPE Samples
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We demonstrate how AFA® technology combined with truXTRAC® and truChIP® effectively recovers chromatin suitable for studying histone modifications and transcription factor binding interaction events.
Download PDFActive Extraction of Native Proteins from Yeast using Covaris Adaptive Focused Acoustics® (AFA®)
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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.
Download PDFActive paraffin removal from FFPE tissues with Adaptive Focused Acoustics
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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.
Download PDFAFA-based Efficient DNA Extraction and Optional Mechanical Shearing from Mycobacteria smegmatis
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DNA Extraction from mycobacteria smegmatis.
Download PDFAFA-based MALDI Biotyper Sample Preparation for Mycobacteria Colonies
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AFA-based MALDI
Download PDFAFA-based MALDI Biotyper™ Sample Prep for MGIT™ Positive Mycobacteria Cultures
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Positive Mycobacteria Cultures
Download PDFAFA-based RNA Extraction from Mycobacteria smegmatis
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RNA Extraction
Download PDFAFA-based Sputum Liquification to Enable Downstream Microbial Analysis
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Sputim Liquification
Download PDFAFA-energetics®- Mediated RNA Extraction from Yeast
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Mediated RNA Extraction from Yeast
Download PDFAFA-energetics®-Mediated DNA Extraction from Yeast and Bacteria Using Scanning in a Labcyte 384-well Plate
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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.
Download PDFAffinity-based Enrichment Analyses of DNA Methylation MCIp, MeDIP, hMeDIP
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MeDIP
Download PDFAmplicon Shearing Using a Covaris® Focused-ultrasonicator
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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.
Download PDFAn Effect of a Shearing Process on the Re-Sequencing of the Arabidopsis thaliana Genome
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Shearing Process of Arabedopis
Download PDFAnalysis of DNA fragments using the Agilent 2100 Bioanalyzer
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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.
Download PDFAssessing FFPE DNA Quality: The “Illumina FFPE QC Kit” Enables Quantitation of Improvements in FFPE DNA Extraction Technologies
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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.
Download PDFAutomated NGS Library Construction with Eppendorf epMotion® 5075t/TMX and Covaris® Focused-ultrasonicators
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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.
Download PDFAutomated NGS Library Preparation with Beckman Biomek FXP and Covaris E220
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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.
Download PDFChromatin Interaction Analysis by Paired-End Tag Sequencing - ChIA-PET
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ChIA-PET
Download PDFChromatin Isolation by RNA Purification - ChIRP
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ChIRP
Download PDFChromosome Conformation Capture Using Biotinylated Oligos - Capture-C
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Capture-C
Download PDFCombining 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
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AFA-TUBE Case study
Download PDFCovaris cryoPREP® with AFA: Enabling High-resolution Diagnostic Metagenomics
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cryoPREP Applications
Download PDFCovaris DNA shearing guide for the Agilent SureSelect Target Enrichment System©
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DNA Shearing
Download PDFCovaris Shearing Guide for 500 Base Pairs using the 96 AFA-TUBE TPX Plate
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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.
Download PDFCovaris truSHEAR Mechanical DNA Shearing for NGS Applications
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Mechanical DNA Shearing
Download PDFCross-linked Yeast Chromatin shearing on the Covaris E210
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Shearing cross-linked yeast samples on the Covaris E210.
Download PDFCross-linked Yeast Chromatin Shearing on the Covaris Focused-ultrasonicator
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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.
Download PDFDNA Extraction from FFPE samples with Covaris Focused-ultrasonicators
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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.
Download PDFDNA Shearing for Next Generation Sequencing (NGS) with the M220 Focused-ultrasonicator
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DNA Shearing for NGS with the ME220 Focused-ultrasonicator.
Download PDFEffective disruption of Pseudomonas aeruginosa biofilms using Adaptive Focused Acoustics™ (AFA)
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AFA was used to effectively disperse Pseudomonas aeruginosa biofilms and disrupt bacterial cells in a low detergent concentration lysis buffer, increasing the efficiency of protein extraction.
Download PDFEvaluation 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.
Download PDFFA-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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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
Download PDFFormaldehyde-Assisted Isolation of Regulatory Elements - FAIRE
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FAIRE
Download PDFHiC Chromatin Immunoprecipitation - Hi-ChIP
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Hi-ChIP
Download PDFHigh-resolution Chromosome Conformation Capture: Hi-C
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Hi-C
Download PDFHigh-Throughput, Low Volume gDNA Extraction from Whole Blood Enabled by Covaris Adaptive Focused Acoustics® (AFA®) and AFA-TUBE® TPX
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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.
Download PDFLysis and Extraction of Biomolecules from Eukaryotic and Prokaryotic Cells Powered by AFA-energetics®
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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.
Download PDFLysis and High Molecular Weight DNA Extraction from Eukaryotic and Prokaryotic Cells Powered by AFA-energetics®
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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.
Download PDFMagnetic Bead-based Clean-up Using AFA-energetics®
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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.
Download PDFMicrobiome Sample Preparation: Efficient DNA Extraction and Optional Mechanical Shearing
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DNA Extraction
Download PDFNuclei EXtraction by SONication - NEXSON
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NEXSON
Download PDFNucleic Acid Extraction from Laser-Capture Microdissected (LCM) FFPE Tissues
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LCM
Download PDFOptimized 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.
Download PDFOptimized 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.
Download PDFOptimizing a Dual Fixation Protocol to Study Protein Complexes Binding to Chromatin in vivo
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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.
Download PDFOptimizing Sample Fixation and Chromatin Shearing for Improved Sensitivity and Reproducibility of Chromatin Immunoprecipitation
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Adaptive Focused Acoustic (AFA) technology provides precise control over mechanical shearing and thermal control during processing to deliver high quality chromatin for sensitive results.
Download PDFPipetting 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.
Download PDFPreparation 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.
Download PDFProtein 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.
Download PDFRelease of Microbial Cells from a Solid Matrix, Cell Lysis, and Shearing of Released Nucleic Acids Performed in a One-Step Procedure
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Release of Microbial Cells
Download PDFRNA Extraction from Mycobacteria smegmatis
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RNA Extraction
Download PDFShallow Whole Genome Sequencing Workflow - sWGS
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sWGS
Download PDFSimplifying ChIP from Primary Cells and Clinical Samples for High-throughput Epigenetic Applications
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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.
Download PDFStreamlined 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.
Download PDFTransitioning from custom amplicon-based parallel sequencing to hybrid capture-based sequencing in molecular pathology routine diagnostics
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Molecular Pahology
Download PDFtruXTRAC® FFPE RNA Extraction and Purification - Quality Metrics for Clinical Applications Powered by Adaptive Focused Acoustics® (AFA®)
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FFPE RNA Extraction
Download PDFVariability in DNA Fragment Size and Distribution Analysis Across Various Fragment Analyzers
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DNA Fragmentation
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