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Automated Clinical Rapid Whole Exome Sequencing with the Covaris R230 Focused-ultrasonicator
This application note presents a case study with Radboudumc using our next generation of plate-based Focused-ultrasonicator, the R230, and a streamlined approach to high-throughput NGS library preparation.
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DNA 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 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 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 PDFAutomated Sample Preparation Combining Adaptive Focused Acoustics® (AFA®) and Single Pot Solid Phase Sample Preparation (SP3)
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Download PDFAutomated Protein Extraction from Clinical Samples with the Covaris ML230 Focused-ultrasonicator
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Download PDFHands-off Sample Preparation Workflow for Laser Capture Microdissection (LCM) Samples using Adaptive Focused Acoustics (AFA)
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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 PDFAutomated Clinical Rapid Whole Exome Sequencing with the Covaris R230 Focused-ultrasonicator
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Covaris Technical Note with RadboudumcDNA fragmentation is a critical step in the preparation of good quality libraries for next-generation sequencing (NGS). Covaris Adaptive Focused Acoustics® (AFA®) technology remains the gold standard in reproducible and robust fragmentation, especially relevant while working with precious clinical samples.
Download PDFCovaris Technical Note with Radboudumc
DNA fragmentation is a critical step in the preparation of good quality libraries for next-generation sequencing (NGS). Covaris Adaptive Focused Acoustics® (AFA®) technology remains the gold standard in reproducible and robust fragmentation, especially relevant while working with precious clinical samples.
AFA-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
The preparation of formalin-fixed and paraffin-embedded (FFPE) tissue for mass spectrometry-based (MS) proteomics relies on efficient removal of paraffin, which commonly involves toxic xylol as gold standard.
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 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 PDFCovaris DNA shearing guide for the Agilent SureSelect Target Enrichment System©
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DNA Shearing
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 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 PDFVariability in DNA Fragment Size and Distribution Analysis Across Various Fragment Analyzers
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DNA Fragmentation
Download PDFRobust Sample Preparation for Label-free or Tandem Mass Tag (TMT) LC-MS with Adaptive Focused Acoustics® (AFA®)
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Download PDFImpact of AFA-energetics™ on Enzymatic Hydrolysis of Proteins
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A novel fully automatable approach to improve trypsin digestion of protein samples is presented.
Download PDFClinical Tumor Tissue Evaluated with Illumina® TruSight™ Oncology 500 (NGS) Assay and Sheared on the Covaris ML230 Focused-ultrasonicator
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Abstract: DNA fragmentation is a critical step in the preparation of high-quality next generation sequencing (NGS) libraries. Covaris Adaptive Focused Acoustics® (AFA®) technology guarantees highly reproducible fragmentation of nucleic acids, which is especially relevant while working with valuable clinical samples for pan-cancer NGS assays such as the Illumina®’s TruSight™ Oncology 500 (TSO 500) panel. This panel was developed jointly by Illumina® and Covaris to provide high quality sequencing results. The DNA fragmentation protocol was previously released for the Covaris E220evolution, LE220-plus, and ME220 Focused-ultrasonicators [1]. In this application note, we present the ML230 and microTUBE-50 protocol to shear DNA to a fragment distribution optimized for the TSO 500 panel.
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 PDFA 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 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 PDFA Robust and Standardized Workflow to Analyze C. albicans Differential Protein Expression using Tandem Mass Tag (TMT)
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Download PDFProtein Extraction from Yeast: Comparison of the Covaris Adaptive Focused Acoustics®(AFA) Process to Conventional Bead Beating and Probe Sonication
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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 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 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 PDFHigh-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.
Download PDFOptimizing 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.
Download PDFNuclei EXtraction by SONication - NEXSON
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NEXSON
Download PDFTumor Tissue Evaluation with the Illumina® TruSight™ Oncology 500 (NGS) Assay using the Covaris R230 Focused-ultrasonicator for Clinical Research Studies
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Abstract: Next-generation sequencing (NGS) library preparation workflows comprise DNA fragmentation as an essential step. Covaris’ Adaptive Focused Acoustics® (AFA®) Technology enables precise and high-quality data from NGS workflows by ensuring efficient, reliable, and reproducible nucleic acid fragmentation. Efficient DNA shearing is particularly important when working with precious clinical research samples for Comprehensive Cancer Profiling (CCP) using pan-cancer NGS assays such as Illumina’s TruSight Oncology 500 (TSO 500) panel. The DNA fragmentation protocol for the TSO 500 panel was initially released for the Covaris Focused-ultrasonicators ME220, E220evolution, LE220, and ML230 (1,2).In this application note, we present a DNA fragmentation protocol with the R230 Focused-ultrasonicator using 96 microTUBE plates to achieve the optimal fragment size for the TSO 500 panel. A comparative sequencing analysis between samples sheared with the Illumina-validated protocol on the LE220 focused-ultrasonicator and those sheared using the Covaris developed protocol on the R230 showed equivalent or better results for samples sheared on the R230, while decreasing the sample processing time by ~30%. The results in this application note highlight that the automatable R230 enables efficient, high-throughput workflows with Covaris AFA Technology resulting in the robust, reproducible, and confident fragmentation needed for comprehensive pan-cancer panels such as Illumina´s TruSight Oncology 500 assay.
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 PDFHigh Quality DNA and RNA Extraction and Purification from FFPE Samples with Covaris truXTRAC® FFPE tNA Ultra Kit – Magnetic Beads
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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 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 PDFAFA-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.
Download PDFNucleic Acid Extraction from Laser-Capture Microdissected (LCM) FFPE Tissues
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LCM
Download PDFMicrobiome Sample Preparation: Efficient DNA Extraction and Optional Mechanical Shearing
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DNA Extraction
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 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 PDFCovaris cryoPREP® with AFA: Enabling High-resolution Diagnostic Metagenomics
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cryoPREP Applications
Download PDFCovaris truSHEAR Mechanical DNA Shearing for NGS Applications
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Mechanical DNA Shearing
Download PDFAFA-energetics®- Mediated RNA Extraction from Yeast
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Mediated RNA Extraction from Yeast
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
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.
Download PDFAssessing 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.
Download PDFAFA-based Sputum Liquification to Enable Downstream Microbial Analysis
Application Notes
Sputim Liquification
Download PDFMagnetic 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.
Download PDFChromatin Isolation by RNA Purification - ChIRP
Application Notes
ChIRP
Download PDFAutomated 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.
Download PDFCross-linked Yeast Chromatin shearing on the Covaris E210
Application Notes
Shearing cross-linked yeast samples on the Covaris E210.
Download PDFAutomated 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.
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 PDFAFA-based MALDI Biotyper Sample Preparation for Mycobacteria Colonies
Application Notes
AFA-based MALDI
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 PDFtruCOLLECT® - Blood Application Note
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Download PDFCross-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.
Download PDFHiC Chromatin Immunoprecipitation - Hi-ChIP
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Hi-ChIP
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 PDFAffinity-based Enrichment Analyses of DNA Methylation MCIp, MeDIP, hMeDIP
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MeDIP
Download PDFHigh-resolution Chromosome Conformation Capture: Hi-C
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Hi-C
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 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 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 PDFCytosine Conversion-based, Genome-wide and Targeted DNA Methylation Analysis
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Targeted DNA Methylation Analysis
Download PDFSingle Cell/Nuclei Isolation from Fresh Frozen Tissue
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Download PDFShearing DNA with Confidence: A Robust Method for Generating 3 kb DNA
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Download PDFChromatin Interaction Analysis by Paired-End Tag Sequencing - ChIA-PET
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ChIA-PET
Download PDFChromosome Conformation Capture Using Biotinylated Oligos - Capture-C
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Capture-C
Download PDFFormaldehyde-Assisted Isolation of Regulatory Elements - FAIRE
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FAIRE
Download PDFEffective disruption of Pseudomonas aeruginosa biofilms using Adaptive Focused Acoustics® (AFA®)
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Download PDFMechanical Fragmentation of RNA using the Covaris Adaptive Focused Acoustics® (AFA®) Technology for Development of mRNA-based Vaccine and Gene Therapy Platforms
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Mechanical Fragmentation of RNA using the Covaris Adaptive Focused Acoustics® (AFA®) Technology for Development of mRNA-based Vaccine and Gene Therapy Platforms
Introduction The emergence of Next-Generation Sequencing (NGS) technologies has greatly contributed to targeted gene discovery for the generation of new mRNA-based vaccines and therapeutics [1,2]. With the advancement in the world of NGS technologies, RNA sequencing (RNA-Seq) has rapidly become the method of choice for analyzing the transcriptomes of disease states [3], of biological processes, and across a wide range of clinical study designs. Synthetic mRNA has been considered an emerging biotherapeutic agent for decades [4]. However, the outbreak of the COVID-19 pandemic promoted the application of mRNA technologies in development of SARS-CoV-2 vaccines, and there has been a huge increase in interest in the research and development of mRNA-based vaccines [5]. Despite the tremendous improvement in RNA-based NGS technologies, the mRNA-based sequencing methods still present some unique challenges in production, characterization, and quality controls, especially when compared to their traditional protein-based counterparts. One critical challenge is obtaining products that are of homogeneous sequence. In this regard, NGS has proved to be a key tool to probe and address this challenge. This study, conducted in collaboration with GreenLight Biosciences, presents a mechanical mRNA fragmentation methodology that uses Covaris’ Adaptive Focused Acoustics (AFA) Technology to generate the right-sized population pivotal for successful Illumina® library preparation and reproducible sequencing data.
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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