AFA Technology

Adaptive Focused Acoustics® (AFA®) Technology

Adaptive Focused Acoustics (AFA) is an advanced acoustic technology enabling the mechanical processing of samples through focused ultrasonication.

AFA employs highly controlled bursts of focused high-frequency acoustic energy to efficiently and reproducibly process samples in a temperature-controlled and non-contact environment.

Sample Preparation Utilizing AFA Technology

In discovery, sample preparation of biological specimens for advanced analytical and diagnostic testing is complex; and poorly controlled. Often the precision of a sample prep process is perceived as the benchmark of a good protocol --- it is independent of the sample. Unfortunately, the accuracy (i.e., the true biological status of a sample) is unknown --- discovery, by definition, does not have internal reference standards.



Covaris designed and engineered a patented acoustic-based technology platform dedicated to rapid, reproducible, and high-recovery pre-analytical sample preparation. The Covaris Adaptive Focused Acoustics (AFA) technology platform, which delivers AFA-energetics, addresses the bottleneck between initial sample collection and downstream analysis across a variety of sample types.



How AFA Technology Works

Sample processing with AFA ultrasonic energy is accomplished by precisely controlling the creation and collapse of millions of cavitation bubbles within the closed sample vessel. The AFA electronics uniquely enables focused bursts of ultrasonic acoustic energy. These acoustic processes are performed in an isothermal, non-contact environment – the water bath maintains sample temperature, and only convergent acoustic energy enters the sample vessel.



The ultra-high frequency electronics and transducer produce a wavelength of only a few millimeters which enables the ultrasonic acoustic energy to converge into a focal zone within a sample vessel immersed in the water bath.
The acoustic energy passing through the water bath causes localized pressure fluctuations which form the cavitation bubbles.  The AFA generated cavitation bubbles oscillate or grow to a critical size and then collapse which creates hydrodynamic shear stress in the sample. The oscillation and collapse of the cavitation bubbles also generates acoustic microstreaming, which generates bulk fluid flow in the sample.

Watch AFA-energetics in action

The tuning of peak incident power, duration, and duty factor control microstreaming and/or the generation of hydrodynamic shearing forces.
The Covaris Focused-ultrasonicator systems have multiple transducer configurations that enable single-sample or parallel processing of multiple samples in the acoustic focal zone.

High Frequency Acoustics

AFA technology delivers high frequency ultrasonic acoustic energy in the same acoustic range as medical applications like diagnostic imaging and ultrasound.
  • AFA technology has a short acoustic wavelength – Short acoustic wavelengths enable a tight focus of acoustic energy delivery.
  • AFA technology is focused – Acoustic energy converges onto a focal zone, improving the efficiency of energy delivery to the sample. Less overall heat is delivered to the sample.
  • AFA technology enables temperature control – Focused energy delivery within the sample enables tight temperature control as the process disrupts thermal boundary layers inside of vessels.

Focused-ultrasonicators vs Probe / Bath Sonicators

The technologically advanced AFA is often confused with more general sonication technologies because both utilize acoustic energy. Probe and Bath Sonication is a simpler technology using low frequency and unfocused acoustic energy.
Ordinary probe and bath sonicators operate at a frequency of 10 to 30 kHz, which is on the edge of the audible (sonic) range. At this frequency, the wavelength is approximately 100 mm which is larger than a typical sample vessel (~10 to 100 mm) and is unable to be controlled and focused into a sample vessel. It is also why sonicators are loud!



In addition, the unfocused acoustic energy of sonicators does NOT dissipate rapidly as the sample, the vessel and the water bath acoustic couplant are all contained in the pressure field; there is minimal thermal differential which would drive heat away from the sample. The result is the sonicator process is converted to heat energy which slowly dissipates… this is particularly deleterious for labile, heat-sensitive biomolecules. The unfocused, dispersed low frequency acoustic energy results in decreased efficiency, and therefore requires much larger amounts of acoustic energy to yield a cavitation event. Heat generated from the excess energy affects the sample, resulting in thermal molecular damage and non-uniform sample processing. In addition, probe sonicators also directly contact the sample, introducing the risk of contamination.
AFA is more reproducible because the acoustic energy is delivered in a non-contact, highly focused manner more closely scaled to the vessel size eliminating the risk of damage from heat or contamination. AFA enables higher quality, higher recovery, rapid sample preparations.

Applications of AFA Technology



AFA technology is well known for shearing DNA and RNA for Next Generation Sequencing (NGS) and is setting new standards in FFPE extraction for nucleic acids and proteins, cfDNA extraction, epigenomics, proteomics, cell lysis and more. When extracting biomolecules from difficult samples, AFA technology can be paired with dry cryopulverization, using the cryoPREP Dry Pulverizers, to disrupt the samples prior to downstream processing in a more efficient manner than current methods such as mortar & pestle. Integrating Covaris into your workflow enables a complete, high-quality, sample preparation solution.
  • : Inline Thermocouple for Flow Cell (500384)

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  • 15µl DNA Shearing with microTUBE-15

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  • 96 AFA-TUBE™ TPX Plate (PN 520272)

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  • 96 Well Mixing powered by Covaris AFA

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

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  • A New Effective Method for the Disruption of Pseudomonas aeruginosa Biofilms Using Adaptive Focused Acoustics™(AFA)

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  • A New Workflow for Small Tissue Sample Preparation: Freeze, Fracture, and Extract

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  • A Novel Solution to FFPE Extraction Challenges for Downstream Clinical Assays

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  • A Paradigm Shift: Desiccated Stabilized Transport System for Viral Specimen Collection

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  • A Streamlined Workflow to Perform ChIP from FFPE Samples

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  • Accurate and Cost-Effective Discovery of Active Gene Regulatory Interactions using Arima-HiChiP

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  • Achieve Highly Reproducible and Accurate Results … Covaris Workflow for DNA Fragmentation

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  • Acoustic Thawing powered by Covaris AFA

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  • Active Deparaffinization Drives Superior Yields, Quality and Sequencing Coverage from FFPE Tissue Samples

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  • Active Extraction of Native Proteins from Yeast using Covaris Adaptive Focused Acoustics® (AFA®)

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  • Active organic solvent-free paraffin removal is the key to efficient extraction of NGSquality DNA and RNA from FFPE tissues

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  • Active paraffin removal from FFPE tissues with Adaptive Focused Acoustics

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  • Adaptive focused acoustic lysis for high-throughput shotgun metagenomics and proximity ligation

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  • Adaptive Focused Acoustics: The One Solution for all shearing needs

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  • AFA microTUBES – engineered for Ultrasonics

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  • AFA ultraCUBE Water Management System USER MANUAL

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

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  • AFA-based MALDI Biotyper Sample Preparation for Mycobacteria Colonies

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  • AFA-based MALDI Biotyper™ Sample Prep for MGIT™ Positive Mycobacteria Cultures

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  • AFA-based RNA Extraction from Mycobacteria smegmatis

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  • AFA-based Sputum Liquification to Enable Downstream Microbial Analysis

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  • AFA-energetics®- Mediated RNA Extraction from Yeast

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  • AFA-energetics®-Mediated DNA Extraction from Yeast and Bacteria Using Scanning in a Labcyte 384-well Plate

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  • AFA-Liposome™ Formation: DOPE Based 2 mL

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  • AFA-Liposome™ Formation: HSPC/PEGDSPE2000/Cholesterol

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  • AFA-Liposome™ Formation: Hydrogenated Egg Lecithin 2 mL

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  • AFA-Liposome™ Formation: Phospholipon 90G 2mL

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  • AFA-Liposome™ Formation: Phospholipon 90G M220 130µL

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  • AFA-Nanocrystal™ Production

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  • AFA-Nanoemulsion™ : Rice Bran Oil in Water 2 mL

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  • AFA-Nanoemulsion™ : Rice Bran Oil in Water Continuous Process Stream 2 mL Process Vessel

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  • AFA-Nanoemulsion™ : Rice Bran Oil in Water Continuous Process Stream 22mL Process Vessel

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  • AFA-Nanoemulsion™: Rice Bran Oil in Water 300µ

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  • AFA-TUBE™ The Family of AFA Consumables Designed for Higher Throughput Automation

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  • AFA-TUBE™ TPX Strip (PN 520275)

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

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  • Amplicon Shearing Using a Covaris® Focused-ultrasonicator

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  • An Automated High-throughput ChIP-Seq Workflow using Covaris Adaptive Focused Acoustics® (AFA®) System for Accelerated IP

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  • An Effect of a Shearing Process on the Re-Sequencing of the Arabidopsis thaliana Genome

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  • An optimized single tube workflow for robust, low input NGS library preparation

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  • Analysis of DNA fragments using the Agilent 2100 Bioanalyzer

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  • Assessing FFPE DNA Quality: The “Illumina FFPE QC Kit” Enables Quantitation of Improvements in FFPE DNA Extraction Technologies

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  • Automated cryoPREP® System User Manual

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

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  • Automated NGS Library Preparation with Beckman Biomek FXP and Covaris E220

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  • CAUTION – CARE OF ACRYLIC TANKS

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  • Cavitation Based Bubble

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  • Cell Lysis Citations on Sample Preparation

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  • Centrifuge 8 microTUBE Strip V2 Adapter

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  • CH05 Chiller and AFA ultraCUBE Water Hose Replacement Warning

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  • Chromatin Brochure

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  • Chromatin Interaction Analysis by Paired-End Tag Sequencing – ChIA-PET

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  • Chromosome Conformation Capture Using Biotinylated Oligos – Capture-C

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  • Co-extraction of RNA and DNA by Covaris Adaptive Focused Acoustics® (AFA®) Enables Genome-scale Analysis for Most FFPE Tissues

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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

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  • Comprehensive Epigenomic Sample Prep Workflow Solutions

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  • Confidently Profile the Epigenetic Landscape within Archived FFPE Samples using truChIP®

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  • Control Microplate Dynamics with Covaris AFA Mixing and Dissolution

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  • Control Nucleation and Crystal Growth During Continuous Flow API Production

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  • Covaris 8 microTUBE Strip V2

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  • Covaris 96 microTUBE Plates

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  • Covaris cryoPREP® with AFA: Enabling High-resolution Diagnostic Metagenomics

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  • Covaris DNA shearing guide for the Agilent SureSelect Target Enrichment System©

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  • Covaris DNA Shearing Verification Kit (PN 520120)

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  • Covaris DNA Shearing Verification Kit for the 96 AFA-TUBE TPX (PN 520291) on the LE220-plus and R230 (PN 520120)

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  • Covaris DNA Shearing Verification Kit for the AFA-TUBE TPX on the LE220-plus

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  • Covaris LE220R-plus integration with Liquid Handler

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  • Covaris M220 Focused-ultrasonicator

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  • Covaris Shearing Guide for 500 Base Pairs using the 96 AFA-TUBE TPX Plate

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  • Covaris truChIP– the Next Generation Technology for Chromatin Shearing

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  • Covaris truSHEAR Mechanical DNA Shearing for NGS Applications

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  • Covaris truSHEAR™ Precision DNA Shearing Enables Precision Medicine

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  • Covaris-certified Consumable Guide

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  • CP01 cryoPREP® Manual Dry Pulverizer User Manual

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  • Cross-linked Yeast Chromatin shearing on the Covaris E210

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  • Cross-linked Yeast Chromatin Shearing on the Covaris Focused-ultrasonicator

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  • cryoPREP Introduction to Tissue Dry-pulverization

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  • cryoPREP® Product Line The non-contact, rapid, dry pulverization system for biological tissue

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  • December 2019 Newsletter

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  • Degas, Thaw, Lysis powered by Covaris AFA

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  • Desiccated Stabilized Transport System: Viral RNA Flyer

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  • Dissolution of a gum powered by Covaris AFA

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  • Dissolution of Carbon Nanotubes powered by Covaris AFA

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  • Dissolution of over-dried sucrose powered by Covaris AFA

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  • DNA Extraction from FFPE samples with Covaris Focused-ultrasonicators

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  • DNA Extraction of Lung Cancer Samples for Advanced Diagnostic Testing

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  • DNA miniTUBE – Clear

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  • DNA miniTUBE – Blue for 220 Series

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  • DNA miniTUBE – Clear for 220 Series

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  • DNA miniTUBE – Red for 220 Series

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  • DNA miniTUBE- Blue

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

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  • DNA Shearing Protocols for Ion Torrent Platforms with the M220 Focused-ultrasonicator

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  • DNA Shearing Quick Guide: microTUBE-15 with S220/E220 Focused-ultrasonicator.

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  • DNA Shearing with microTUBEs (<1.5kb fragments)

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  • DNA Shearing with microTUBEs (<1.5kb fragments) S220/E220

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  • E-series Robotic User Manual

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  • E/LE220 Series SonoLab 7 User Manual

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  • E220 / E220x (E-Series) High Performance Multi-Sample Preparation System

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  • E220evolution

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  • E220evolution User Manual

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  • Effective disruption of Pseudomonas aeruginosa biofilms using Adaptive Focused Acoustics™ (AFA)

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  • Evaluation of a New Protein Extraction Method Using an Advanced Acoustic Technology for Identification of Filamentous Fungi by MALDI-TOF MS

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  • Evaluation of Next Generation Library Preparation using DNA Extracted from Dried Blood Spots using truXTRAC® DBS DNA kit

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  • Experienced User Quick Guide: truXTRAC® FFPE total Nucleic Acid Plus Kit – Column

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  • Experienced User Quick Guide: truXTRAC® FFPE total Nucleic Acid Plus Kit –Magnetic Beads

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  • Extraction and Purification of NGS Grade DNA and RNA from FFPE

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  • Extraction of RNA from Laser-Capture Microdissected Clinical FFPE Samples

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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

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  • February 2019 Newsletter

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  • February 2020 Newsletter

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  • FFPE RNA Quality

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  • FFPE Sample Preparation with Covaris

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  • Five-Minute Ultrasonic Inactivation and Protein Extraction of Mycobacteria for Identification by MALDI-ToF MS

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  • Focused-ultrasonicators Standardize Sample Preparation for a Variety of Application Areas

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  • Formaldehyde-Assisted Isolation of Regulatory Elements – FAIRE

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  • Formulation and Drug Delivery Breakthrough processing for poorly soluble API’s

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  • Four Minute Mycobacterium sp. Sample Preparation Process for MALDI-TOF Identification

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  • g-TUBE for DNA Shearing

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  • Hi Power Mixing powered by Covaris AFA

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  • HiC Chromatin Immunoprecipitation – Hi-ChIP

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  • High Molecular Weight DNA Extraction and Purification from Whole Blood – Fully-automatable and High-Throughput

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  • High Molecular Weight DNA Sample and Library Preparation For Long-Read Sequencing Using Clinical Tissue Specimens

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  • High Performance Multiplexed Target Enrichment Sequencing from FFPE Tissues

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  • High Throughput nucleic acid fragmentation for High Throughput next-gen sequencing applications

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  • High value tissue samples deserve high quality preparation, prior to committing to high cost analysis

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  • High-resolution Chromosome Conformation Capture: Hi-C

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  • High-throughput High Molecular Weight DNA Extraction from Human Tissues for Long-read Sequencing

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  • High-Throughput, Low Volume gDNA Extraction from Whole Blood Enabled by Covaris Adaptive Focused Acoustics® (AFA®) and AFA-TUBE® TPX

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  • How Adaptive Focused Acoustics® Works

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  • How to Use the Covaris cryoPREP System

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  • Improved workflow for FFPE tissue Nucleic Acid extraction

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  • Incorporating Covaris Focused-ultrasonication into a Fully Automated Diagnostic NGS Workcell

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  • January 2019 Newsletter

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  • June 2019 Newsletter

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  • KingFisher™ Duo Prime Purification in combination with the truXTRAC® FFPE total NA Kit

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  • KingFisher™ Duo Prime Purification in combination with the truXTRAC® FFPE total NA Plus Kit

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  • KingFisher™ Duo Prime Purification in combination with the truXTRAC® cfDNA Kit

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  • LE220 (-plus, R-plus, and Rsc) Setup & Instruction Manual

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  • LE220-plus Adding A Method via Admin Privileges

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  • LE220-plus Enabling Barcode Scanning

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  • LE220-plus Focused-ultrasonicator

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  • LE220-plus Pulsing Method Creation

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  • LE220R-plus Flyer

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  • LE220Rsc Focused-ultrasonicator: High-performance, Scalable, Automated Sample Preparation

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  • Liquid Biopsy truXTRAC cfDNA

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  • Loading and Rebuilding Process Vessel SST 2ml (500350) Using Prep-Station (500345)

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  • Loading and Rebuilding Process Vessel SST 300µl (500328) Using Prep Station (500333)

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  • Loading and unloading Process Vessel SST 2ml (500350) onto Holder Process Vessel SST 2ml (500347)

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  • Loading and unloading Process Vessel SST 300µl (500328) onto Holder Process Vessel SST 300µl (500319)

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  • Low Power Mixing powered by Covaris AFA

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

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  • Lysis and High Molecular Weight DNA Extraction from Eukaryotic and Prokaryotic Cells Powered by AFA-energetics®

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  • M-Series Focused-ultrasonicators

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  • M220 Focused-ultrasonicator Setup & Instruction Manual

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  • Magnetic Bead-based Clean-up Using AFA-energetics®

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  • Maintaining SonoLab 7 Log and History Files

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  • Maintaining SonoLab 7 Log and History Files

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  • March 2019 Newsletter

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  • ME220 Continuous Method Creation

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  • ME220 Focused-ultrasonicator New User Set-up

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  • ME220 Focused-ultrasonicator overview

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  • ME220 Pulsing Method Creation

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  • ME220 User Manual

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  • Microbiome Sample Preparation: Efficient DNA Extraction and Optional Mechanical Shearing

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  • Microbiome Samples: Reveal the Hidden Diversity Using Adaptive Focused Acoustics® (AFA®)

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  • microTUBE-500 AFA Fiber Screw-Cap

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  • ML230 DNA Shearing Protocols

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  • ML230 Flyer

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  • ML230 Focused-ultrasonicator The Parallel Sample Processing PlatformPowered by Covaris Adaptive Focused Acoustics® (AFA®)

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  • ML230 User Manual

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  • Muscle Tissue Disruption powered by Covaris AFA

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  • Nano-suspension formation via crystallization (Felodipine based)

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  • NGS Quality Sample Preparation with Covaris Adaptive Focused Acoustics (AFA)

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  • NGS-Quality DNA and RNA Extraction from FFPE Tissue

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  • Non-contact mixing from Covaris

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  • Novel, Automated Co-extraction of High-quality DNA and RNA from a Single FFPE Sample

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  • Nuclei EXtraction by SONication – NEXSON

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  • Nucleic Acid Extraction from Laser-Capture Microdissected (LCM) FFPE Tissues

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  • October 2019 Newsletter

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  • Optimized Covaris truXTRAC® FFPE RNA Protocol for Isolating RNA from Laser-Capture Microdissected (LCM) FFPE Tissue for Next Generation Sequencing

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  • Optimized Protocol for Robust Chromatin Shearing and Immunoprecipitation of Human Pancreatic Islets using the Covaris® Focused-ultrasonicator

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  • Optimizing a Dual Fixation Protocol to Study Protein Complexes Binding to Chromatin in vivo

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  • Optimizing a Dual Fixation Protocol to Study Protein Complexes Binding to Chromatin in vivo

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  • Optimizing Sample Fixation and Chromatin Shearing for Improved Sensitivity and Reproducibility of Chromatin Immunoprecipitation

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  • Parallel Processing (Top View) powered by Covaris AFA

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  • Performing ChIP Using Low Amounts of Frozen Mouse Brain Tissue

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  • Pipetting Best Practices for Covaris 96 microTUBE Plate and 8 microTUBE Strip in Automated Liquid Handlers

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  • Poster Presentation from ASMS 2020: Standardized Sample preparation Workflows for Clinical Proteomics

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  • Preparation of whole body Caenorhabditis elegans extracts for chromatin immunoprecipitation using the Covaris® S220 Focused-ultrasonicator

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