Application Notes

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

Application Notes

DNA Shearing for NGS with the ME220 Focused-ultrasonicator.

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.

Automated Sample Preparation Combining Adaptive Focused Acoustics® (AFA®) and Single Pot Solid Phase Sample Preparation (SP3)

Application Notes

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.

Covaris DNA shearing guide for the Agilent SureSelect Target Enrichment System®

Application Notes

DNA Shearing

Variability in DNA Fragment Size and Distribution Analysis Across Various Fragment Analyzers

Application Notes

DNA Fragmentation

Robust Sample Preparation for Label-free or Tandem Mass Tag (TMT) LC-MS with Adaptive Focused Acoustics® (AFA®)

Application Notes

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.

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.

Clinical Tumor Tissue Evaluated with Illumina® TruSight™ Oncology 500 (NGS) Assay and Sheared on the Covaris ML230 Focused-ultrasonicator

Application Notes

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.

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.

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.

A Robust and Standardized Workflow to Analyze C. albicans Differential Protein Expression using Tandem Mass Tag (TMT)

Application Notes

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

Application Notes

cryoPREP Applications

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.

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.

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.

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.

Chromatin Isolation by RNA Purification - ChIRP

Application Notes

ChIRP

Measuring Sodium Dodecyl Sulfate Carryover In Protein Hydrolysates Prepared via Protein Aggregation Capture

Application Notes

The Covaris PAC workflow is a method for extracting and purifying nucleic acids and liquid chromatography mass spectrometry (LC-MS) ready peptide digests from cultured cells and human tissue. The PAC process was originally designed to function as a protein isolation and purification technique that could be performed in a single vessel. The workflow utilizes paramagnetic beads to indiscriminately bind proteins and to enable the removal of harsh chemicals which are often essential for lysis and solubilization. PAC is highly compatible with a wide range of sample inputs as well as detergents, chaotropes, salts, and solvents [3]. Proteolytic cleavage is performed on-bead, and allows for highly efficient and unbiased sample recovery. The Covaris PAC workflow requires minimal liquid transfer; the workflow starting from cell culture and deparaffinized FFPE tissue can be performed in a single plate format and is fully automatable. The extraction process is facilitated through the use of lysis buffers which contain chaotropic agents or detergents like sodium dodecyl sulfate. While PAC is reputed to generate samples with a high degree of purity, carryover of SDS into the final peptide lysate remains a possible concern due to its suppressive effects on analyte ion signal and fouling of equipment during LC-MS [4]. A method was published describing the colorimetric quantitation of SDS in biological samples [5]. The reported approach relies on measuring the interaction of SDS with the extraction efficiency of methylene blue into chloroform. This application note describes the quantitation of SDS carryover in final tryptic digests of the Covaris PAC workflow to determine if they contain any significant degree of contaminating detergent.

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.

HiC Chromatin Immunoprecipitation - Hi-ChIP

Application Notes

Hi-ChIP

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.

Single Cell/Nuclei Isolation from Fresh Frozen Tissue

Application Notes

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.

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

Application Notes

Shearing Process of Arabedopis

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

Application Notes

MeDIP

High-resolution Chromosome Conformation Capture: Hi-C

Application Notes

Hi-C

Cytosine Conversion-based, Genome-wide and Targeted DNA Methylation Analysis

Application Notes

Targeted DNA Methylation Analysis

Covaris truCOVER Library Prep Kit: A Streamlined, PCR-Free WGS Workflow for Enhanced NGS Library Performance and Data Quality

Application Notes

The truCOVER WGS PCR-free Library Prep Kit was developed to overcome the challenges of modern WGS workflows by offering a streamlined, scalable, and cost-effective solution. Its simplified workflow, compatibility with diverse sample types, and consistent performance make it a reliable tool for researchers seeking high-quality sequencing data. Sequencing analysis conducted in-house and in collaboration with Dana-Farber Cancer Institute Molecular Biology Core Facilities and Genique Lifesciences demonstrated improved genome coverage and enhanced variant detection accuracy with the Covaris workflow as compared to leading supplier workflows.

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

Application Notes

ChIA-PET

Mechanical Fragmentation of RNA using the Covaris Adaptive Focused Acoustics® (AFA®) Technology for Development of mRNA-based Vaccine and Gene Therapy Platforms

Application Notes

Mechanical Fragmentation of RNA using the Covaris Adaptive Focused Acoustics® (AFA®) Technology for Development of mRNA-based Vaccine and Gene Therapy Platforms

Formaldehyde-Assisted Isolation of Regulatory Elements - FAIRE

Application Notes

FAIRE

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

Application Notes

High-throughput RNA-Seq of Low Input and Clinically Derived FFPE Samples using Covaris Adaptive Focused Acoustics® (AFA®) Technology

Application Notes

RNA-Seq data not only reveal gene expression levels but also provide insight into RNA processing patterns and allele-specific expression. However, due to the variable quality and quantity of RNA obtained from FFPE and single-cell samples, the library preparation process often presents challenges and requires significant improvements. To address these challenges, Covaris Adaptive Focused Acoustics (AFA) Technology offers a flexible solution for customers with varying throughput, batch, and automation needs. This technology enables the routine implementation of large-scale RNA sequencing for degraded samples by using a novel method of RNA fragmentation combined with reduced sample volumes for library preparation.

Optimizing Laboratory Efficiency with truCOVER WGS PCR-Free Library Prep Through Pooling by Mass

Application Notes

Key Advantages of Mass Pooling with truCOVER Features: • High quantification concordance between Qubit and qPCR [1] • Enables Qubit-only pooling, eliminating time- consuming qPCR-based QC steps Benefits: • Reduces preparation and pooling time by up to 30% [1], while lowering overall costs by eliminating qPCR-based QC steps—saving both time and reagent expenses • Delivers robust and reproducible >30X coverage across diverse sample types—with ±6% coverage variation and ±1.9% insert size variation at 99% confidence—ensuring highly reliable and unbiased sequencing metrics [2, 3].

Optimization of Insert Sizes for Illumina’s WGS with a Combination of Covaris AFA-based Shearing and Bead-based Size Selection

Application Notes

In this study, we provide a short technical note on optimization of insert size using Covaris Adaptive Focused Acoustics® (AFA®) technology in conjunction with bead-based size selection for more robust and reproducible library prep to improve overall NGS results.

High-Fidelity Whole-Genome Sequencing from Low-Input, Formalin-Fixed Paraffin-Embedded (FFPE) DNA using the truCOVER® WGS Library Prep with Amplification

Application Notes

Formalin-fixed, paraffin-embedded (FFPE) FF12878 represents an invaluable resource for clinical and translational research, linking genomic data to long-term clinical outcomes. However, the fixation process is known to severely damage DNA, causing fragmentation, chemical modifications such as cytosine deamination, and DNA-protein cross-linking [1]. These damage types present significant challenges for next-generation sequencing (NGS), often leading to low library complexity, high duplication rates, sequencing artifacts, and biased amplification across the genome leading to confounding identification of single nucleotide variants (SNV) [2]. Consequently, genomic data derived from FFPE samples can be unreliable, complicating the accurate detection of variants, particularly in clinically relevant regions [3].

truCOLLECT® Solution: High-Fidelity Genomic DNA Extraction from Decentralized, Dry-Stabilized Whole Blood for Biomarker Identification

Application Notes

Blood-quality genomic data from decentralized sample collection

Saliva and other minimally invasive collection methods can introduce variability, contamination, and sequencing failure, driving up cost and delaying results.The truCOLLECT® Solution enables decentralized blood collection while maintaining the data quality required for high-performance sequencing workflows. See how Ambry Genetics achieved blood-quality genomic data without the failure risk of alternative collection methods.

Unlock Your FFPE Samples. Unleash Your Comprehensive Genomic Profiling Workflow.

Application Notes

Comprehensive Genomic Profiling (CGP) is a powerful tool to identify somatic mutations and/or other genetic changes in tissue samples through the analysis of hundreds of genes. CGP testing activities are rapidly growing as they fuel advances in oncology research, clinical studies, and medical care. However, the effectiveness of genomic characterization is often limited by the critical upstream step of nucleic acid extraction, particularly from Formalin-Fixed Paraffin-Embedded (FFPE) tissues. These samples are challenging to process due to variability in quality caused by tissue size, fixation conditions, block age, tumor heterogeneity, and position within the block, often resulting in low-quality or insufficient genetic material (Quantity Not Sufficient, or QNS) [1–4]. This can lead to high sample failure rates, costly rework, and critical delays in testing. Some CGP tests have shown assay failure rates as high as 17% [5].

Optimizing Laboratory Efficiency with truCOVER™ WGS PCR-Free Library Prep: Pooling by Volume

Application Notes

The truCOVER WGS PCR-free Library Prep Kit leverages Covaris Adaptive Focused Acoustics® (AFA®) technology to ensure precise DNA fragmentation. The kit supports both mass-based and volume-based pooling methodologies, providing flexibility tailored to diverse laboratory workflows. Robust quality control measures and streamlined pooling protocols further simplify sample preparation.

When Less is More — truCOVER™ Library Amplification Kit: Empowering Next-Generation Sequencing (NGS) with Superior Amplification

Application Notes

Challenges in DNA Amplification for Next-Generation Sequencing Next-Generation Sequencing (NGS), encompassing methodologies such as Whole Genome Sequencing (WGS) and Whole Exome Sequencing (WES), has profoundly advanced genomic research and clinical diagnostics [1]. Nevertheless, a persistent bottleneck within NGS workflows pertains to the efficient and accurate amplification of DNA, particularly when dealing with limited or degraded sample inputs [2]. Conventional amplification techniques often introduce biases, leading to non-uniform coverage, preferential amplification of regions with extreme GC content, and a subsequent compromise in data quality and variant calling precision [3].

Whole Transcriptome Sequencing from Degraded FFPE Samples: A Fast Workflow to Deliver Robust Gene Fusion Detection

Application Notes

This technical note highlights the downstream impact and economic value of integrating Whole Transcriptome Sequencing (WTS) into precision oncology workflows, particularly for degraded FFPE samples. It demonstrates how the Covaris truCOVER® Total RNA Library Prep Kit, powered by Adaptive Focused Acoustics® (AFA®) technology, delivers a streamlined ~4-hour workflow with reduced hands-on time, broad input compatibility (10–500 ng; DV200 ≥30%), and ultra-efficient rRNA depletion (<1%).

Validation data show high alignment rates, strong strand specificity, and superior exonic read distribution compared to alternative RNA library prep workflows, maximizing informative transcript coverage for differential gene expression and structural variant analysis. Notably, the workflow enables Robust gene fusion detection, achieving 100% sensitivity (18/18 targets) in reference FFPE standards while maintaining library complexity and optimal insert sizes critical for spanning fusion junctions.

Overall, the study supports truCOVER Total RNA Library Prep as a reproducible, cost-efficient, and automation-ready solution for extracting high-quality transcriptomic insights from challenging and degraded samples.

Is Phlebotomy a Bottleneck for Genomics Studies? Rethinking and Redesigning Blood Collection Infrastructure for Large Scale Biology

Application Notes

Advances in detection technologies have enabled better molecular insights across a wide array of Omics studies – from genomics to transcriptomics, and from proteomics to metabolomics. A combination of the data from all the omics studies are increasingly applied to large population cohorts, longitudinal clinical studies, and decentralized clinical trials. While the end-detection technologies experienced some significant developments in the last two to three decades, the sample collection and preparation approaches continue to be challenging, complex, time consuming, and lack standardization protocols. The infrastructure used to obtain biospecimens, especially, whole blood has evolved far more slowly than the analytical technologies used to study them. Most blood samples used in research and diagnostics are still obtained through venous phlebotomy performed in clinical environments. While historically adequate for diagnostic testing and small studies, this model presents growing limitations for large scale studies. Workforce shortages, geographic constraints, cold-chain logistics and variability in sample handling collectively limit the scalability of blood-based molecular profiling. Emerging remote blood collection technologies, including stabilized capillary blood sampling systems such as Covaris’ truCOLLECT® Whole Blood Collection Solution offer a potential pathway toward decentralized biospecimen infrastructure compatible with modern analytical workflows. Here we examine how evolving blood collection technologies may reshape biological sampling for the laboratories focused on Genomics.

Maximizing Insights from Minimal Input: High-Quality WGS Libraries from as Little as 0.1 Nanograms of DNA using the truCOVER® WGS Library Prep Kit with Amplification

Application Notes

The ability to perform whole-genome sequencing (WGS) from samples with limited DNA input remains a significant challenge in genomics [1,2]. Conventional library preparation kits often fail to generate high-quality sequencing libraries from low nano- and sub-nanogram amounts of DNA, frequently resulting in sample loss, decreased depth of coverage, and inconclusive sequencing outcomes [3]. These difficulties are further compounded when working with microbial genomes that exhibit variable GC content, as amplification and coverage biases are particularly noticeable under low-input conditions [4].