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Chromatin Fragmentation and Shearing

Covaris workflows enable standardized chromatin shearing from versatile samples such as primary cells, cultured cells, tissues, and FFPE samples. Covaris Adaptive Focused Acoustics® (AFA®) technology guarantees efficient and random chromatin fragmentation and supports nuclei extraction from hard to lyse specimens.

Contents



Covaris truChIP®: A Different Approach to Chromatin Shearing

Epigenetic characterization provides a powerful tool to better understand cell-fate changes during development and disease. However, standardizing the sample preparation steps in chromatin assays is crucial to retrieve meaningful genome-wide epigenomic data that can be compared against different experimental set-ups and different laboratories.
Covaris technology has enabled the standardization of chromatin preparation and shearing from virtually any sample input with consistent results. AFA technology in combination with optimized reagents provide researchers an easy, fast, reproducible and scalable workflow to retrieve high-quality sheared chromatin to analyze the epigenetic make-up of their sample on genome-wide scale.
Chromatin shearing with truChIP and AFA has many benefits including:
  • Lower cell number requirement​
    • Reduced cell culturing​, enable analysis of scarce clinical samples
  • Controlled shearing size range​
    • Reproducible ChIP-seq results
  • Isothermal processing​
    • Maintaining epitope integrity and no reversal of crosslinks during shearing​
  • Low detergent requirement (reduced SDS 0.1%)​
    • Suitable for all IP protocols​ and less chromatin dilutions
  • Gentle shearing​
    • Lower fixation time to avoid epitope masking
  • Universal protocol guaranteed to work with all mammalian cells​


Watch the video case study, Standardization of the ChIP Workflow Using Covaris Adaptive Focused Acoustics (AFA) to Study the Transcriptional Regulation of SOD1 in ALS Pathogenesis, presented by Byung Woo Kim, PhD Candidate, Johns Hopkins University and Hamid Khoja, PhD, Covaris
Download the Chromatin Preparation and Shearing Brochure, a presentation of Chromatin Applications enabled by AFA-energetics®
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Downstream Epigenomic Applications: Translational Discoveries Powered by AFA-energetics®

Covaris instruments powered by Adaptive Focused Acoustics® (AFA®) are the well established and trusted high-throughput chromatin platforms available that allow chromatin shearing in a 96 well format. Sample types supported include cultured cell lines, primary cells, fresh/ frozen tissues, and FFPE Fixed tissues.
AFA is widely used by scientists to decipher the regulatory potential of chromatin landscape at several layers including histone modifications, DNA methylation patterns as well as interactions with biomolecules like transcription factors, epigenetic regulators and ncRNAs. The Covaris technology has further been proven beneficial to restore multi-subunit complexes from chromatin and to study 3D chromatin organization.
AFA is the method of choice in NuGEN’s Ovation® platform and Agilent’s SureSelectXT Methyl-Seq protocols for profiling 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). It is also cited as the preferred sample prep method for meDIP-Seq, ChIP-Seq, HI-C, HI-ChIP, ChIRP-Seq, and other epigenomics applications.



Click here to download our Comprehensive Epigenomic Sample Prep Flyer
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“In the past we struggled to get reproducible chromatin shearing to a size range suitable for ChIPseq experiments. However, we were relieved that using the Covaris E220 Focused-ultrasonicator enabled us to optimize a chromatin sample preparation protocol in less than 2 weeks. The fast optimization and high degree of reproducibility in shearing, without day to day or sample to sample variation, has made our scientific life much easier.”
Stefanie Dichtl, PhD

Max-Planck-Institut für Biochemie

Resources

Chromatin Shearing Protocols
Protocols for using truChIP® Chromatin Shearing Kits with Covaris Adaptive Focused Acoustics (AFA) technology.
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Chromatin Shearing Application Notes
Case studies, tech notes and app notes to support chromatin shearing workflows powered by Covaris Adaptive Focused Acoustics (AFA) technology.
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Chromatin Shearing Videos
Learn more about Chromatin Shearing with Covaris through customer driven presentations and webinars.
LEARN MORE
Chromatin Preparation and Shearing Brochure
A Presentation of Chromatin Applications Enabled by AFA-energetics®
DOWNLOAD

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