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Chromatin and DNA Shearing
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Let us help you select the appropriate Sonicator model and accessory for your application. Call us at 203.426.0101 or
fill out a Contact Form.

DNA and Chromatin Shearing Solutions

Qsonica offers several devices routinely used for shearing chromatin and DNA. The Q800R system is our most advanced option and offers the highest throughput. In addition, the Q700 and Q125 are very popular and effective alternatives.

Q800R System

For individual samples the easiest method is to insert a small probe directly into a sample. At Qsonica, we call this direct probe sonication. Energy is transmitted from the probe directly into the sample and the entire volume is processed very quickly.

Indirect sonication is a great option for processing very small samples as well as multiple samples. Contact a Qsonica representative to find out which option is best for you.

Platinum Genome DNA Shearing
Yeast Chromatin Prep

Introducing the New Q800R3 Sonicator System

Q800R2 Sonicator System

The Q800R3 is our 2nd generation DNA and chromatin shearing system. Improvements include an enhanced user-friendly design and quieter operation while remaining thousands of dollars less than the competition.

The system is compatible with commercially available sample tubes and is capable of processing up to 18 samples at one time.

Find out why customers like NIH, Harvard and Genentech have adopted our technology for use with multiple NGS platforms and see the new Illumina® technical note highlighting the Q800R3 system.

Publications and Protocols

Mammalian Chromatin Prep
Mammalian Chromatin prep and ChIP
Chromatin Prep
Broad Institute report
C. elegans Chromatin Prep and ChIP
C. elegans Chromatin Prep and ChIP
E. coli Genomic DNA Shearing
E. coli Genomic DNA Shearing
Illumina Technical Note
Illumina® Technical Note
Human Genomic DNA Shearing
Human Genomic DNA Shearing

Customer Reviews

“We’ve been using Qsonica Q800R in our NGS library preparation pipeline for more than two years. Over that time, we processed hundreds of samples and Q800R has proven to be an exceptionally reliable machine producing consistent results with little variability from run to run. Q800R allows us to finely control the size distribution of sheared fragments. Its ability to process up to 18 samples at a time provides more than sufficient capacity for our workflow.”

Dr. Igor Antoshechkin, Caltech

Chromatin/DNA Shearing Publications and Protocols

Q800 Protocols



Museum Genomics Illuminate the High Specificity of a Bioluminescent Symbiosis for a Genus of Reef Fish
Alison L. Gould, Allison Fritts-Penniman and Ana Gaisiner, Frontiers in Ecology and Evolution, Feb. 2021.

Isolation of extracellular vesicles from intestinal tissue in a mouse model of intestinal ischemia/reperfusion injury
Xiao-Dong Chen, Jin Zhao, et al., Biotechniques, 2020.

Adsorption of double-stranded ribonucleic acids (dsRNA) to iron (oxyhydr-) oxide surfaces: comparative analysis of model dsRNA molecules and deoxyribonucleic acids (DNA)
Katharina Sodnikar, Kimberly M. Parker, et al., Royal Society of Chemistry, 2021

More than 50% of Clostridium difficile Isolates from Pet Dogs in Flagstaff, USA, Carry Toxigenic Genotypes
Stone, N.E., et al., PLOS ONE | DOI:10.1371/journal.pone.0164504 October 10, 2016

The complete mitochondrial genome of Cerion uva uva (Gastropoda: Panpulmonata: Stylommatophora: Cerionidae)
Harasewych, M. G. et al., Mitchondrial DNA Part B: Resources, 2017 VOL. 2, NO. 1, pp 159–160, DOI: 10.1080/23802359.2017.1303343

Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis
Xindan Wang, Tung B.K. Le, Bryan R. Lajoie, et al., Genes & Dev. 2015 29: pp 1661-1675, Cold Spring Harbor Laboratory Press

Phylogenomics, biogeography and diversification of obligate mealy bug tending ants in the genus Acropyga
Blaimer et al., Molecular Phylogenetics and Evolution, Vol. 102, September 2016, pp 20-29

Sequence Capture and Phylogenetic Utility of Genomic Ultraconserved Elements Obtained from Pinned Insect Specimens
Bonnie B. Blaimer, et. al., PLoS ONE 11(8):e0161531.doi:10.137

An RNF168 fragment defective for focal accumulation at DNA damage is proficient for inhibition of homologous recombination in BRCA1 deficient cells
Munoz, et. al., 2014; Nucleic Acids Research, doi: 10.1093/nar/gku421

Enhanced virome sequencing using targeted sequence capture
Wylie, et. al., 2016; Genome Research, 25: 1910-1920

Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) Using mitochondrial genome data and insight into their mitochondrial transcription
Kayal, et. al., 2015; PeerJ, 3: e1403; doi 10.7717/peerj.1403

Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage
Sass, et. al., 2016; PeerJ, 4:e1584; doi 10.7717/peerj.1584

CXCL8 histone H3 acetylation is dysfunctional in airway smooth muscle in asthma: regulation by BET
Clifford, et. al., Am J Physiol Lung Cell Mol Physiol Vol. 308: L962–L972, February 2015

IƙB Kinase β (IKBKB) Mutations in Lymphomas That Constitutively Activate Canonical Nuclear Factor ƙB (NFƙB) Signaling*
Kai, et. al., Journal of Biological Chemistry Vol. 289, No. 38, pp26960-26972, September 2014

Farnesoid X receptor regulates forkhead Box O3a activation in ethanol-induced autophagy and hepatotoxicity
Manley, et. al., Redox Biology Vol. 2, pp991-1002, August 2014

Inhibition of mutant EGFR in lung cancer cells triggers SOX2-FOXO6-dependent Survival pathways
Rothenberg, et. al., eLife, 2015; 4:e06132. DOI: 10.7554/eLife.

DNA Damage Response Factors from Diverse Pathways, Including DNA Crosslink Repair, Mediate Alternative End Joining
Howard, et. al., PLOS Genetics, 11(1): e1004943, 2015; doi:10.1371/journal.pgen.1004943

KDM4A Lysine Demethylase Induces Site-Specific Copy Gain and Rereplication of Regions Amplified in Tumors
Black, Cell, Volume 154, Issue 3, 541-555, 18 July 2013

Enhanced in vivo Fitness of Carbapenem-resistant oprD mutants of Pseudomonas Aeruginosa Revealed Through High-throughput Sequencing
Skurnika et al., PNAS, Volume 110 No. 51, 20747–20752, 17 December 2013

Coupling Mutagenesis and Parallel Deep Sequencing to Probe Essential Residues in a Genome or Gene
Robins et al., PNAS, Volume 110 No. 9, E848–E857, 26 February 2013

TP53 supports basal-like differentiation of mammary epithelial cells by preventing translocation of deltaNp63 into nucleoli
Munne, P.M., Nature Sci. Rep., 4, 4663; DOI: 10.1038/srep04663 (2014)

Rediscovery of an Endemic Vertebrate from the Remote Islas Revillagigedo in the Eastern Pacific Ocean: The Clarion Nightsnake Lost and Found
Mulcahy et al., PLOS ONE, Volume 9 Issue No. 5, E97682, 2 May 2015

MELK is an oncogenic kinase essential for mitotic progression in basal-like breast cancer cells Wang et al., eLife 2014; 3:e01763. DOI:10.7554/eLife.01763

SH2B1 in _-Cells Promotes Insulin Expression and Glucose Metabolism in Mice
Chen, et. al., Molecular Endocrinology, Volume 28, Issue 5, 696-705, May 2014

O-GlcNAcase expression is sensitive to changes in O-GlcNAc homeostasis
Zhang, et. al., Frontiers in Endocrinology, Volume 5, Article 206, December 2014

Lysine Demethylase KDM4A Associates with Translation Machinery and Regulates Protein Synthesis
Van Rechem, AACR Cancer Discovery 2015, Volume 5, 255-263 DOI: 10.1158/2159-8290.CD-14-1326

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera
Faircloth, Molecular Ecology Resources, Volume 15, 489-201, 2015


SOX4 enables oncogenic survival signals in acute lymphoblastic leukemia
Ramezani-Rad, Blood Journal, Volume 121 (1), 1-9, October 2012

ZASC1 Stimulates HIV-1 Transcription Elongation by Recruiting P-TEFb and TAT to the LTR Promoter
Bruce, PLOS Pathogens, Volume 9, Issue 10, 1-19, October 2013

Activation of TGF-b1 Promoter by Hepatitis C Virus-Induced AP-1 and Sp1: Role of TGF-b1 in Hepatic Stellate Cell Activation and Invasion
Presser, PLOS ONE, Volume 8, Issue 2, 1-19, February 2013

Allelic Imbalance Assays to Quantify Allele-Specifi c Gene Expression and Transcription Factor Binding
Luca, Pharmacogenomics: Methods and Protocols, Methods in Molecular Biology, vol. 1015, DOI 10.1007/978-1-62703-435-7_13, 201-211, (2013)

Cdk1 Regulates the Temporal Recruitment of Telomerase and Cdc13-Stn1-Ten1 Complex for Telomere Replication
Liu, Molecular and Cellular Biology, Volume 34, Number 1, 57-70 , January 2014


Wnt Signaling Inhibits Adrenal Steroidogenesis by Cell-Autonomous and Non–Cell-Autonomous Mechanisms
Walczak et. al., Molecular Endocrinology, Volume 28, No. 9, pp 1471-1486; September 2014

Tissue-specific regulation of Igf2r/Airn imprinting during gastrulation
Marcho et. al., Epigenetics and Chromatin, Volume 8, No.10, 2015; DOI 10.1186/s13072-015-0003-y

Parasitology Canonical histone H2Ba and H2A.X dimerize in an opposite genomiclocalization to H2A.Z/H2B.Z dimers in Toxoplasma gondii
Bogado, Molecular and Biochemical Parasitology, 197 (2014) 36-42

Genome-wide Mapping and Characterization of Notch-Regulated Long Noncoding RNAs in Acute Leukemia
Trimarchi, Cell, Volume 158, 593-606, July 2014


The capacity of target silencing by Drosophila PIWI and piRNAs
Post, Cold Spring Harbor Laboratory Press, RMA Volume 20: 1977-1986, April 2015

Discontinued Models (e.g. S-4000, S-3000)

Chromatin Immunoprecipitation with Fixed Animal Tissues and Preparation for High-Throughput Sequencing
Cotney, Cold Spring Harbor Laboratory Press (2015)
Cold Spring Harb Protoc; doi: 10.1101/pdb.prot084848



Tips & Info for Chromatin/DNA Shearing

  • Sonication with a cup horn will allow you to process smaller volumes than would be possible with a standard probe-style horn. A cup horn will also reduce heat addition and eliminate any cross-contamination risk. Cup horns will also increase throughput, allowing you to process multiple samples simultaneously.
  • Direct probe sonication will result in a faster processing time for individual samples of at least 200 µl.
  • Utilizing a method to cool the samples, for instance processing in an ice bath or using a recirculating chiller, is highly recommended to prevent heat-based degradation of chromatin / DNA samples. This is particularly important when looking to assess protein-DNA interactions.
  • For general best practices, see Best Practices for Ultrasonic Homogenization.


Contact Us
Contact an Expert Contact an Expert >
Let us help you select the appropriate Sonicator model and accessory for your application. Call us at 203.426.0101 or
fill out a Contact Form.