DNA Methylation Analysis
Discover how DNA methylation influences gene expression levels
Epigenetics modifications are reversible changes that influence gene function that do not alter the DNA sequence. Importantly, these modifications have been shown to play a role in the regulation of diseases, such as cancer and neurological disorders.
DNA methylation is the most widely studied epigenetic modification. It is an important function in cellular processes, such as development, X-chromosome inactivation, and chromosome stability. In addition, methylation of certain sequences can lead to inappropriate gene silencing, such as the silencing of tumor suppressor genes in cancer cells.
DNA methylation analysis is accomplished by treating DNA with bisulfite to convert unmethylated cytosine residues to uracil while methylated cytosines remain unchanged for both capture-based and genome-wide sequencing analysis.
The Adaptive Focused Acoustics® (AFA) technology by Covaris is part of the most widely used DNA methylation analysis protocols for NGS including the Illumina TruSeq Methyl Capture EPIC Library Prep Kit and the Agilent SureSelect Methyl-Seq Target Enrichment protocol.
DNA Methylation Sample Preparation Workflow
AFA Workflow Advantage
- Fully validated workflows to process 500 ng to 3 µg of gDNA
- The only high-throughput (up to 96 samples) sample preparation workflow available
- Robust shearing for accurate methylation (CpG) profiling
|Part Number||Description||M220 Holder & Insert||ME220 Holder & Insert||S-Series Holder||E220 Evolution Rack||E220 Rack||LE220 Rack|
|520045||microTUBE AFA Fiber Pre-Slit Snap-Cap||500414 & 500489||500514 & 500526||500114||500433||500111||NA|
|520052||microTUBE AFA Fiber Crimp-Cap||NA||500514 & 500526||500114||500433||500282||500282|
|520053||8 microTUBE Strip V1||NA||500514 & 500526||NA||500430||500191||500191|
|520217||8 microTUBE-130 AFA Fiber Strip V2||NA||500518 & 500526||NA||NA||NA||NA|
|520078||96 microTUBE Plate||NA||NA||NA||NA||NA||500329|
|520130||milliTUBE-1 mL with AFA Fiber||500414 & 500422||500520 & 500534||500371||500368||500368||500368|
- Isobe K, Jung HJ, Yang CR, et al. Systems-level identification of PKA-dependent signaling in epithelial cells. Proc Natl Acad Sci USA. 2017;114(42):E8875-E8884. DOI: 10.1073/pnas.1709123114
- Donaghey J, Thakurela S, Charlton J, et al. Genetic determinants and epigenetic effects of pioneer-factor occupancy. Nat Genet. 2018;50(2):250-258. DOI: 10.1038/s41588-017-0034-3
- Gong S, Johnson MD, Dopierala J, et al. Genome-wide oxidative bisulfite sequencing identifies sex-specific methylation differences in the human placenta. Epigenetics. 2018;:1-12. DOI: 10.1080/15592294.2018.1429857
- Galonska C, Charlton J, Mattei AL, et al. Genome-wide tracking of dCas9-methyltransferase footprints. Nat Commun. 2018;9(1):597. DOI: 10.1038/s41467-017-02708-5
- Janssens S, Schotsaert M, Karnik R, et al. Zika Virus Alters DNA Methylation of Neural Genes in an Organoid Model of the Developing Human Brain. mSystems. 2018;3(1) DOI: 10.1128/mSystems.00219-17
- Kernaleguen M, Daviaud C, Shen Y, et al. Whole-Genome Bisulfite Sequencing for the Analysis of Genome-Wide DNA Methylation and Hydroxymethylation Patterns at Single-Nucleotide Resolution. Methods Mol Biol. 2018;1767:311-349. DOI: 10.1007/978-1-4939-7774-1_18
- Charlton J, Downing TL, Smith ZD, et al. Global delay in nascent strand DNA methylation. Nat Struct Mol Biol. 2018;25(4):327-332. DOI: 10.1038/s41594-018-0046-4
- Zhang YL, Sun JW, Xie YY, et al. Setd2 deficiency impairs hematopoietic stem cell self-renewal and causes malignant transformation. Cell Res. 2018;28(4):476-490. DOI: 10.1038/s41422-018-0015-9
- Olova N, Krueger F, Andrews S, et al. Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data. Genome Biol. 2018;19(1):33. DOI: 10.1186/s13059-018-1408-2
- Ziller MJ, Ortega JA, Quinlan KA, et al. Dissecting the Functional Consequences of De Novo DNA Methylation Dynamics in Human Motor Neuron Differentiation and Physiology. Cell Stem Cell. 2018;22(4):559-574.e9. DOI: 10.1016/j.stem.2018.02.012
- Rhie SK, Schreiner S, Farnham PJ. Defining Regulatory Elements in the Human Genome Using Nucleosome Occupancy and Methylome Sequencing (NOMe-Seq). Methods Mol Biol. 2018;1766:209-229. DOI: 10.1007/978-1-4939-7768-0_12
- Olohan L, Gardiner LJ, Lucaci A, et al. A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample. BMC Genomics. 2018;19(1):250. DOI: 10.1186/s12864-018-4640-y
Covaris provides tools and technologies to improve pre-analytical sample preparation, enable novel drug formulations, and manage compounds in the drug discovery process.