Methylation mapping is inherently more complex than genome sequencing, because the methylome exhibits much more variability than the genome. While each of us has only one genome, methylomes vary with age and between tissues, are altered by environmental factors, and show aberrations in diseases. Thus, mapping a person’s methylome at different ages, in different tissue types, and in various disease states is expected to yield valuable information about the mechanisms that lead to aging and disease.

Methods for DNA Methylation Analysis

A variety of methods to tackle the complex question of DNA methylation have evolved over time including bisulfite conversion, digestion with methylation-sensitive restriction enzymes, and antibody- or 5-methylcytosine binding protein–based purification of methylated DNA.

The 5500xl Genetic Analyzer enables accurate, ultra–high-throughput sequencing, mapping, and counting of short DNA reads and, in combination with any of the above methylation profiling strategies, can be used for comprehensive, genome-wide mapping of methylation sites.

Three genome-wide methylation profiling strategies are available for the 5500xl Genetic Analyzer. The size of the target genome and the level of resolution you require will determine which solution will best suit your needs.

Enzymatic Genome Partitioning

Methylation-sensitive and methylation-dependent restriction enzymes are used to compartmentalize the genome into methylated and unmethylated fractions. This method allows the methylation status of both unique and repetitive DNA sequences to be analyzed, which is not possible using microarrays. Deep sequencing with the 5500xl Genetic Analyzer then allows comprehensive, genome-wide methylation profiles to be constructed.

Learn more at genome.cshlp.org.

 

Enriching for Methylated DNA

MethylMiner™ Methylated DNA Enrichment Kit employs the methylCpG binding domain (MBD) of the human MBD2 protein to enrich double-stranded DNA based on CpG methylation density, with increased sensitivity over antibody-based methods. The MethylMiner™ Methylated DNA Enrichment Kit combined with ultra-deep sequencing on the 5500xl Genetic Analyzer provides a cost-effective and seamless method for profiling genome-wide methylation patterns.

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Bisulfite Conversion

All unmethylated cytosines in the genome are converted to uracil when treated with bisulfite (methylated cytosines are unaltered by this treatment). In this way, bisulfite conversion preserves the methylation status of every CpG prior to sequencing using the 5500xl Genetic Analyzer. The accuracy and throughput of the 5500xl Genetic Analyzer gives you the power to interrogate every CpG in the genome for whole-methylome analysis. Bisulfite conversion can also be coupled with the MethylMiner™ Methylated DNA Enrichment Kit for individual CpG analysis of the methylated fraction of the genome.

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Step-by-Step Guide to DNA Methylation Analysis

The three traditional methylation profiling strategies can be successfully adapted onto SOLiD® System for a much more complete epigenomic mapping. Depending upon your specific scientific question, you might consider the following approaches:

  • Enzymatic Genomic Partition
    Separate the genome into methylated and unmethylated compartments with methylation sensitive or dependent restriction enzymes.
  • Bisulfite Conversion
    Chemical modification of the unmethylated cytosines in the genome.
  • Enrichment of Methylated DNA
    Purification of methylated genomic fragments.

For help choosing the best strategy for your research, please contact your field application specialist.

Ordering Information

Sku Name Size Price Qty
ME10025 MethylMiner™ Methylated DNA Enrichment Kit 1 kit USD 485.00

Ordering Information

Sku Name Size Price Qty
4463592 AB Library Builder™ System, self installation 1 instrument Request a Quote  
4463794 AB Library Builder™ System, service installation 1 instrument Request a Quote  
4465657 AB Library Builder™ Barcode Reader 1 instrument Request a Quote  
4463776 AB Library Builder™ Tip and Tube Rack 1 unit USD 1,294.00
4463762 Library Builder™ Fragment Core Kit for the SOLiD™ 4 System 1 kit USD 1,312.00
4465602 AB Library Builder™ Builder D-Rings 1 unit USD 48.90
4465603 AB Library Builder™ Builder D-Ring Tool 1 unit USD 91.75
4463763 Library Builder™ Fragment Core Kit for 5500 Genetic Analysis Systems 1 kit USD 1,312.00
4464412 5500 SOLiD™ Fragment Library Core Kit 1 kit USD 1,100.00
4464411 5500 SOLiD™ Fragment Library Standard Adaptors 1 kit USD 458.00
4464404 5500 SOLiD™ Fragment Library Barcode Adaptors 1ndash;96 1 kit USD 5,090.00
4464405 5500 SOLiD™ Fragment Library Barcode Adaptors 1-16 1 kit USD 1,018.00
4464406 5500 SOLiD™ Fragment Library Barcode Adaptors 17ndash;32 1 kit USD 1,018.00
4464407 5500 SOLiD™ Fragment Library Barcode Adaptors 33ndash;48 1 kit USD 1,018.00
4464408 5500 SOLiD™ Fragment Library Barcode Adaptors 49ndash;64 1 kit USD 1,018.00
4464409 5500 SOLiD™ Fragment Library Barcode Adaptors 65ndash;80 1 kit USD 1,018.00
4464410 5500 SOLiD™ Fragment Library Barcode Adaptors 81ndash;96 1 kit USD 1,018.00
4449637 SOLiD™ Fragment Library Barcoding Kit 1-96, includes all 6 DNA Barcoding Modules 96 barcodes USD 6,040.00
4444836 SOLiD™ Fragment Library Barcoding Kit Module 1-16 16 barcodes USD 1,208.00
4449636 SOLiD™ Fragment Library Barcoding Kit Module 17-32 16 barcodes USD 1,208.00
4449635 SOLiD™ Fragment Library Barcoding Kit Module 33-48 16 barcodes USD 1,208.00
4449641 SOLiD™ Fragment Library Barcoding Kit Module 49-64 16 barcodes USD 1,208.00
4449642 SOLiD™ Fragment Library Barcoding Kit Module 65-80 16 barcodes USD 1,208.00
4449643 SOLiD™ Fragment Library Barcoding Kit Module 81-96 16 barcodes USD 1,208.00
4449639 SOLiD™ Library TaqMan® Quantitation Kit 250 reactions USD 1,086.00
A12127 SOLiD™ Library TaqMan® qPCR Module 250 reactions USD 810.00
A12126 SOLiD™ Library qPCR Standard 10 µL USD 307.00
4453093 SOLiD™ EZ Bead™ E10 System Consumables 4 packs USD 2,645.00
4453094 SOLiD™ EZ Bead™ E20 System Consumables 4 pack USD 3,340.00
4453095 SOLiD™ EZ Bead™ E80 System Consumables 4 pack USD 3,915.00
4465571 SOLiD™ EZ Bead™ E120 System Consumables 4 packs USD 5,940.00
4452720 SOLiD™ EZ Bead™ Emulsifier E10 Reagents Kit 1 kit USD 96.75
4452721 SOLiD™ EZ Bead™ Emulsifier E20 Reagents Kit 1 kit USD 184.00
4452722 SOLiD™ EZ Bead™ Emulsifier E80 Reagents Kit 1 kit USD 504.00
4465555 SOLiD™ EZ Bead™ Emulsifier E120 Reagents Kit 1 each USD 790.00
4453065 SOLiD™ EZ Bead™ Emulsifier E10 Accessories Kit 1 kit USD 102.00
4453076 SOLiD™ EZ Bead™ Emulsifier E20 Accessories Kit 1 kit USD 102.00
4453070 SOLiD™ EZ Bead™ Emulsifier E80 Accessories Kit 1 kit USD 112.00
4465569 SOLiD™ EZ Bead™ Emulsifier E120 Accessories Kit 1 each USD 112.00
4457185 SOLiD™ EZ Bead™ Emulsifier Oil Pack Kit 1 kit USD 81.50
4453071 SOLiD™ EZ Bead™ Amplifier E10 Accessories Kit 4 packs USD 112.00
4453077 SOLiD™ EZ Bead™ Amplifier E20 Accessories Kit 4 packs USD 112.00
4453072 SOLiD™ EZ Bead™ Amplifier E80 Accessories Kit 4 packs USD 143.00
4452723 SOLiD™ EZ Bead™ Enricher E10 Reagent Kit 1 kit USD 102.00
4452724 SOLiD™ EZ Bead™ Enricher E20 Reagent Kit 1 kit USD 189.00
4452725 SOLiD™ EZ Bead™ Enricher E80 Reagent Kit 1 kit USD 534.00
4465564 SOLiD™ EZ Bead™ Enricher E120 Reagents Kit 1 each USD 1,068.00
4444140 SOLiD™ EZ Bead™ Enricher Buffer Reagent Kit 1 kit USD 117.00
4453073 SOLiD™ EZ Bead™ Enricher Accessories Kit 1 kit USD 204.00

Learn More:

User documentation for the 5500 Series Genetic Analysis Systems can be found on the SOLiD Community.  Access is through the 5500 Series User Hub.  Access is limited to 5500 Series Genetic Analysis Systems users who are registered on the solid community and have been authenticated through the process of requesting permission to join the 5500 Series User Hub.

Ordering Information

Sku Name Size Price Qty
4460730 5500xl Genetic Analyzer 1 instrument Request a Quote  
4452865 5500 Genetic Analyzer 1 instrument Request a Quote  
4461826 SOLiD™ 6-Lane FlowChip 1 kit USD 678.00
4463011 SOLiD™ FWD1 SP Kit 1 kit USD 167.00
4463012 SOLiD™ FWD2 SP Kit 1 kit USD 167.00
4463019 SOLiD™ REV1 (RNA) SP Kit 1 kit USD 209.00
4463020 SOLiD™ REV1 (DNA) SP Kit 1 kit USD 209.00
4463013 SOLiD™ Small RNA SP Kit 1 kit USD 167.00
4463030 SOLiD™ REV SR Kit, Double 1 kit USD 3,225.00
4463032 SOLiD™ FWD ECC Module, Double 1 kit USD 1,146.00
4461840 SOLiD™ Run Cycle Buffer Kit, Double 1 kit USD 642.00
4463027 SOLiD™ REV Buffer, Double 1 kit USD 78.50
4458935 SOLiD™ Buffer D, Double 1 kit USD 78.50

The tools you need for each step in the Methylation data analysis workflow:

 
Data Analysis Step Applied Biosystems Software 3rd-Party Software***
1. Align reads to reference in color space
  • ICS
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
  • LifeScope™ Cloud
2. Generate quality metrics
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
  • LifeScope™ Cloud
3. Generate sequencing and alignment statistics
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
  • LifeScope™ Cloud
4. Identify Polymorphisms
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
  • LifeScope™ Cloud
5. Translate color space to base space  
6. Visualize in context of annotation
  • LifeScope™ Genomic Analysis Software
  • LifeScope™ Cluster
  • LifeScope™ Workstation
  • LifeScope™ Cloud
7. Convert to SRF for publishing    
*** Need XSQ --> csfasta/qual converter

Learn more

Targeted Methylation Analysis using Capillary Electrophoresis

For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use.