Methylation Analysis
The mapping of the human epigenome is seen by many scientists as the logical follow-up to the completion of the Human Genome Project. This epigenomic information will be important in understanding how the function of the genetic sequence is implemented and regulated. Since the epigenome is less stable than the genome, it is thought to be important in gene-environment interactions.
Epigenomic mapping is inherently more complex than genome sequencing, since the epigenome is much more variable than the genome. While each of us has only one genome, our epigenome varies with age, differs between tissues, is altered by environmental factors, and shows aberrations in diseases. So mapping a person’s epigenome at different ages, in different tissue types and disease states, would yield valuable information on the mechanisms leading to aging and disease.
Current Methods
For the targeted analysis of methylation for specific regions, the gold standard technique is bisulfite sequencing using automated capillary electrophoresis instruments. Measuring genome-wide DNA methylation, however, is only feasible using other techniques, such as restriction landmark genomic scanning, which involves labeling DNA with radioactive phosphorus 32.
Methylation Analysis and the SOLiD™ System
The SOLiD™ System provides a high-throughput method for analyzing genome-wide DNA methylation with a much higher level of resolution than traditional methods.
Experimental Workflow: Find the Products You Need for Every Step
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Step 1: Design Experiment
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.
Step 2: Prepare DNA
Depending on the method of choice and the quantity of sample, DNA can either be digested with restriction enzymes for SOLiD™ mate paired library construction, or bisulfite converted for SOLiD™ fragment library construction. Alternatively, sample DNA can be subject to shearing and methylated DNA can be captured.
Products for Step 2: Prepare DNA
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View more reagents, kits and bench-top devices on invitrogen.com
MethylMiner™ Methylated DNA Enrichment Kit
The MethylMiner™ Methylated DNA Enrichment Kit enables differential fractionation of DNA based on methylation density. The enriched methylated DNA can be to construct a DNA library for sequencing in the SOLiD™ System.
For research use only. Not intended for any animal or human therapeutic or diagnostic use.
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Step 3: Construct DNA Library
The library construction approach is dependent upon the methylation profiling strategy used.
Products for Step 3: Construct DNA Library
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SOLiD™ Mate-Paired Library Oligos Kit
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These kits are used to construct mate-paired libraries for sequencing on the SOLiD™ System. The SOLiD™ Mate-Paired Library Oligos Kit contain oligonucleotide adaptors and primers for mate-paired library construction.
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SOLiD™ Fragment Library Construction Kit
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This kit provides a fully optimized complete set of reagents, columns, and our new SizeSelect™ gels to generate 10 fragment libraries using the SOLiD™ System standard fragment library protocol.
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Step 4: Amplify & Sequence
After you construct your libraries, amplify the DNA using standard emulsion PCR. Next, deposit the beads on a slide for sequencing on the SOLiD™ Analyzer.
Products for Step 4: Amplify & Sequence
Sequencing
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SOLiD™ 4 System
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The Applied Biosystems SOLiD™ 4 System is a revolutionary genetic analysis platform that enables massively parallel sequencing of clonally-amplified DNA fragments linked to beads. The sequencing methodology is based on sequential ligation with dye-labeled oligonucleotides. The SOLiD™ 4 System enables researchers to obtain higher-quality genomes at lower cost without the purchase of a new instrument.
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Fragment Library Sequencing Reagents for SOLiD™ 4 System, Main Kits
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These kits contain sequencing master mixes in an easy-to-use strip tube format for ligation sequencing of fragment libraries on the SOLiD™ 4 System. Reagent mixing is not required, minimizing tube mix ups and providing a convenient automated method for sequencing reagent handling.
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Mate-Paired Library Sequencing Reagents for SOLiD™ 4 System, Main Kits
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These kits contain sequencing master mixes in an easy-to-use strip tube format for ligation sequencing of mate-paired libraries on the SOLiD™ 4 System. Reagent mixing is not required, minimizing tube mix ups and providing a convenient automated method for sequencing reagent handling.
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Instrument Buffers for SOLiD™ 4 System
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This kit contains a set of buffers needed for ligation sequencing on the SOLiD™ 4 System and is sufficient for 110 cycles. The product is compatible only with the SOLiD™ 4 System. Store components at ambient, 2 °C to 8 °C, and at -15 °C to -25 °C.
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Workflow Analysis Reagents for SOLID™ 4 System
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This kit is for accurate qualification and quantitation of templated beads prior to your sequencing run. Use this kit to perform a workflow analysis (WFA) run on the SOLiD™ 4 Analyzer.
Emulsion PCR (ePCR)
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SOLiD™ ePCR Kits
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The SOLiD™ ePCR Kits contain the components needed for amplifying short library inserts by emulsion PCR on beads. Each kit includes reagents for performing PCR, reagents for generating emulsions, and P1 DNA beads for clonal amplification.
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SOLiD™ Buffer Kits
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These kits contain buffers needed for emulsion PCR, bead enrichment, and bead deposition onto slides for ligation sequencing. These kits are available a 10 full-scale reaction size and a 20 mini-reaction size.
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Thermocycler Systems
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We have a full range of thermal cyclers for every budget, including our award-winning Veriti® thermal cycler series.
Bead Deposition
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SOLiD™ Bead Deposition Kits
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These kits contains components for depositing templated beads onto a slide for ligation sequencing on the SOLiD™ Analyzer. The kits contain reagents for performing a 3’ end modification and buffers. These kits are available in a 10 full-scale reaction size and a 20 mini-reaction size.
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SOLiD™ Bead Enrichment Kits
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These kits contain components to enrich templated beads amplified by emulsion PCR. The kit includes enrichment beads and reagents. These kits are available in a 10 full-scale reaction size and a 20 mini-reaction size.
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SOLiD™ Slide Kits
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These kits contain activated slides and storage buffer for ligation sequencing on the SOLiD™ Analyzer.
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Step 5: Analyze Data
Please view the learn more publications below.
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