Methylated DNA Immunoprecipitation (MeDIP) combined with sequencing (MeDIP-seq) is a good start. Not as comprehensive as MethylC-seq (it's not single base-pair resolution and enrichment slightly favours higher 5mC density), but it is considerably cheaper, less labour intensive, and can be set up with as little as 50ng of DNA (though I prefer to start with 200ng). Our paper may help: http://www.ncbi.nlm.nih.gov/pubmed/22402632. Enrichment with CpG-binding domain proteins is also an option, but it can't detect non-CpG methylation (if that's of any interest to you).
Check this out: Taiwo et al., nature protocols 2012: 'methylome analysis usibg MeDIP-seq with low DNA concentrations'. This works just fine , even with very low DNA input (pay attention to specificity/ and recovery though). The procedure might get a little tedious when processing manually more than 24 samples in a row. In that case pay special attention to washing of magnetic beads because incubation times may overlap. Good luck !
MeDIP-seq, nature protocol Methylome analysis using MeDIP-seq with low DNA concentrations
I know a new qPCR-based method. It directly measures the percentage of global methylation in DNA samples, which even enables researchers to study the global methylation changes in a single cell level (pg level gDNA) and capable to identify 0.5% of global methylation difference between samples.
Hi Alan
I work at NXT-Dx, a company specialized in epigenetics and transcriptomics testing services and we offer a whole range of methylation techniques.
There is a range of options you could consider for your project. MeDIP-seq and MBD-seq have already been mentioned. They are very similar in approach but know that the downstream analysis in MBD-seq will be easier than for MeDIP-seq.
You can also consider RRBS or even the agilent methylseq kit to capture 3,7 million CpGs combined with bisulfite sequencing (only human samples though).
Anotther option you might consider if you are planning to run human samples is the infinium 450K array, which will be the cheapest solution you can probably find for a genome-wide study.
We offer all the mentioned techniques and more, so if you would want to know more on which technique to use in your project (either through our service or on your own), please let me know. I would be happy to assist you. You can contact me directly on [email protected].
Below the list of our related services:
- MBD-seq or MeDIP-seq
- Infinium 450K array
- RRBS
- (oxidative) bisulfite sequencing (whole genome, genome-wide or targeted)
- MSRE-qPCR
- RNA-seq (mRNA, small RNA or total RNA)
- miRNA expression profiling
- lncRNA & mRNA expression array
Good luck with your project.
Maarten
Dear Alan,
I believe that Bisulfite treatment will be important step to change the methylation information to sequence information first. This way you will be able to amplify the sample you have as much as you want by making a genomic library (eg. for next generation sequencing).
To my knowledge other techniques will have to sacrifice the sample without having an reproducible backup.
but be careful, the bisulfite treatment also degrades part of the sample. if your sample is very small, you can add carrier DNA (e.g. whale sperm) to increase your yield.
kindly, - Yazan
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