Hello! We want to do some methylation experiments but only have a limited amount of sample which also is needed for other applications. Anybody know what amount of DNA is needed both for target-specific and genome-wide assays? The HumanMethylation27 Beadchip by illumina proposes 500 ng to 1 µg, is that particularly low or par for the course?
We've done the illumina 450k array with 500ng DNA. (500ng input for the bisulfite conversion, some is lost in there ofcource)
for MSP and BSA-like validation tests I've gone down to 50 ng DNA input for bisulfite conversion (and then elute in 10ul, use 1ul per PCR)
These numbers are all for high quality DNA. If you are using FFPE samples you might want to be a bit higher, as you have degraded samples. I would not go too low with DNA input, as you also want to make sure you have a descent amount of template to ensure your sample is a representative aliquote (especially if you have degraded DNA).
Hi,
For genome-wide assay, Diagenode propose the RRBS service. It's a cost-effective method to cover up to 4 million CpG (compare to 450K) with reduced sequencing cost. You can start with only 400ng of DNA or slightly less if necessary.
https://www.diagenode.com/categories/rrbs-service
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