I was wondering if anyone has ever used the illumina MiSeq for meDIP experiments. I know meDIP can be performed on a HiSeq but never tried it on a MiSeq.
Hi Nizar, I'm relatively new to NGS myself, so I would take my advice with a caution. I can't see why you couldn't use MiSeq for MeDIP in principle, but you probably won't get enought coverage. MiSeq produces about 25M reads per lane. I'm not sure how much coverage you need for MeDIP, but if global histone methylation marks (such as H3K27 methylation) are anything to go by, I'd say you need 15-20M reads per sample for reliable differential methylation analysis. So you might end up running a sample per lane, while you could multiplex 9-10 samples per lane of HiSeq.
I hope it helps.
Yes. MiSeq can most certainly be used for sequencing of meDIP. Has a lower coverage, but I'm sure you must have already realized the same.
Hi Nizar, I am currently asking myself the same question. Did you ever try sequencing your MeDIP on the MiSeq?
- Badges
- Science method