small amount of DNA material for Helicos?

[danf1985]

We tried Helicos for ChIP-Seq with small amount of DNA (less than 1ng). As it claimed, Helicos should work well with small amount of DNA samples, yet it did not seem to be the case. What is your experience and how do you think about this?

We are currently using Illumina, but has been interested in Helicos for the reason that it claims to be more accurate and use less material (sometimes we don't get a lot of DNA out of ChIP). However, the more I learned about it, the more concerns I have. It does not seem to be as good as they advertise. The sample prep is not very easy, and the results is not that accurate, or at least not really superior to Illumina. The reads are short compared with Illumina. And it would be a big investment with one machine, 1 million dollars. What's your opinion?

[angelawu]

I currently use Helicos for my low quantity samples (picogram level) and it is working far better than Illumina. The reason is because the tSMS allows you to get individual reads, whereas for Illumina I get jackpotting (that is, repeated reads from the same DNA fragment) from the pcr amplification I have to do to get enough DNA for the GA, whereas for Helicos, I don't do any amplification... Also the end repair and ligation for Illumina library prep has not worked well for me. It appears much less effficient than the Helicos library prep polyA tail method, and caused my DNA to be lost in the library prep process. Let me know if this makes sense. For me the Helicos wins by far for small quantity DNA sequencing.

If you are doing ChIP-seq, the quality of the DNA can highly affect the sequencing outcome as well...