mouse miRNA seq with SOLiD, help with coverage needed desperately!

[bisrat]

Hello,

I am a novice member with a novice question

I plan to conduct a mouse miRNA sequencing project with the SOLiD platform. The platform I would use gives 250million reads in a single run, and there are 590 mouse miRNAs listed on miRbase as of now. I have an option of multiplexing my samples, with the 16 barcodes available presently. The major headache I have now comes from having to decide on the number of samples I need to run in order to get a decent biological information without compromising the coverage .

I could not find a proper literature to help me calculate the minimum coverage I would need for mouse miRNA seq. Does anyone have an idea? How can I calculate my coverage from the information I mentioned above? or what exactly do I need to know?

I would be very grateful should someone explain to me in simple terms the issue of coverage in the SOLiD (mouse) miRNA sequencing context.

thanks in advance

[scooter]

You should only need ~5 million mappable tags to essentially saturate a small RNA library from Human samples, so I think mouse would be fairly similar. This all depends on the purpose of your experiments. If you want only to profile known miRNAs and their isomir variants than the 5 million number should allow you to get pretty full coverage. This would mean that if you can get 250 million in a SOLiD run you could sequence up to 50 samples and probably saturate all of them. I think you can easily get away with running all 16 barcodes on 1/2 to a full slide and get more than enough data.

However, if you are looking for rare and unknown small RNA transcripts, you may want to go quite a bit higher in coverage (maybe up to ~15-20 million or so per sample).

[bisrat]

Scooter, thanks a lot for the tips!