study design small RNAs

[Conny]

Hi!

We want to sequence small RNAs and I'm wondering how many reads (or coverage?) are needed for a sample from a mammal to obtain a realistic small RNA profile?

I know that it is possible to multiplex a number of samples in one lane (~60 million reads in total) on the Illumina. Is it reasonable to multiplex, for example, 6 samples in one lane for smallRNAs? This would give me ~10 million reads per sample. However, is this enough or do I need more reads?

Thanks a lot in advance for your help!

Cheers,

Conny

[pfranchini]

Hi Conny,

I am planning to sequence many small RNA libraries with an Illumina GA and I have your same questions? Did you receive some feedback?

Thanks in advance

Paolo

[Conny]

study design - small RNAs

Hi Paolo,

unfortunately, no one has replied yet, but it is vacation time, I guess. I'm discussing things with some other people and as soon as I have some answers, I will post them on SEQanswers. It seems that the literature out there is not really helpful in this regard or I'm not finding the appropiate articles....

Cheers,

Conny

[GenomicIBK]

Bringing this thread up, I have the same question.

I was talking to people and they told me 50 million reads for total transkription analysis should be enough.
But, how you can downscale this for small RNA analysis, I have no idea.

Informations about this would be highly appreciated.


Have a nice day

[GenomicIBK]

Just found the following thread:

http://seqanswers.com/forums/showthread.php?t=5724

[Conny]

Hi!

Thanks a lot for the link! That helps a lot!

I've heard similar numbers before, so it is probably some kind of guideline. Also, it means that it is possible to multiplex several samples and make the most of each run....I'll post updates, if I find some other info.

Have a nice weekend,

Conny

Bringing this thread up, I have the same question.

I was talking to people and they told me 50 million reads for total transkription analysis should be enough.
But, how you can downscale this for small RNA analysis, I have no idea.

Informations about this would be highly appreciated.


Have a nice day