I'm in the initial stages of planning a miRNA seq experiment using human cultured cells and decided on TRIzol extraction, Truseq small RNA prep kit, using an illumina HiSeq2500. The illumina webinar suggests 10-20 Million reads for discovery, the QandA support page suggests 2-5M, and I wrote the tech support to ask, who suggested I do up to 100M reads for rare transcripts. Exiqon guide to miRNA discovery manual says there is not really any benefit on going over 5M reads. I was hoping to save money by pooling more samples in a lane, so I was hoping someone with experience might be able to suggest a suitable number of reads.
Having 5M You should see changes in expression of majority of, or all conserved, well expressed miRs. Dicovery of new human miRs ? Then You should carefully select a specific tissue of interest. Different RNA extraction methods sometimes give different miRNA populatins. Good Luck!
Just in case you haven't read the reference paper from QandA support materials, here is the link. They discuss the depth in a bigger detail.
http://journal.frontiersin.org/Journal/10.3389/fgene.2013.00020/full
I agree with Przemyslaw that starting from 5M (mapped miRNA) reads you should be able to get reasonable results. But the word "mapped" plays a big role. Depending on your skills and experience you might produce 10M reads which would give you 1M miRNA mapped reads or 6M reads which would give you 5.5M miRNA mapped reads....so consider this as well. Sören's suggested paper discusses this for sure (although I haven't read it yet).
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