Multiplexed Rnaseq

Question

[Yannick Wurm]

So now that Illumina HiSeq can produce a gazillion bp of sequence per lane, what's the deal with multiplexing RNA samples? Say with this kit.

Has anyone had experience with data from a multiplexed RNAseq run? Do the data look ok? Is the cost of preparing 12 tagged libraries = 12x the cost of preparing one normal library?

Answer 1

[Istvan Albert]

I have asked our lab manager about this (we have experience with ChiP-Seq if that matters at all), she tells me that:

The cost of preparing 12 tagged libraries (by which I am assuming you mean 12 tagged samples pooled into 1 library) is the same as preparing 1 single library.

[Yannick Wurm]

Thanks Istvan. Our core facility manager seems to differ: He says the cost of preparing a library of 12 tagged samples is closer to the cost of preparing 12 libraries than to the cost of preparing one single library...

[Istvan Albert]

Interesting - I wonder if the discrepancy is due to perhaps accounting for the actual sequencing cost as well (in our case at least).