1 lane per treatment vs. multiplexing for rnaseq

[nsl]

Hi all,

I ran a pilot for an experiment which had 3 treatments using 1 lane per treatment . We have funds to pay for 3 more full lanes of sequencing. My question is

Should I run each treatment as I did for the pilot ( using 1 lane per treatment)

or

Should I multiplex and run all 3 treatments on each of the sequencing lanes?

Would I roughly get the same coverage as running a single treatment per lane?

Any insight would be greatly appreciated.

nsl

[lukas1848]

you should multiplex to prevent any technical bias from the lane.

Have a look at this very nice paper on that.

Auer, P. L., & Doerge, R. W. (2010). Statistical design and analysis of RNA sequencing data. Genetics, 185(2), 405–416. doi:10.1534/genetics.110.114983

[nsl]

thank you