RNA seq expt design

[jul31]

Hello,

I am trying to design an experiment :
and my question is can I put together my 3 reps of RNA before doing the library and then sequence the 3 reps as one. I will compare to a non treated samples and to different times points
ending with 6 libraries instead of 18.

I am looking only for very strong differences I can then verify my datas by qPCR on the single samples.

1-Is there any problem with this design?
2- what am I loosing against doing separate libraries for each reps beside the statistical ?

thanks

[dpryan]

As a general principal, if you can avoid pooling, you'll be better of. If pooling results in you not having biological replicates, then you'll likely be screwed if you pool.

[chadn737]

Lots of problems with this design. You loose all information about biological variation. Don't do it.