Paired end RNA-seq library preparation question

[happye321]

Hi there,
I am gonna work on gene expression profiling in a non-model plant species, my advisor suggested using ScriptSeqTM Complete Kit*(plant) for sequencing libraries construction and then do a paired end sequencing(Supposed to be better than single end sequencing for the purpose of de novo assemble ?) using illumina Hiseq-2000.
Without a reference genome, I guess I will need either to use ref genome from a close related species or do a de novo assemble.
According to the library construction protocol, there is no size selection step for the final sequencing library, though they suggested to use bioanalyzer to estimate the size distribution in the library. So, my question is: will it be necessary to add a size selection step (200~400bp?) before sending out the library for a paired-end sequencing?
Any suggestion will be greatly appreciated!
Thanks !

[dblyons]

the scriptseq chemical fragmentation step works well. we start with ~50ng ribominus RNA and do the frag step at 90 degrees C for 10 minutes (rather than what they suggest in the protocol we have). We get a mean fragment size around 500bp following library prep, with a pretty broad peak maxing out at about 800 bp. No need for size selection.

[happye321]

the scriptseq chemical fragmentation step works well. we start with ~50ng ribominus RNA and do the frag step at 90 degrees C for 10 minutes (rather than what they suggest in the protocol we have). We get a mean fragment size around 500bp following library prep, with a pretty broad peak maxing out at about 800 bp. No need for size selection.

Thanks for your help!