Dear Florence,

it is technically possible to pool different type of libraries and have them sequenced on the same lane. the obvious issue with miRNA is the very short insert size. Reads from miRNA molecules will typically contain adapter sequences, these need to be trimmed before analysis. Also any further sequence that the sequencer software may identify after the adapter region needs to be discarded as it consists of optical artefacts. Finally, I would not recommend the RNA and the miRNA libraries in equimolar ratio but have more of the RNA one as it will be more complex and will require more reads.

hope this helps

best of luck 

Thanks for your answer. To be clear, you do not think that I will get, lets say, 100M reads for small RNA-seq (shorter so better amplification) and 1M reads for classical RNAseq ? It should be correct ?

Does anybody have experienced such mixes?

Theoretically, the technical issues can be compromised to sequence the RNA and miRNAs in the same lane. But you will sacrifice several things when you choose to do it in the same lane.

As you say "the size of fragments to sequence will differ". So, if you choose small RNA-seq, which is short in length, then you need to shear mRNA into short fragments for library construction and sequencing. This will cause problems in following contig assembly. If you choose to perform it through RNA-seq then you will waste lot of sequencing reagents for the short reads of small RNAs and cause signal noise for base calling. 

It does not show any advantage to do them in the same lane. : )