PGM for mtDNA transcriptome

[le.nono]

Hi,

Still new in the field but my lab is about to acquire a PGM or a Proton. our projects turn around the mitochondrie. I'd like to know if a PGM ihas enough capacity enough with the 318 chips for instance to perform sequencing such as whole transcriptome RNA-Seq (including mito transcripts and nuclar transcripts from the mito compartment) and a whole cell Chips-Seq analysis with a good coverage (30-40x)?

Thank you.
A

[jonathanjacobs]

Probably not. You'll get about 5M reads on a good day with the Ion318 - which is good enough for polyA+ transcriptome sequencing; comparable to what you might expect from an Affymetrix array. We also do a lot of small RNA sequencing on the PGM - and it (316/318) seems to work quite well, but For total Transcriptome you are going to be better off with an Ion Proton or a MiSeq. You simply need more reads for that type of sample.

[le.nono]

even with a rRNA depletion step ?