PGM for mtDNA transcriptome

le.nono · 07-10-2013, 03:50 AM

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 · 07-15-2013, 04:22 AM

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 · 07-15-2013, 11:32 PM

even with a rRNA depletion step ?

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07-10-2013, 03:50 AM	#1
le.nono Member Location: Montpellier- France Join Date: Sep 2012 Posts: 17	PGM for mtDNA transcriptome 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 __________________ Gene R' Us!

07-15-2013, 04:22 AM	#2
jonathanjacobs Member Location: Rockville, MD Join Date: Apr 2011 Posts: 23	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. __________________ @bioinformer http://www.linkedin.com/in/jonathanjacobs

07-15-2013, 11:32 PM	#3
le.nono Member Location: Montpellier- France Join Date: Sep 2012 Posts: 17	even with a rRNA depletion step ? __________________ Gene R' Us!