SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Ion Torrent



Similar Threads
Thread Thread Starter Forum Replies Last Post
mtDNA genome assembly problems leftisthominid Illumina/Solexa 10 01-09-2014 05:44 AM
PGM flows aahardikar RNA Sequencing 0 11-14-2012 06:53 PM
PubMed: High-throughput sequencing of complete human mtDNA genomes from the Philippin Newsbot! Literature Watch 0 12-15-2010 11:20 AM
Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequenci krobison Literature Watch 0 04-16-2010 08:35 AM
PubMed: Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep- Newsbot! Literature Watch 0 04-14-2010 03:01 AM

Reply
 
Thread Tools
Old 07-10-2013, 04:50 AM   #1
le.nono
Member
 
Location: Montpellier- France

Join Date: Sep 2012
Posts: 17
Default 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!
le.nono is offline   Reply With Quote
Old 07-15-2013, 05:22 AM   #2
jonathanjacobs
Member
 
Location: Rockville, MD

Join Date: Apr 2011
Posts: 23
Default

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.
jonathanjacobs is offline   Reply With Quote
Old 07-16-2013, 12:32 AM   #3
le.nono
Member
 
Location: Montpellier- France

Join Date: Sep 2012
Posts: 17
Default

even with a rRNA depletion step ?
__________________
Gene R' Us!
le.nono is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:37 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO