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Old 11-16-2010, 09:13 PM   #1
sp20040
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Location: pittsburgh

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Question HiSeq versus Solid for DGE

Dear All,
this is my first post.
I have to make purchasing decision for a sequencer for the my lab in the next two months.
My need is simple - replace microarray gene expression profiling for formalin fixed paraffin embedded samples with DGE to get more reproducible data.
I looked at most recent protocols using DSN from Illuimina and SAGE-Seq from ABI. Illumina protcol looks simpler but new ABI 5500 seems to be very flexible since it allows sequencing in each lane and may be helpful for us to experiment with different conditions because we have to deal with samples from many different institutions.
Any recommendations?
thanks!
Soon Paik
NSABP
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Old 11-17-2010, 06:13 AM   #2
pmiguel
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We do not yet own an Illumina sequencer, so I can't give you a direct comparison. But my impression is that the Solid beats Illumina at price per base (for reagents and instrument service contract costs) and in accuracy. But no good method for de novo transcriptomics exists for solid reads. Also, part of what makes the solid accurate -- color space base calls, also makes analysis with standard tools somewhat more complex. (But this is supposed to be largely solved in the solid 5500.)

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Old 11-17-2010, 06:28 AM   #3
NextGenSeq
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Note Nugen is coming out with a FFPE RNA-Seq kit. I know it works with Illumina not sure with the SOLiD or 5500.

Also, Illumina just released the HiSeq 1000 (single flowcell). I don't know it's price tho.
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Old 11-17-2010, 05:50 PM   #4
sp20040
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pmiguel and NexGenSeq,
thanks for the replies..
any experience with illumina barcoding with DGE? are they easy to use?
thanks again
Soon Paik
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Old 11-18-2010, 06:01 AM   #5
NextGenSeq
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I find Illumina's library kits to be vastly overpriced. Check out Nugen, Epicentre or NEB for their kits.
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Old 11-18-2010, 04:29 PM   #6
sp20040
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thanks again NextGenSeq,
i have a situation - we just got notified that from our award we can use only 480k for infrastructure - so our choice for the sequencer is limited unless we get a great deal from illumina for HySeq1000. We do not need big server since we will use cloud and collaborate with bioinformatics group overseas for sequence analysis part. We will have to make choices among GA IIx (refurbished - and very cheap) vs HiScan with sequencing module vs HySeq1000 (if we get discount) vs Solid. For SAGE type application, I am not sure which one we should get even after having extensive discussions with both company's application specialists.
any advice would be greatly appreciated
thanks
Soon Paik
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Old 11-19-2010, 05:30 AM   #7
NextGenSeq
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The SOLiD is being replaced by the 5500. For your budget I think only the 5500, the refurbished GAIIX, the HiScan or possibly the HiSeq 1000 (what is the price of this?) fit.

If you get the 5500 make sure you get the EZ Bead. The reagent cost of the 5500 is now cheaper than the Illumina systems. LIFE is aggressively pursuing the next gen market and is more likely to deal.
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