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Old 12-06-2010, 06:47 AM   #1
BenEvans
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Default Equpment Cost in setting up NGS core

Hello all,

I am currently trying to weigh the pros/cons in buying different equipment to support library prep and pre-run quality control for illumina/454/SOLiD as well as possibly upcoming ion torrent etc etc.

So I would like to draw from collective experience and put together a wish list of sorts from people that now routinely run these pipelines. Are there any instruments that you all view as indispensable? What about those that are versatile enough to be helpful for more than one tech?

I'm starting a list, but would like input from all the experts here.

Thanks!
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Old 12-06-2010, 11:53 PM   #2
simonandrews
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In common with most other labs which run Illumina sequencers we make extensive use of a bioanalyzer to do basic library QC and a real time PCR machine to do the quantitation of the libraries prior to sequencing. I guess that similar checks would be appropriate for other sequencing technologies.

Other than that there's nothing which wouldn't be found in any molecular biology lab.
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Old 12-07-2010, 12:35 AM   #3
niceday
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We also have a Qubit. Very useful and quite inexpensive to buy and use. A nanodrop is also required for SOLiD long mate pair. Try and get use of someone elses as we dont use a nanodrop for anything else but circularised DNA.

If you are not going to use SPRI beads get an e-gel setup. 10 to 15 minutes rather than 30mins to 1 1/2 hours for a normal gel.
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Old 12-08-2010, 01:24 AM   #4
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I agree with the previous answers, and would probably add the Covaris as well.
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Old 12-08-2010, 06:04 AM   #5
NextGenSeq
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If you use Q-PCR to quantify your libraries you don't need a Qubit. A NanoDrop is still useful though, as well as a Bioanalyzer.
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Old 12-08-2010, 10:26 AM   #6
BenEvans
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Thanks for the input! Does anyone know if the Qubit uses RiboGreen for quantification, or is that another Fluorometer? From everyone's experience, which do you prefer based on time/reliability/sensitivity/cost: Qubit/qPCR/bioanalyzer?

I also haven't done much with e-gel, but hear that the pippin prep is quite nice for separation & size selection. Has anyone used both? Could you get away with standard agarose gels if needed and the pippin prep for 'gel extractions' & size selection?

What model Covaris do most people use? S2?
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Old 12-09-2010, 10:42 PM   #7
james hadfield
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I would agre with the Bioanalyser and Qubit. Standard manual gels are fine, if run carefuly so as to reduce variability between gels.

The Bioruptor is an alternative to the Covaris.

I would also recommend a disposable, gel cutting tips. These are indespensible in gettting the same amount of gel/DNA into the ceanup column.

You might also consider something like Beckmans SPIworks or a Tecan, Beckman or even Illumina robot to automate the TruSeq library kits.

Pippin Prep and Calipers system are both eary days instruments and it wil be interesting to see how they work out compared to manual or SPI based selections.

Have fun.

Oh, and dont forget the largest stress relieveing device you can find!
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Old 12-13-2010, 10:00 AM   #8
VanessaS
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Quote:
Originally Posted by james hadfield View Post
Oh, and dont forget the largest stress relieveing device you can find!
Yeah but we can't have scotch in the lab......
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Old 12-14-2010, 07:18 AM   #9
rglover
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Originally Posted by VanessaS View Post
Yeah but we can't have scotch in the lab......
...there's always absolute ethanol for those desperate enough
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Old 12-14-2010, 07:50 AM   #10
VanessaS
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Originally Posted by rglover View Post
...there's always absolute ethanol for those desperate enough
Don't think it hasn't crossed my mind, albeit briefly, a time or two.
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Old 12-14-2010, 08:14 AM   #11
GW_OK
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Here is my list, in decreasing order of indispensability:
Bioanalyzer
qPCR instrument
Covaris
Qubit
Robot (We've got a SPRI-TE)
Size selection system (We don't have one, but if you're robot can't size select for you it might be nice)
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Old 02-08-2011, 11:18 PM   #12
jo_mason
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Quote:
Originally Posted by GW_OK View Post
Here is my list, in decreasing order of indispensability:
Bioanalyzer
qPCR instrument
Covaris
Qubit
Robot (We've got a SPRI-TE)
Size selection system (We don't have one, but if you're robot can't size select for you it might be nice)
How useful do you find your SPRI-TE. We are considering buying one but I have concerns as we do alot of RNAseq. I've considered other options but they all have a fairly large footprint and we are rapidly running out of benchspace for equipment!
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Old 03-02-2011, 11:03 AM   #13
BTS
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There is some very useful information here. Has anyone used Bio-rad's Gel Doc EZ system in place of a bioanalyzer?
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Old 01-17-2012, 01:23 AM   #14
chrisv
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wrong post sorry..
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Old 01-17-2012, 04:22 AM   #15
TonyBrooks
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Quote:
Originally Posted by NextGenSeq View Post
If you use Q-PCR to quantify your libraries you don't need a Qubit. A NanoDrop is still useful though, as well as a Bioanalyzer.
Qubits are also useful to quantitate starting material. We've seen the Nandrop overspec by 10 fold on some samples.
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Old 01-19-2012, 09:00 AM   #16
epistatic
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Quote:
Originally Posted by BTS View Post
There is some very useful information here. Has anyone used Bio-rad's Gel Doc EZ system in place of a bioanalyzer?
Do you mean the Experion™ Automated Electrophoresis Station? That would be Bio-Rad's BioA. We tried it out due to the lower price point but decided to return it and go with the BioA. They run the same Caliper chips but have a lower number of samples per well. Our unit had the chip vortexer's speed capped off and would throw the sample out of the well. They tried to tell us we didn't know how to pipet and then it was because our building "moved too much for the laser". We had to put dye into the chips and show how it was really failing.

The Gel Doc EZ system is good for taking pics of gels and doing other work but you can't beat the bioanalyzer's ability to handle different sample types like the High Sensitivity/DNA1000 chips for DNA and nano/pico for RNA. We use it multiple times a day for sample QC -> QC through library preps.
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Old 02-10-2012, 08:46 AM   #17
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Ben, did you ever set up the new lab? If yes, what did you purchase? Thanks!
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