Equpment Cost in setting up NGS core

[BenEvans]

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!

[simonandrews]

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.

[niceday]

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.

[mboth]

I agree with the previous answers, and would probably add the Covaris as well.

[NextGenSeq]

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.

[BenEvans]

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?

[james hadfield]

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!

[VanessaS]

Oh, and dont forget the largest stress relieveing device you can find!

Yeah but we can't have scotch in the lab......

[rglover]

Yeah but we can't have scotch in the lab......

...there's always absolute ethanol for those desperate enough

[VanessaS]

...there's always absolute ethanol for those desperate enough

Don't think it hasn't crossed my mind, albeit briefly, a time or two.

[GW_OK]

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)

[jo_mason]

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!

[BTS]

There is some very useful information here. Has anyone used Bio-rad's Gel Doc EZ system in place of a bioanalyzer?

[chrisv]

wrong post sorry..

[TonyBrooks]

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.