[ngsnewbie]

Ben, did you ever set up the new lab? If yes, what did you purchase? Thanks!

[epistatic]

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.

[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.

[chrisv]

wrong post sorry..

[BTS]

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

[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!

[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)

[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.

[rglover]

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

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

[VanessaS]

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

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

[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!

[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?

[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.

[mboth]

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

[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.