tape station

[dummyseq]

Has anyone used tape station from Agilent ? It's very cool ,gives the molecular weights of your DNA,cool electrophoresis,unit -all in 10minutes.

But how does the ladder read concentrations??/ Ladder is for molecular weight,so how does the software calculate concentration of my DNA???

Any input is appreciated.
Thanks
dummyseq

[kwaraska]

For concentration it uses a combination of the ladder and the marker. Don't fully understand it, but I know it works. We have gone to running all our 1st pass QC on it instead of the Bioanalyzer for two main reasons. One is the speed which you mentioned. The other is that since each sample runs in its own "gel tube" lane, if one is overloaded it does not affect the others that on a BioA would run after it.

The fact that it runs 15 sample plus a ladder at once isn't bad either!

[ECO]

I have one and really like it so far.

It's a mini agarose gel in a capillary that is loaded by a mini robot directly from a 96-well plate or strip tubes. Runs all 16 simultaneously, then takes a picture of all at the same time (runtime is ~12 minutes).

You can also apply a previously run ladder so you don't have to run a ladder with each tape/strip (but I haven't validated the sizing from saved ladders yet).

The analysis software is a little clunky and takes some getting used to, but it seems to do the job. Haven't automated any parsing of the output files yet.

[dummyseq]

But how does it calculate concentration when the upper range is only 6.6ng/ul and our results are between 20-120ng/ul

[kwaraska]

There are differing tapes. The D1K HS only goes to 1ng/ul, the D1K goes to 50ng/ul.

Beyond that, you can dilute to get into the correct range, the same as you would for a Bioanalyzer

[microgirl123]

We're demo-ing a tapestation right now, and I'm not super impressed. I love the ease of use and that fact that you don't need an entire $50 chip for one sample, but the size range and sensitivity don't seem to compare well to the Bioanalyzer. We're running high-sensitivity DNA kits on both and, while I can see distinct adapter dimer and unligated adapter peaks on the Bioanalyzer, I can't see them on the TapeStation. And since those stupid teeny tiny adapter dimers are causing me an immensely huge headache on the MiSeq, I really want to see them!

[northpaw]

You should check out the Fragment Analyzer from Advanced Analytical. They have a fast migrating lower marker designated at 1 bp that gets down out of the way of most low molecular weight molecules in the sample enabling quantitation.

Illumina uses the Fragment Analyzer (FA) now. They evaluated all systems on the market to improve reliability, throughput, and dynamic range of analysis for their workflows. This of course included the TapeStation. Illumina doesn't recommend the TapeStation, they have recommended the BA as you know for years.

Do a google search for the Illumina Automation Partners webpage. Scroll down and you will find the Advanced Analytical Fragment Analyzer (FA).

Illumina R&D has integrated the FA into multiple divisions including Consumables Product Development, Diagnostics, and Oncology. They are even starting to release new sample prep kits with the FA as a recommended QC platform.

The latest was the TruSeq RNA Access kit. They have a tech note for degraded RNA sample analysis that describes how they use custom software settings on the FA to streamline analysis of a new critical QC metric for RNA samples they call DV200.

You can find this in a google search on the Illumina website:

[PDF]Evaluating RNA Quality from FFPE Samples - Illumina
res.illumina.com/documents/.../technotes/technote-truseq-rna-access.pdf
Technical Note: RNA Sequencing. Introduction. The TruSeq® RNA Access Kit provides an exon-capture, RNA-Seq approach for difficult samples such as RNA …

If you work with FFPE or any samples prone to degradation by digestive enzymes, you should definitely check out this new kit from Illumina. Its pretty amazing.

[kmcarr]

Northpaw,

How many times are you going to post the same advertisement for the Fragment Analyzer?

[northpaw]

Spreading the word about this system, Advanced Analytical is a great company with amazing support of their products. Its lame that Agilent leverages the fact that Illumina recommends the BioAnalyzer to promote the TapeStation and then does things like refuse to replace a box of their special tips that are crazy expensive that were spilled by hard working academics trying to cure cancer with tax payers money. People should know there is a better alternative that is ACTUALLY recommended by Illumina.

[kmcarr]

Spreading the word about this system, Advanced Analytical is a great company with amazing support of their products.

Are you an employee, agent or vendor for Advanced Analytical?

...tips that are crazy expensive that were spilled by hard working academics trying to cure cancer with tax payers money.

Hyperbole much?

Resurrecting four dormant threads just this morning to post your endorsements is a bit much don't you think?

[pmiguel]

Are you an employee, agent or vendor for Advanced Analytical?



Hyperbole much?

Resurrecting four dormant threads just this morning to post your endorsements is a bit much don't you think?

Completely agree with you. Looks like "northpaw" went on a posting (spamming?) spree this morning. Posting four similar messages of adulation for this system.

--
Phillip