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Old 01-05-2015, 07:01 AM   #1
shay covo
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Default Tapestation or Fragment analyzer

I am now about to buy tapestation of agilent or fragment analyzer of AATI

I will use both to QC libraries genomic DNA and RNA

We will not process many samples a week but we need a reliable low maintenance machine
What would you recommend? Do you have any clear bias towards any one of them? why
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Old 01-07-2015, 09:51 AM   #2
pmiguel
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We only have the bioanalyzer. I think it is preferable for us because the high sensitivity chips are more sensitive than the tapestation.
That said, the down side of a bioanalyzer is that you have to run samples 10-12 at a time. So if you only have a couple of samples to run the reagent costs become quite outrageous. And the kits themselves have a limited shelf life, so that can make the cost even worse if you don't run the instrument fairly heavily.

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Old 06-02-2015, 05:16 PM   #3
GagneUW1
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I am making the same decision between a tape station and a AATI fragment analyzer. What did you end up deciding on this and why? Any information helps. Thank you!
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Old 06-06-2015, 01:55 PM   #4
shay covo
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Default I chose tapestation

It is much easier to operate. Other members of the department were very negative about the fragment analyzer.
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Old 06-06-2015, 02:48 PM   #5
bilyl
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Quote:
Originally Posted by shay covo View Post
I am now about to buy tapestation of agilent or fragment analyzer of AATI

I will use both to QC libraries genomic DNA and RNA

We will not process many samples a week but we need a reliable low maintenance machine
What would you recommend? Do you have any clear bias towards any one of them? why
Why not a Labchip GX? It can run 96-well plates of samples and can perform regular NGS quant as well as genomic DNA assays.
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Old 06-18-2015, 01:54 AM   #6
seqdx
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Quote:
Originally Posted by shay covo View Post
It is much easier to operate. Other members of the department were very negative about the fragment analyzer.
Really? Did you run any samples? The TapeStation is easier to use than the Fragment Analyzer for small sample sets, but the benefits stop there. Data quality matters most. The lack of resolution, sensitivity, and dynamic range will limit applications and worse, force you to keep using slab gels and the BioAnalyzer you hoped to get away from.

See the attached restriction digest comparison of the TapeStation versus the Fragment Analyzer. Data speaks volumes, resolution is critical for sizing accuracy.

NGS read lengths are getting longer and longer. If you demo the two also explore sensitivity limitations for samples over 2 kb.
Attached Files
File Type: pdf FragmentAnalyzer_vs_Tapestation.pdf (135.8 KB, 502 views)
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Old 06-18-2015, 11:39 AM   #7
Ingeneious
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I have used the BA a lot in the past and recently switched to the TapeStation. For convenience, it is pretty simple and accuracy is good enough to use for NGS library prep. My previous lab was using it for hundreds of clinical samples, after calibrating it with a BA. It also gives you the option between running a few or many samples, which can lead to reduced costs against the BA. If you run without a ladder and use expired tapes (they only last 2 weeks after first use), you can really cut down costs.

On the flip side, you can buy around 3 BA's for 1 TapeStation and the per sample cost may be higher (off the top of my head ~$41 for 16 sample D1000 tapes/reagents, $65 for HSD1000 tapes/reagents vs ~$30? for 1 x 12 sample BA D1000 chip/reagents). I also do notice the resolution loss between the BA.

Someone else in our group was an advocate of the LabChip GX, but she said prep time was ~50 minutes vs 10 minutes for the BA and about 5 minutes for the TapeStation. You can have results for the TapeStation in as few as 10 minutes vs 30 for the BA. That can certainly help with development.

No one that I know has experience with the Fragment Analyzer, but I do know we had one sitting idle, while BA's and TapeStations were being used frequently...

Some of the major downsides have been that with only 25 - 1000bp resolution for the D1000, some samples may bleed into the ladder and give inaccurate concentrations. The BA offered a chip with up to 7500bp.

We have used the gDNA tape only once and it was good enough to check the overall integrity, plus gave a DIN number for accuracy. Based on seqdx, if you need the resolution, it looks like that might be a problem.

Last edited by Ingeneious; 06-18-2015 at 11:46 AM.
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Old 06-18-2015, 02:49 PM   #8
barrmur
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New tape station, 4200, to be released soon, likely shipping in September. May be wise to wait and see what the offer is....

Looks like it will be capable of running 96 samples in "walk away" mode.
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Old 06-18-2015, 10:34 PM   #9
Ingeneious
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Yeah, my boss said a new one was coming out that would do 96 samples. Good to hear details.
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Old 06-19-2015, 04:30 AM   #10
Smoki
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The comment about Labchip GX prep time is silly. I have used both the BA and the GX, and the latter requires less hands-on work and skill.

You would get to 50 min only if you take into account that you have to put the chip and reagents on room temp half an hour before using them.
Not to mention that you prep the chip once and then it's good for the whole day. You just add samples to the microplate. That certainly helps with development.

And I absolutely love the GX software.
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Old 06-19-2015, 05:58 AM   #11
Ingeneious
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So same as BA and TapeStation + 20min prep. What's the per sample cost of the LapChip GX with reagents/chips?
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Old 06-19-2015, 06:18 AM   #12
Smoki
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Unless you will have a very low throughput in the lab (i.e. always less than 10 samples per day), the reagents cost should be considerably lower on the GX. But the initial investment in the instrument is higher.
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Old 06-19-2015, 05:41 PM   #13
seqdx
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Quote:
Originally Posted by barrmur View Post
New tape station, 4200, to be released soon, likely shipping in September. May be wise to wait and see what the offer is....

Looks like it will be capable of running 96 samples in "walk away" mode.
Agilent should focus on the resolution and sensitivity limitations of the TapeStation. The instrument simply lacks the resolution needed for accurate sizing of large NGS libraries, and the lack of sensitivity for samples over 2 kb make it useless for single-cell applications such as Fluidigm C1 transcriptomics (Clonetech). Why spend hard earned capital funds on a system that can't handle the diverse assay requirements of a rapidly evolving field.
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Old 01-28-2016, 05:11 AM   #14
Mini
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Quote:
Originally Posted by Ingeneious View Post
Yeah, my boss said a new one was coming out that would do 96 samples. The 3 week diet from https://skinnyexpress.com/the-3-week-diet-review is good to hear details.
Oh really? Any idea when this is coming out?

Last edited by Mini; 05-22-2016 at 02:10 PM.
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Old 01-28-2016, 05:47 AM   #15
GenoMax
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Quote:
Originally Posted by Mini View Post
Oh really? Any idea when this is coming out?
Looks like it is already available: http://www.genomics.agilent.com/en/p...questid=859015
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Old 01-30-2016, 12:40 PM   #16
luc
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Have you heard of any improvements over the previous system (other than the 96 sample capability)?
The agilent page is not very informative.
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Old 01-30-2016, 06:18 PM   #17
Ingeneious
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I think that is it, other than the walk away capability. Pricing is about $5k more than the old system. Uses the same tapes and allows selecting specific wells. Not sure if that requires two at a time. This was from someone who attended their booth.

Last edited by Ingeneious; 01-30-2016 at 06:21 PM.
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Old 01-30-2016, 07:42 PM   #18
luc
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Thanks a lot Ingeneious!
Quote:
Originally Posted by Ingeneious View Post
I think that is it, other than the walk away capability. Pricing is about $5k more than the old system. Uses the same tapes and allows selecting specific wells. Not sure if that requires two at a time. This was from someone who attended their booth.
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