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Old 09-29-2014, 09:12 AM   #1
IshSeq
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Default Agilent Bioanalyzer vs AATI fragment analyzer

Hello Seqers,

We use the Agilent Bioanalyzer to perform QC on our DNA samples, pre and post library preparation.

However, on several occasion we have had issues with this system, from data not being reproducible, one sample being affected by the other during the run and the fact that you have to use an entire chip even when there are only 5 samples to run (the chips and the reagents are quite expensive).

Therefore, we are looking into a new system and are considering the AATI fragment analyzer.I would like to know if anyone has done a comparison of the bioanalyzer and the fragment analyzer and know how they stack against each other in terms of performance and cost.

Thanks
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Old 09-30-2014, 08:04 AM   #2
NextGenSeq
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The AATI Fragment Analyzer is more sensitive and can detect lower amounts of RNA and DNA.

Illumina has switched to AATI from Agilent for all their in house library QC.
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Old 09-30-2014, 09:44 AM   #3
der_eiskern
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Default re:

i'm very concerned about AATI's inability to provide specs for their DNA quantitation abilities. Is it still recommended to use picogreen for library quantitation and only use microcapillaries for size range validation?
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Old 09-30-2014, 12:27 PM   #4
NextGenSeq
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We don't use the Agilent for quantification either. I do know that we can detect much lower amounts of Illumina libraries.

Also, the AATI does not have an upper marker which interferes with Oxford Nanopore libraries. We make ONT libraries ranging from 8kB to 20kB and the 10 kB Agilent marker screws up the quantification on the Bioanalyzer.

The AATI has a 100 kB marker. Since we are about to try to make 50 kB libraries this will be useful for sizing and quantification.
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Old 10-01-2014, 07:47 AM   #5
der_eiskern
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Good to know!

so you do use the AATI (not Agilent) for quantitation?
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Old 10-01-2014, 08:28 AM   #6
NextGenSeq
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ONT libraries are hard to quantify since the adapters have proteins tethered to them.

The MinION is less sensitive to DNA quantity though since there is no cluster amplification or emulsion PCR.

Basically if you have enough to see your library on the Bioanalyzer or AATI you have enough.
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Old 10-01-2014, 10:43 AM   #7
northpaw
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Illumina R&D has indeed transitioned away from chip-based systems and is now releasing new sample prep kits recommending the AATI Fragment Analyzer:

http://res.illumina.com/documents/pr...rna-access.pdf

Illumina recently announced Advanced Analytical as an automation partner for their Fragment Analyzer system:

http://applications.illumina.com/app...utomation.html

AATI Fragment Analyzer specs are available on their website:

www.aati-us.com
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Old 10-01-2014, 06:52 PM   #8
nucacidhunter
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Quote:
Originally Posted by northpaw View Post
Illumina R&D has indeed transitioned away from chip-based systems and is now releasing new sample prep kits recommending the AATI Fragment Analyzer:

http://res.illumina.com/documents/pr...rna-access.pdf

Illumina recently announced Advanced Analytical as an automation partner for their Fragment Analyzer system:

http://applications.illumina.com/app...utomation.html

AATI Fragment Analyzer specs are available on their website:

www.aati-us.com
Your Illumina links are not working.
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Old 10-01-2014, 07:18 PM   #9
northpaw
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Try these:

http://res.illumina.com/documents/pr...rna-access.pdf

http://applications.illumina.com/app...utomation.html

If links don't work you can find the Illumina Automation Partners page using Google.

The most recent technical note by Illumina recommending the AATI Fragment Analyzer is the TruSeq RNA Access Kit. They developed a new critical QC metric they call the DV200 using the Fragment Analyzer:

Google search:

[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 ...
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Old 10-01-2014, 09:38 PM   #10
dannydesloover
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Default Aati

Had used the original system before the face-lift and thought it was great.

Now in a new role, just purchased the new AATI system and can't wait to put it through its paces.
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