Re: [DIYbio] Re: Agilent 2100 Bioanalyzer Issues

I am running both RNA and DNA chips at different intervals and using a different cartridge for each one. This is why I concluded that it doesn't seem to be the cartridge itself, but could perhaps be an issue with cleaning (not drying beforehand, not rinsing for long enough, etc.), because we have been seeing the same issues for both RNA and DNA.

I haven't kept track of how closely the instances occur to the prep of new gel dye, but I'll be sure to look out for that in the future. Most times new gel is prepared almost weekly because we use this machine every day, but it's good to note.

The document you sent over is the standard protocol we have adapted, and we have even made a few further modifications ourselves. We vortex at just under 2000 RPM to ensure no splashing, and cleaning (both standard rinse and deep cleaning) is done on a regular basis. My current thought is that the diodes aren't fully drying, and that is what's causing voltage/migration issues. I'll be sure to let you know if that fixes the issue.

Thank you for the help.

-SG

On Thu, Sep 28, 2017 at 12:24 AM, Tobias Viehböck <tobi92.v@gmail.com> wrote:
Hey,
I also had problems during my first run, I even run expired chips. Are you running DNA or RNA chips? Does the problem also occur if you prepare the gel fresh?
This troubleshooting guide might be also useful https://biosci-batzerlab.biology.lsu.edu/Genomics/documentation/Mastering_the_Bioanalyzer_DNA-HS_assay.docx
although I modified it, e.g. I do all the pipetting with filter tips.

Hope that helps!

Am Montag, 25. September 2017 22:06:43 UTC+2 schrieb Skyler Gordon:
Hello all, 

I'm not sure if anyone out there has any experience with this particular machine, but I've been having some issues with an Agilent 2100 Bioanalyzer. The machine is functioning very strangely, and I'm hoping someone might be able to help me figure out why. 

Here's some background:
The machine has been serviced recently
The cartridge is relatively new (less than 1 year old)
The chips are not expired

Here is the issue:
When running samples on a chip, some will not read correctly. Extremely high fluorescence peaks, incorrect concentrations, and even the ladder will be incorrectly read on a regular basis. I have run some diagnostics using just ladder and just marker/reporter, and have determined that the machine will not malfunction on a consistent basis. This leads me to believe that the diodes within the cartridge are not damaged or functioning incorrectly.

Here's the rub:
When the machine does malfunction, I have had good success with just re-running the machine. I DO NOT change my samples, AT ALL. The chip, cartridge, software, etc. will all remain exactly the same. I do not even open the machine, I simply press start again and it tends to run successfully after a few runs. But the same issue occurs on subsequent runs, but not consistently across the different samples (i.e. sample well 2 will be incorrect on the initial run, but sample well 5 will be incorrect on the secondary run).

Again, not sure if there is anyone out there who has dealt with this, but I'm starting to get annoyed with this machine and I REALLY don't want to have to replace it. 

-SG 

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