Agilent¶
How to use a BioAnalyzer Agilent DNA Kit
Find the centrifuge arm length here. Calculation to convert RPM to RCF here.
First read the Agilent DNA 1000 Kit Quick Start Guide. This protocol uses the kit for DNA of size between 25 and 1000bp with a concentration range between 0.5 to 50 ng/μl. You can use a NanoDrop or PicoGreen to quantify the DNA.
Some additions to the protocol¶
1 chip can do 12 samples. In 1 box (e.g. Agilent DNA 1000 kit), you can do 25 chips of 12 samples each (300 samples total!)
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You can install the software on many computers (Windows only)
Do NOT use “filter tips”. These WILL once in a while AFFECT the results. At least, be aware that it might create spikes in the analysis.
Maintenance¶
You can clean the equipment using water, and/or ethanol
Please wipe the white ring that enters in contact with the chip
A Kit is good for 4-6 months. After that, the quality is not necessarily guaranteed
Clean the interior of the BioAnalyzer with the “cleaning chip” (transparent one). Just put distilled water inside the chip and put the chip inside the BioAnalyzer. Then close the lid for 30 sec to 1 min. Toss the water in the sink after you’re done. Clean the BioAnalyzer before and after using it.
Once you’re done with your run, do NOT leave the chip for more than 30 minutes in the machine. Beyond this time, there is a risk that the gel dries and crystallizes on the electrode. Usually, you should remove the chip in less than 5 minutes of the run and rinse the electrodes with the cleaning chip (water should dissolve the gel). If you want to clean the electrodes of the BioAnalyzer, you can use KimWipes (with a little bit of water) between the electrodes. You can also use a very soft toothbrush with water between the electrodes.
Chip Priming station¶
Test the syringe
Mount the Chip Priming Station and raise the syringe to 1.0 and press the plunger all the way down until you hear a “click” (the plunger will be locked).
Wait 5 seconds and release the plunger. The plunger should come back (at least) to the mark “3.0”
The syringe should be changed about every 25 run (so it’s good for 1 kit, don’t reuse it)
Be certain that the position of he syringe clip is properly positioned and that the base plate is at the proper position.
Chip tricks!¶
Cleaning chip: the cleaning chip can be reuseé
DO NOT REUSE a loading chip.
Try to avoid as much as possible the amount of air that can be put inside the chip
On step 7 of the protocol under “Loading the Gel-Dye Mix (“Wait for 5s, then slowly pull back the plunger to the 1 ml position”). Please, do it VERY SLOWLY. You do not want to disturb the gel.
Under the title Loading the Marker, “Pipette 5 μl of marker in all sample and ladder wells (not the Gs). DO NOT LEAVE ANY WELLS EMPTY.” You CAN’T leave any well empty (otherwize, the bioanalyzer doesn’t detect the chip). If you forgot to fill a well, you can add water by increment of 1μl. If you don’t know which well is missing liquid for the machine to detect that a well contains a sample, add 1μl in all wells. Iterate until you reach a level where the machine can read.
Reagents¶
The reagent with the blue dot (DNA dye concentrate) is light sensitive!! Avoid as much as you can exposure to light. Exposing the DNA dye concentrate will affect performance in the long run.
Some reagents need to beat room temperature.This is important as the viscosity of the reagents will affect the performance of the protocol (if not enough warm, it’s going to be too viscous)