Making the gel

Secure the gel tray on the loading block.
Measure 100 mL of 1X TAE buffer in a graduated cylinder. For a thick gel, use 200 mL.
Measure out agarose to the intended percentage using the analytical balance — 1% gel is 1.0 g per 100 mL, 2% gel is 2.0 g per 100 mL.
Add agarose and 1X TAE to an Erlenmeyer flask and mix by gently swirling. Microwave for ~2 minutes, monitoring for boil-over.
When the mixture starts to boil, stop the microwave, remove the flask using a hot pad, and swirl slightly.
Return to the microwave and continue until the mixture comes back to a boil, about 5 seconds. Remove using hot pads and swirl once more. All agarose should be dissolved.
Place on the benchtop and monitor the temperature using the thermometer in the gel rig area.
Once the mixture has reached ~70°C, add 10 μL of ethidium bromide and swirl.
Pour the agarose into the gel mold slowly to avoid bubbles. Place the appropriate comb and pop any bubbles using a pipette tip. Allow to cool until solid — 15–30 minutes for a 100 mL gel.
Once solid, remove the gel tray from the loading block and place it in the gel rig, orienting the wells at the negative electrode. Black is negative, red is positive — run to red.
Fill the gel rig to the max line with 1X TAE buffer. Carefully remove the comb so as not to destroy any wells.

Loading and running the gel

Load 10 μL of DNA ladder into the wells furthest to the left.
Add 5 μL of one tube of PCR product into a well. Repeat until all PCR product has its own well. Note which product went into which well.
- Mix PCR product with loading dye before placing it into the gel well, if dye is not already a component of the PCR reaction.
Always store leftover nucleic acids at 4°C until the gel has finished running, in case the gel fails.
Run the gel at 80–150 V for 1–1.5 hours, or until the dye line is 75% down the gel.