May 12, 2026

Running Gels

DOI
https://dx.doi.org/10.17504/protocols.io.4r3l2dk3qg1y/v1
  • Jordan Sims1
  • 1UC Berkeley
  • Cryptic Pocillopora FP
Jordan Sims
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DOI: https://dx.doi.org/10.17504/protocols.io.4r3l2dk3qg1y/v1
Protocol Citation: Jordan Sims 2026. Running Gels. protocols.io https://dx.doi.org/10.17504/protocols.io.4r3l2dk3qg1y/v1
License: This is an open access  protocol  distributed under the terms of the  Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: April 28, 2026
Last Modified: May 12, 2026
Protocol  Integer ID: 315919
Keywords: running gels load, gels load, running time, active time, hour total time, made gel, total time, hour, sample, ladder
Abstract
Load 44 samples + 4 ladders onto a pre-made gel and run it
Active time: ~1 hour
Running time: 1 hour
Total time: ~2 hours
Materials
Equipment required
  • Power supply
  • Blue light transilluminator
  • Transilluminator cover
  • Phone camera
  • Laptop
  • 10µL pipette
  • 20µL pipette
 
Consumable materials (per sample)
  • 1µL 6X loading dye
  • One 20µL pipette tip
 
Consumable materials (per batch)
  • One prepared 2% agarose gel
  • Large square parafilm
  • 20µL 50bp DNA Ladder (NEB, cat. #N0556S)
  • One 10µL pipette tip (for aliquoting loading dye)
  • Four 20µL pipette tips (for loading ladder into gel)
Troubleshooting
Problem
Low bands not visualizing on gel
Solution
Pause gel run after first 30 minutes and visualize/photograph the low bands clearly. Then return the gel to the gel box and run for another 30 minutes. Visualize/photograph again to capture the higher bands clearly.
Create one well per sample in a sheet of parafilm by pressing parafilm down over a 1.5mL tube rack
Pipette 1µL 6X Loading Dye into each parafilm well
Add 5µL digested amplicons to each parafilm well and pipette up and down several times to mix with loading dye
Load digested amplicons with loading dye into an empty gel lane, leaving the first and last lane of each row empty
After all samples have been loaded onto gel, load 5µL 50bp DNA Ladder into the first and last lane of each row on the gel
Run the gel at 100V for one hour
Visualize on blue light visualizer and photograph with phone camera
Immediately upload gel image to laptop, annotate, and save
Note: Record date, SampleIDs, and enzyme on each annotated gel image. Provide a key that clearly connects the wells to the SampleIDs