May 12, 2026

Preparing Gels

DOI
https://dx.doi.org/10.17504/protocols.io.36wgqx8m3lk5/v1
  • Jordan Sims1
  • 1UC Berkeley
  • Cryptic Pocillopora FP
Jordan Sims
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DOI: https://dx.doi.org/10.17504/protocols.io.36wgqx8m3lk5/v1
Protocol Citation: Jordan Sims 2026. Preparing Gels. protocols.io https://dx.doi.org/10.17504/protocols.io.36wgqx8m3lk5/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: 315918
Keywords: preparing gel, cooling time, ladders active time, sample, total time, minute, minutes total time, maximum capacity
Abstract
Pour a 2% agarose gel with two rows with maximum capacity of 44 samples + 4 ladders
Active time: ~10 minutes
Cooling time: ~25 minutes
Total time: ~35 minutes
Materials
Equipment required
  • 250mL Erlenmeyer flask
  • Weigh boat
  • Scoopula
  • 150mL graduated cylinder
  • Analytical balance
  • Microwave
  • Hot hands gripper
  • Gel box
  • Two 24-well gel combs
  • 10µL pipette
 
Consumable materials (per batch)
  • 2g agarose
  • 100mL 1X TAE (clean)
  • 10µL 10,000X SYBR Safe (FisherSci, cat. #S33102)
  • One 10µL pipette tip
  • 1X TAE to cover gel (can be reused between gels)
Troubleshooting
Problem
Bubbles in agarose after pouring gel
Solution
After pouring, but before gel has time to cool, pop bubbles using the wide end of a 10 or 20µL pipette tip or use the pipette tip to push bubbles to the edges of the gel before adding combs
Transfer 2g agarose and 100mL 1X TAE to a 250mL Erlenmeyer flask. Swirl gently to mix
Place flask in microwave for 30 seconds. Use hot hands gripper to remove flask and swirl gently. Place back in microwave for 30 seconds. Watch for boiling and remove flask using hot hands gripper once bubbles are large and solution is clear. *Do not let the liquid boil over!!*
Allow solution to cool on the bench until steam is no longer visible and flask can be held indefinitely without the hot hands gripper
Transfer 10µL 10,000X SYBR safe to the flask. Swirl gently to mix, and try not to introduce bubbles
Pour gel solution into the gel box, place combs, and cover the gel. Allow to cool for ~25 minutes
Prepare the gel to run by submerging in enough 1X TAE to cover the gel