Protocol Title: General for the Technique

Goal or reason for the technique, and conceptual description of the method (if applicable).

Example 1: Methyl binding domain enrichment of DNA for highly methylated regions. Sheared DNA is hybridized with the methyl binding domain protein that binds to regions of DNA with a lot of CpG methylation. The protein is attached to co-molecules and to a magnetic bead, so that un-bound DNA can be washed away, and the bound DNA can be released and ethanol precipitated as the highly methylated regions of your DNA sample.

Example 2: Air brushing and homogenization technique for Montipora coral fragments. Air brushing tissue off fragments and subsequent homogenization (blending) of tissue removes tissue in the most complete manner for complex structured corals for later surface area analysis, and homogenization breaks open coral host cells for further diagnostic assays.

Materials and Equipment

List ALL the materials and equipment you need for the protocol.

• For reagents/kits provide a link to the company website and the catalog number.
• If it is a really basic lab material (ie. sterile 1.5mL tube), then just say that without a link.
• For equipment, list the equipment, specifications (like centrifuge that can go to 4 degrees, air brusher with however much psi), and company that made the equipment and model number we have in the lab.

If there is a company protocol (like with an extraction kit from Zymo), save it as a pdf to your notebook github, and link it here. These are likely going to be less specific than the one you write.

Protocol Steps

Make headings for separate sections of the protocol (if applicable)

• Bullet or number list all steps.
• Be specific about what is being added to what and clear, don’t shorten names of reagents in different ways.
• Be consistent with your language of techniques and materials.

Specifics

• Try to remember to include things that are simple/second nature, ie. every vortex, spin down or pipette mix.
• If a lot of different tubes are happening, you can write in that you labeled a set of tubes something, and call on that name later on when referring to those tubes.
• If you are discarding a liquid, where did it go? Hazardous Waste bottle, trough, container that can be poured down the sink?
• If you use a thermocycler program, list the entire program even if it is a crazy one. And say what it is called in our machines and what login it’s under. Ex:
  • 8 degrees for 4 minutes
  • 16 degrees for 1 minute with 3% ramp rate
  • 22 degrees for 1 minute with 3% ramp rate
  • 28 degrees for 1 minute with 3% ramp rate
  • 36 degrees for 1 minute with 3% ramp rate
  • 36.5 degrees for 1 minute with 3% ramp rate
  • 37 degrees for 8 minutes
  • repeat back from the first step one time through again
• Photos can be really helpful!
• Include all troubleshooting tips, ie. some samples become foamy or mucusy at this step, carefully watch your pipette tip and aspirate very slowly to avoid the chunks. Or bubbles at this stage are not a concern because after the next centrifugation step they will be pushed down.
• If there are master mixes in the protocol, use some sort of place holder like n for number of samples to put in to the description of the calculation.

QC Steps

• List what steps to do for QC (if applicable).
• List data/sample type you arrive at when you’re done, ex: absorbance values, extracted DNA, sequencable libraries, etc etc.

Any final notes you want to provide!