Notes on protocol and process in post. Testing again with correct mussel tissue weights.

Why am I doing this again?

Well… it turns out I messed up the decimals when I was weighing my tissue during the first FHL 2025 mussel tissue DNA extraction test, and was testing out 100mg, 150mg, 200mg, and 250mg of tissue instead of 10mg, 15mg, 20mg, and 25mg. So I am re-doing the test with the correct weights.

GitHub Issue with response from SR: #2507

Kit and Protocol Notes:

Protocol notes: here

The kit reagents that I got from Olivia Graham is missing extra Proteinase K, so a previous notebook post explains that I can use the proteinase K from old Zymo kits, so long as it’s in the correct concentration (20mg/mL).

I looked back at the Zymo Quick DNA/RNA Microprep Plus Kit (D7005) protocol and saw that the aliquots I made for that kit are in the correct concentration (20mg/mL). So I am using those moving forward. I have a bunch aliquoted out! Stored in the FTR 213 freezer.

Samples Extracted

I grabbed 4 mussels from the 2025 FHL pilot experiment that were not actually from the experiment at all… but were exposed to Vibrio pectenicida for a couple days.

The samples are:

M2A; M2B; M3A; M3B

Qubit and Nanodrop results:

Qubit

Nanodrop

Ran 2ul of each sample on the nanodrop.

Goal is to have “Nanodrop is still useful for the purity ratios. Look at 260/280 (target about 1.8) and 260/230 (target about 2.0 to 2.2). A low 260/230 would point to carryover”

For my actual samples:

I have n=32 samples from the actual FHL 2026 Experiment (experiment info here).