See details in post.
Experiment details: here
Samples and Notes
| sample_id | treatment_id | treatment | sample_type | mussel_weight_processed_g | vol_filtered_mL | sample_location |
|---|---|---|---|---|---|---|
| M_EM_01 | EM | eelgrass + mussel + sw | mussel | 0.1571 | NA | -80 UW FTR |
| M_EM_02 | EM | eelgrass + mussel + sw | mussel | 0.1552 | NA | -80 UW FTR |
| M_EM_04 | EM | eelgrass + mussel + sw | mussel | 0.157 | NA | -80 UW FTR |
| M_EM_08 | EM | eelgrass + mussel + sw | mussel | 0.1538 | NA | -80 UW FTR |
| M_EMVP_02 | EMVP | eelgrass + mussel + vp | mussel | 0.1517 | NA | -80 UW FTR |
| M_EMVP_03 | EMVP | eelgrass + mussel + vp | mussel | 0.1563 | NA | -80 UW FTR |
| M_EMVP_05 | EMVP | eelgrass + mussel + vp | mussel | 0.1518 | NA | -80 UW FTR |
| M_EMVP_06 | EMVP | eelgrass + mussel + vp | mussel | 0.155 | NA | -80 UW FTR |
| M_MVP_03 | MVP | mussel + vp | mussel | 0.1513 | NA | -80 UW FTR |
| M_MVP_04 | MVP | mussel + vp | mussel | 0.1592 | NA | -80 UW FTR |
| M_MVP_05 | MVP | mussel + vp | mussel | 0.1536 | NA | -80 UW FTR |
| M_MVP_07 | MVP | mussel + vp | mussel | 0.151 | NA | -80 UW FTR |
| M_MSW_03 | MSW | mussel + sw | mussel | 0.1545 | NA | -80 UW FTR |
| M_MSW_04 | MSW | mussel + sw | mussel | 0.1523 | NA | -80 UW FTR |
| M_MSW_05 | MSW | mussel + sw | mussel | 0.1531 | NA | -80 UW FTR |
| M_MSW_06 | MSW | mussel + sw | mussel | 0.15 | NA | -80 UW FTR |
| M_BLANK1 | BLANK | NA | NA | NA | NA | NA |
| M_BLANK2 | BLANK | NA | NA | NA | NA | NA |
Protocol notes: google doc
What I did this afternoon:
- Wiped down benchtop and pipet tips and tube racks with dilute bleach and DNA/RNA Eliminase stuff
- Got the mussels from the -80C and let thaw at room temp for ~1.5hours.
- Using sterile tools (dip in 10% bleach, 70% ethanol, flame between uses) I swab each mussel shell and save at -80C, then open the mussel and scrape out all the mussel tissue into a labeled 1.5ml tube. I use the pokey tool thing from my dissection kit to mash the mushy tissue. Then, I weigh ~15mg of tissue from each mussel into a new 1.5ml tube.
- I was going to continue on to the extraction protocol steps (linked in google doc above)… but the bottle that Chris mentioned was extra Proteinase K that I could use is actually Solution CD2… unless I truly am not looking in the right place. I messaged her so I’ll see what she says. In the meantime, I put the 15mg of weighed tissue samples back inthe -80C for storage.
Proteinase K issue –> I have some proteinase K from old kits from Zymo Research… which online says it’s roughly the same thing as the proteinase K from the Qiagen Blood and Tissue Kit… but I’m unsure if it’s a good idea to mix and match from different kits. I’ll wait to hear what Chris says and if she doesn’t actually have extra Proteinase K from the Qiagen Blood and Tissue kit for me to use, then I’ll post a GitHub issue (after doing more research) to see if it would be ok for me to use the Proteinase K from the Zymo research kit in replacement.
Proteinase K from Qiagen Blood and Tissue Kit cat 19131: link
Proteinase K from Zymo Research that I have extra of from old kits: link