See post for details on extracting DNA from eelgrass swabs from the FHL 2026 V. pec., eelgrass and mussel experiment - PART 3!!
Background info on the project
Post: FHL 2026 Experiment Details
DNA Extraction of Eelgrass Swabs Info:
Samples processed –> all done after this batch with eelgrass swabs!
| sample_id | treatment_id | treatment | sample_type |
|---|---|---|---|
| S_ESW_02 | ESW | eelgrass + sw | eelgrass_swab |
| S_ESW_04 | ESW | eelgrass + sw | eelgrass_swab |
| S_ESW_07 | ESW | eelgrass + sw | eelgrass_swab |
| S_ESW_08 | ESW | eelgrass + sw | eelgrass_swab |
| S_EVP_01 | EVP | eelgrass + vp | eelgrass_swab |
| S_EVP_02 | EVP | eelgrass + vp | eelgrass_swab |
| S_EVP_08 | EVP | eelgrass + vp | eelgrass_swab |
| S_EM_02 | EM | eelgrass + mussel + sw | eelgrass_swab |
| S_EM_04 | EM | eelgrass + mussel + sw | eelgrass_swab |
| S_EM_07 | EM | eelgrass + mussel + sw | eelgrass_swab |
| S_EM_08 | EM | eelgrass + mussel + sw | eelgrass_swab |
| S_EMVP_01 | EMVP | eelgrass + mussel + vp | eelgrass_swab |
| S_EMVP_03 | EMVP | eelgrass + mussel + vp | eelgrass_swab |
| S_EMVP_04 | EMVP | eelgrass + mussel + vp | eelgrass_swab |
| S_Blank_05 | NA | NA | NA |
| S_Blank_06 | NA | NA | NA |
Protocol notes:
Extraction Kit: Qiagen DNeasy PowerSoil Pro Kit (Cat: 47014)
Extraction Notes: here
Protocol was modified by Becca Maher specifically for swabs from eelgrass tissue (see link to notes above).
Eelgrass swab sampling protocol: here
Note on sample S_EVP_08: during the extraction for step 7 where you transfer 500ul of the liquid to a tube that has 200ul of CD2… I have been having to remove the swab using sterile tweezers because otherwise the P1000 tip doesn’t fit in the tube to access the liquid. For this one sample (S_EVP_08), I accidentally put the swab in the tube with the 200ul CD2 and threw out the tube with the 500ul of liquid. I realized my mistake immediately. I used sterile tweezers to remove the swab, then fished the tube out of the trash (was on top of the trash and on a kimwipe) and transferred the 500ul of liquid to the tube with 200ul of CD2. Everything else from then on was the same and normal for that sample and all other samples.
Results
Stay tuned for when I run 2ul of each sample on qPCR targetting V. pec!
Kit note
There are now 11 preps remaining in the kit! Another kit is on the way so that I can process mussel shell swabs.