Notes on DNA extractions of the first batch of 0.45um 1/2 water filters from FHL 2026 experiment.
background info
Experiment info: Lab Notebook Post
DNA extraction info
Samples
–> extracted DNA from n=17 0.45um water filters (cut in half –> remaining half of filter is in FTR -80C) and 1 blank sample (DNA extraction control).
Samples extracted:
| sample_id | treatment_id | treatment | sample_type | vol_filtered_mL | sample_location | extraction_batch | DNAextract_date | amount_sample_processed | extraction_kit | DNA_location | elution_liquid | elution_vol_ul | notes |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| F_T0_03 | NA | 0.22um filtered SW + Vpec | 0.45um filter | 150 | FTR -80 | 1 | 2026-07-06 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_ESW_02 | ESW | eelgrass + sw | 0.45um filter | 150 | FTR -80 | 1 | 2026-07-06 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_ESW_05 | ESW | eelgrass + sw | 0.45um filter | 150 | FTR -80 | 1 | 2026-07-06 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_EVP_04 | EVP | eelgrass + vp | 0.45um filter | 150 | FTR -80 | 1 | 2026-07-06 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_EVP_06 | EVP | eelgrass + vp | 0.45um filter | 150 | FTR -80 | 1 | 2026-07-06 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_VPSW_02 | VPSW | vp + sw | 0.45um filter | 150 | FTR -80 | 1 | 2026-07-06 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_VPSW_05 | VPSW | vp + sw | 0.45um filter | 150 | FTR -80 | 1 | 2026-07-06 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_EM_07 | EM | eelgrass + mussel + sw | 0.45um filter | 150 | FTR -80 | 1 | 2026-07-06 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_MVP_07 | MVP | mussel + vp | 0.45um filter | 150 | FTR -80 | 1 | 2026-07-06 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_MSW_02 | MSW | mussel + sw | 0.45um filter | 150 | FTR -80 | 1 | 2026-07-06 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_MSW_04 | MSW | mussel + sw | 0.45um filter | 100 | FTR -80 | 1 | 2026-07-06 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_MSW_05 | MSW | mussel + sw | 0.45um filter | 150 | FTR -80 | 1 | 2026-07-06 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_MSW_06 | MSW | mussel + sw | 0.45um filter | 125 | FTR -80 | 1 | 2026-07-06 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | May 28th 12:03am - right before inoc - mussel spawning (female) ; half filter remaining in -80C; DNA from half filter |
| F_ShSW_03 | ShSW | mussel shell + sw | 0.45um filter | 150 | FTR -80 | 1 | 2026-07-06 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_ShSW_06 | ShSW | mussel shell + sw | 0.45um filter | 150 | FTR -80 | 1 | 2026-07-06 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_SW_02 | SW | seawater + media | 0.45um filter | 150 | FTR -80 | 1 | 2026-07-06 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_SW_06 | SW | seawater + media | 0.45um filter | 150 | FTR -80 | 1 | 2026-07-06 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| BLANK1 | BLANK | BLANK | BLANK | NA | NA | 1 | 2026-07-06 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 |
Kit and protocol info:
ZymoBIOMICS DNA MiniPrep Kit –> D4300
Extraction protocol notes: Protocol_eDNA-extraction_protocol_GAC_2026Samples
Note for future self - centrifuge can only hold 18 tubes at a time (n=17 samples + 1 extraction blank).
Maybe there’s another one I can use tomorrow and Wednesday to run 24 tubes at a time.
Up next
- Finish extracting DNA from remaining water filters (n=58 remaining)
- Run 2ul of each sample’s DNA on qPCR looking for V. pectenicida <– this will happen later July (out of town July 10-20, also the TaqMan hasn’t arrived yet…)