Notes on DNA extractions of the third 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_ESW_01 | ESW | eelgrass + sw | 0.45um filter | 150 | -80 FHL | 3 | 2026-07-08 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_ESW_03 | ESW | eelgrass + sw | 0.45um filter | 150 | -80 FHL | 3 | 2026-07-08 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_EVP_01 | EVP | eelgrass + vp | 0.45um filter | 150 | -80 FHL | 3 | 2026-07-08 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_EVP_05 | EVP | eelgrass + vp | 0.45um filter | 150 | -80 FHL | 3 | 2026-07-08 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_VPSW_01 | VPSW | vp + sw | 0.45um filter | 150 | -80 FHL | 3 | 2026-07-08 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_VPSW_04 | VPSW | vp + sw | 0.45um filter | 150 | -80 FHL | 3 | 2026-07-08 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_VPSW_06 | VPSW | vp + sw | 0.45um filter | 150 | -80 FHL | 3 | 2026-07-08 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_EM_06 | EM | eelgrass + mussel + sw | 0.45um filter | 150 | -80 FHL | 3 | 2026-07-08 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_EMVP_06 | EMVP | eelgrass + mussel + vp | 0.45um filter | 150 | -80 FHL | 3 | 2026-07-08 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_EMVP_07 | EMVP | eelgrass + mussel + vp | 0.45um filter | 90 | -80 FHL | 3 | 2026-07-08 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | May 28th 12:17am (at time of inoc) mussel was spawning (male); half filter remaining in -80C; DNA from half filter |
| F_MVP_03 | MVP | mussel + vp | 0.45um filter | 150 | -80 FHL | 3 | 2026-07-08 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_MVP_04 | MVP | mussel + vp | 0.45um filter | 150 | -80 FHL | 3 | 2026-07-08 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_MVP_06 | MVP | mussel + vp | 0.45um filter | 150 | -80 FHL | 3 | 2026-07-08 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_MSW_07 | MSW | mussel + sw | 0.45um filter | 150 | -80 FHL | 3 | 2026-07-08 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_ShSW_05 | ShSW | mussel shell + sw | 0.45um filter | 150 | -80 FHL | 3 | 2026-07-08 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_SW_01 | SW | seawater + media | 0.45um filter | 150 | -80 FHL | 3 | 2026-07-08 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| F_SW_08 | SW | seawater + media | 0.45um filter | 150 | -80 FHL | 3 | 2026-07-08 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half filter remaining in -80C; DNA from half filter |
| BLANK3 | BLANK | BLANK | BLANK | NA | NA | 3 | 2026-07-08 | 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
I’m using the Eppendorf Centrifuge 5418 in FTR 213 that holds 18 tubes.
I took up the protocol for the optional stopping point after Step 2 Page 6 to eat and do some emails. Other than that, everything went smoothly and the DNA is in the same box as the other two batches in the -80C in FTR.
Up next
- Finish extracting DNA from remaining water filters (n=18 remaining) week of July 21 (I’ll be out of town July 10-20).
- Run 2ul of each sample’s DNA on qPCR looking for V. pectenicida <– late July