Final batch of DNA from half of the 0.45um filters (as in cut-in-half) from 2026 FHL experiment!
background info
Experiment info: Lab Notebook Post
DNA extraction info
Samples
–> extracted DNA from n=18 0.45um water filters (cut in half –> remaining half of filter is in FTR -80C) and 2 blank samples (DNA extraction control - needed to do 2 to keep centrifuge balanced).
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_02 | NA | 0.22um filtered SW + Vpec | 0.45um filter | 150 | -80 FHL | 4 | 2026-07-21 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half of filter remains in -80C |
| F_ESW_07 | ESW | eelgrass + sw | 0.45um filter | 150 | -80 FHL | 4 | 2026-07-21 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half of filter remains in -80C |
| F_EVP_02 | EVP | eelgrass + vp | 0.45um filter | 150 | -80 FHL | 4 | 2026-07-21 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half of filter remains in -80C |
| F_EVP_07 | EVP | eelgrass + vp | 0.45um filter | 150 | -80 FHL | 4 | 2026-07-21 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half of filter remains in -80C |
| F_VPSW_08 | VPSW | vp + sw | 0.45um filter | 150 | -80 FHL | 4 | 2026-07-21 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half of filter remains in -80C |
| F_EM_03 | EM | eelgrass + mussel + sw | 0.45um filter | 100 | -80 FHL | 4 | 2026-07-21 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half of filter remains in -80C |
| F_EM_08 | EM | eelgrass + mussel + sw | 0.45um filter | 150 | -80 FHL | 4 | 2026-07-21 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half of filter remains in -80C |
| F_EMVP_02 | EMVP | eelgrass + mussel + vp | 0.45um filter | 150 | -80 FHL | 4 | 2026-07-21 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half of filter remains in -80C |
| F_EMVP_03 | EMVP | eelgrass + mussel + vp | 0.45um filter | 150 | -80 FHL | 4 | 2026-07-21 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half of filter remains in -80C |
| F_MVP_01 | MVP | mussel + vp | 0.45um filter | 150 | -80 FHL | 4 | 2026-07-21 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half of filter remains in -80C; about 1/10 of 1/2 the filter fell out |
| F_MVP_05 | MVP | mussel + vp | 0.45um filter | 150 | -80 FHL | 4 | 2026-07-21 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half of filter remains in -80C |
| F_MSW_01 | MSW | mussel + sw | 0.45um filter | 150 | -80 FHL | 4 | 2026-07-21 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half of filter remains in -80C |
| F_MSW_03 | MSW | mussel + sw | 0.45um filter | 150 | -80 FHL | 4 | 2026-07-21 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half of filter remains in -80C |
| F_MSW_08 | MSW | mussel + sw | 0.45um filter | 150 | -80 FHL | 4 | 2026-07-21 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half of filter remains in -80C |
| F_ShSW_01 | ShSW | mussel shell + sw | 0.45um filter | 150 | -80 FHL | 4 | 2026-07-21 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half of filter remains in -80C |
| F_ShSW_02 | ShSW | mussel shell + sw | 0.45um filter | 150 | -80 FHL | 4 | 2026-07-21 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half of filter remains in -80C |
| F_ShSW_07 | ShSW | mussel shell + sw | 0.45um filter | 150 | -80 FHL | 4 | 2026-07-21 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half of filter remains in -80C |
| F_SW_05 | SW | seawater + media | 0.45um filter | 150 | -80 FHL | 4 | 2026-07-21 | half_filter | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | half of filter remains in -80C |
| F_BLANK4A | BLANK | BLANK | BLANK | NA | NA | 4 | 2026-07-21 | NA | ZymoBIOMICS DNA Miniprep Kit (D4300) | FTR -80C | water | 50 | |
| F_BLANK4B | BLANK | BLANK | BLANK | NA | NA | 4 | 2026-07-21 | NA | 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 used the Eppendorf Centrifuge 5424 in FTR 209 that holds 24 tubes.
I took up the protocol for the optional stopping point at Step 2 Page 6 to have a check-in meeting with Drew… but as a note, the stoppage point was pre-bead-beating, but post-lysis solution addition. Other than that, everything went smoothly and the DNA is in the same box as the other three batches in the -80C in FTR.
Up next
- Run 2ul of each sample’s DNA on qPCR looking for V. pectenicida <– n=80 samples (with all the DNA extraction blanks) will be split up across 4 qPCR plates (have done by Aug 4th meeting with Drew)
- Start eelgrass swab DNA extractions (n=32 samples, will also do blanks for each DNA extraction batch)