Since we have a working qPCR for detecting the withering syndrome bacteriophage (RLOv), Carolyn wanted to see how detection/quantification compared to withering syndrome detection/quantification on water samples collected from various farms and their nearest wild abalone site.
DNA samples used were extractions from water filters collected for the Ab Endo Project in 2011.
Ran qPCR using the RLOv DNA helicase standard curve from 20151106.
All samples were run in duplicate.
Master mix calcs are here (Google Sheet): 20151228 – qPCR RLOv 2011 H2O Filters
Plate layout, cycling params, etc. can be found in the qPCR Report (see Results below).
| qPCR LABEL | FULL DESCRIPTION | FARM/WILD SITE | NEAREST FARM/WILD SITE |
| CI_SCI_PC_1A | Painted Cave SCI 1A | Wild | The Cultured Abalone |
| CI_SRI_PC_1B | Painted Cave SCI 1B | Wild | The Cultured Abalone |
| CI_SCI_PC_2B | Painted Cave SCI 2B | Wild | The Cultured Abalone |
| CI_SCI_PC_2A | Painted Cave SCI 2A | Wild | The Cultured Abalone |
| CI_SCI_PRIS_1A | Prisoner’s 1A | Wild | The Cultured Abalone |
| CI_SCI_PRIS_2A | Prisoner’s 2A | Wild | The Cultured Abalone |
| CI_SCI_PRIS_1B | Prisoner’s 1B | Wild | The Cultured Abalone |
| CI_SCI_PRIS_2B | Prisoner’s 2B | Wild | The Cultured Abalone |
| RM_0M_SW | Rancho Marina 0M SW | Wild | The Abalone Farm |
| RM_0M_SW_#1 | Rancho Marina 0M SW #1 | Wild | The Abalone Farm |
| PSN_0M_#2 | Pt. Sierra Nevada 0M #2 | Wild | The Abalone Farm |
| PSN_0M_#1 | Pt. Sierra Nevada 0M #1 | Wild | The Abalone Farm |
| CARMEL_0M_2 | Carmel 0M 2 | Wild | American Abalone |
| AMER_DRAIN_1A | American Abalone Drain 1A | Farm | Carmel |
| AMER_DRAIN_2A | American Abalone Drain 2A | Farm | Carmel |
| AMER_DRAIN_1B | American Abalone Drain 1B | Farm | Carmel |
| AMER_DRAIN_2B | American Abalone Drain 2B | Farm | Carmel |
| AMER_0M_OUT_1A | American Abalone 0M Outfall 1A | Farm | Carmel |
| AMER_0M_OUT_2A | American Abalone 0M Outfall 2A | Farm | Carmel |
| AMER_0M_OUT_1B | American Abalone 0M Outfall 1B | Farm | Carmel |
| AMER_0M_OUT_2B | American Abalone 0M Outfall 2B | Farm | Carmel |
| TAF_DRAIN_DUP2B | The Abalone Farm Drain Dup 2B | Farm | Pt. Sierra Nevada/Rancho Marina |
| TAF_DRAIN_2C | The Abalone Farm Drain Dup 2C | Farm | Pt. Sierra Nevada/Rancho Marina |
| TAF_DRAIN_DUP2D | The Abalone Farm Drain Dup 2D | Farm | Pt. Sierra Nevada/Rancho Marina |
| TAF_DRAIN_1D | The Abalone Farm Drain Dup 1D | Farm | Pt. Sierra Nevada/Rancho Marina |
| TAF_DRAIN_DUP2A | The Abalone Farm Drain Dup 2A | Farm | Pt. Sierra Nevada/Rancho Marina |
| TAF_DRAIN_DUP1A | The Abalone Farm Drain Dup 1A | Farm | Pt. Sierra Nevada/Rancho Marina |
| TAF_DRAIN_1B | The Abalone Farm Drain Dup 1B | Farm | Pt. Sierra Nevada/Rancho Marina |
| TAF_DRAIN_1C | The Abalone Farm Drain Dup 1C | Farm | Pt. Sierra Nevada/Rancho Marina |
| CAB_N.OUT_1A | The Cultured Abalone North Outfall 1A | Farm | Santa Cruz Islands |
| TCA_N.OUT_1B | The Cultured Abalone North Outfall 1B | Farm | Santa Cruz Islands |
| CAB_N.OUT_1C | The Cultured Abalone North Outfall 1C | Farm | Santa Cruz Islands |
| CAB_N.OUT_1D | The Cultured Abalone North Outfall 1D | Farm | Santa Cruz Islands |
| TCA_S.OUT_1A | The Cultured Abalone South Outfall 1A | Farm | Santa Cruz Islands |
| TCA_S.OUT_1B | The Cultured Abalone South Outfall 1B | Farm | Santa Cruz Islands |
| CAB_S.OUT_1C | The Cultured Abalone South Outfall 1C | Farm | Santa Cruz Islands |
| CAB_S.OUT_1D | The Cultured Abalone South Outfall 1D | Farm | Santa Cruz Islands |
Results:
qPCR Report (PDF): Sam_2015-12-28 15-44-35_CC009827.pdf
qPCR Data File (CFX96): Sam_2015-12-28 15-44-35_CC009827.pcrd
Overall, data looks good. Will enter copy numbers into the Ab Endo master sheet for later analysis (Google Sheet): Ab Endo Samples
