Return to study ST001895 main page
MB Sample ID: SA176009
| Local Sample ID: | Acatenella 5 |
| Subject ID: | SU001973 |
| Subject Type: | Other organism |
| Subject Species: | Alexandrium catenella; Alexandrium tamarense |
| Taxonomy ID: | 2925; 2926 |
| Genotype Strain: | CCMP 1719; CCMP 2023 |
| Gender: | Not applicable |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001973 |
| Subject Type: | Other organism |
| Subject Species: | Alexandrium catenella; Alexandrium tamarense |
| Taxonomy ID: | 2925; 2926 |
| Genotype Strain: | CCMP 1719; CCMP 2023 |
| Gender: | Not applicable |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| Acatenella 5 | SA176009 | FL021830 | Alexandrium_catenella | Treatment |
Collection:
| Collection ID: | CO001966 |
| Collection Summary: | Alexandrium cells were collected by vacuum filtration onto GF/F filters and quenched with liquid nitrogen. Frozen cells with filters were stored in foil (previously muffled for 3 h at 450 °C) at -80 °C until extraction. |
| Collection Protocol Filename: | Differentiating_toxic_and_nontoxic_congeneric_harmful_algae_using_the_non-polar_metabolome_protocol.pdf |
| Sample Type: | Algae |
| Collection Method: | Filtration and Freeze |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001985 |
| Treatment Summary: | Metabolomes of toxic versus non-toxic species were compared using the following experimental pairings: A. tamarense (n=15) with A. catenella (n=15) (Experiment 1) and A. tamarense (n=15) with A. pacificum (n=15) (Experiment 2). The same non-toxic strain of A. tamarense was used in both experiments but the two experiments were conducted separately, in different months, to make the experiment manageable based on availability of batches grown from stock cultures. For both experiments, Alexandrium spp. cultures at a cell density of 12,000 to 13,000 cells mL-1 were split into fifteen 300 mL subcultures of each species which grew for two days. At the end of each experiment, during harvesting, a 1.0 mL aliquot from each culture was preserved with Lugol’s solution to measure cell concentrations |
| Treatment Protocol Filename: | Differentiating_toxic_and_nontoxic_congeneric_harmful_algae_using_the_non-polar_metabolome_protocol.pdf |
| Treatment: | Species comparison |
Sample Preparation:
| Sampleprep ID: | SP001979 |
| Sampleprep Summary: | Non polar extracts were dissolved with volumes calculated to account for different cell densities at the time of harvesting, to a concentration equivalent to 1.62 x 10^7 Alexandrium cells mL-1 in dimethyl sulfoxide d6 (99.9% atom d6-DMSO; Cambridge Isotope Labs) containing 0.1% trimethylsilane (TMS) as internal standard for 1H nuclear magnetic resonance (NMR) spectroscopy analysis. The extracts were transferred to 3 mm NMR tubes. Extracts from Experiment 1 (A. tamarense-A. catenella) were analyzed using a Bruker Avance IIIHD 800 MHz NMR spectrometer equipped with a 3 mm triple resonance broadband cryoprobe. Spectra of non-polar extracts from both experiments were acquired using a Bruker zg30 pulse sequence 1H NMR experiment compiled from 320 scans. Due to poor NMR spectral quality one A. tamarense replicate spectrum was removed from analysis of Experiment 1 (A. tamarense-A. catenella. |
| Sampleprep Protocol Filename: | Differentiating toxic and nontoxic congeneric harmful algae using the non-polar metabolome_protocol.pdf |
| Extract Storage: | -80℃ |
Analysis:
| MB Sample ID: | SA176009 |
| Analysis ID: | AN003076 |
| Analysis Type: | NMR |
| Results File: | Preprocessed_binned_Experiment1_AcvAt_NMRmetabolomics.txt |
| Units: | area under the curve |
NMR:
| NMR ID: | NM000212 |
| Analysis ID: | AN003076 |
| Instrument Name: | Bruker Avance IIIHD |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D-1H |
| Spectrometer Frequency: | 800 MHz |
| NMR Probe: | 3 mm triple resonance broadband cryoprobe |
| NMR Solvent: | Dimethyl sulfoxide d6 (99.9% atom d6-DMSO; Cambridge Isotope Labs) containing 0.1% trimethylsilane |
| NMR Tube Size: | 3 mm |
| Pulse Sequence: | zg30 |
| Number Of Scans: | 320 |
| Baseline Correction Method: | Spline |
| Binned Increment: | 0.005 ppm |
