Summary of Study ST001645
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000747. The data can be accessed directly via it's Project DOI: 10.21228/M8469M This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST001645 |
| Study Title | Variability in metabolomic profiles among unique genotypes of Acropora cervicornis (part -III) |
| Study Type | intraspecific variability |
| Study Summary | This project aims to identify differences in metabolomic profiles among seven known, unique genotypes of the threatened staghorn coral Acropora cervicornis. |
| Institute | University of Florida |
| Department | SECIM |
| Last Name | Patterson |
| First Name | Joshua |
| Address | Florida Aquarium Center for Conservation, 529 Estuary Shore Lane, Apollo Beach, FL 33572 |
| joshpatterson@ufl.edu | |
| Phone | (813) 419-4917 |
| Submit Date | 2020-12-22 |
| Num Groups | 7 |
| Total Subjects | 41 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | fid |
| Analysis Type Detail | NMR |
| Release Date | 2021-06-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000747 |
| Project DOI: | doi: 10.21228/M8469M |
| Project Title: | Variability in metabolomic profiles among unique genotypes of Acropora cervicornis |
| Project Type: | intraspecific variability |
| Project Summary: | This project aims to identify differences in metabolomic profiles among known, unique genotypes of the threatened staghorn coral Acropora cervicornis. Previous studies have shown that the three genotypes selected for study possess unique phenotypes related to growth and thermotolerance. Improved understanding of metabolomic differences could aid in selection of A. cervicornis genotypes for use in restoration. |
| Institute: | University of Florida |
| Department: | Department of Fisheries and Aquatic Sciences |
| Last Name: | Patterson |
| First Name: | Joshua |
| Address: | Florida Aquarium Center for Conservation, 529 Estuary Shore Lane, Apollo Beach, FL 33572 |
| Email: | joshpatterson@ufl.edu |
| Phone: | 8134194917 |
Subject:
| Subject ID: | SU001722 |
| Subject Type: | Other organism |
| Subject Species: | Acropora cervicornis |
| Taxonomy ID: | 6130 |
| Genotype Strain: | U77, U44, U41, U25, K1, K2, K3 |
Factors:
Subject type: Other organism; Subject species: Acropora cervicornis (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype |
|---|---|---|
| SA151460 | K1_C1 | K1 |
| SA151461 | K1_C2 | K1 |
| SA151462 | K1_B2 | K1 |
| SA151463 | K1_B1 | K1 |
| SA151464 | K1_A2 | K1 |
| SA151465 | K1_A1 | K1 |
| SA151466 | K2_A2 | K2 |
| SA151467 | K2_A1 | K2 |
| SA151468 | K2_B1 | K2 |
| SA151469 | K2_B2 | K2 |
| SA151470 | K2_C1 | K2 |
| SA151471 | K2_C2 | K2 |
| SA151472 | K3_C1 | K3 |
| SA151473 | K3_C2 | K3 |
| SA151474 | K3_B2 | K3 |
| SA151475 | K3_A2 | K3 |
| SA151476 | K3_A1 | K3 |
| SA151477 | K3_B1 | K3 |
| SA151478 | U25_C2 | U25 |
| SA151479 | U25_C1 | U25 |
| SA151480 | U25_B2 | U25 |
| SA151481 | U25_A1 | U25 |
| SA151482 | U25_A2 | U25 |
| SA151483 | U25_B1 | U25 |
| SA151484 | U41_A2 | U41 |
| SA151485 | U41_A1 | U41 |
| SA151486 | U41_B2 | U41 |
| SA151487 | U41_C1 | U41 |
| SA151488 | U41_C2 | U41 |
| SA151489 | U44_A2 | U44 |
| SA151490 | U44_A1 | U44 |
| SA151491 | U44_B1 | U44 |
| SA151492 | U44_C2 | U44 |
| SA151493 | U44_B2 | U44 |
| SA151494 | U44_C1 | U44 |
| SA151495 | U77_B1 | U77 |
| SA151496 | U77_A2 | U77 |
| SA151497 | U77_B2 | U77 |
| SA151498 | U77_C2 | U77 |
| SA151499 | U77_A1 | U77 |
| SA151500 | U77_C1 | U77 |
| Showing results 1 to 41 of 41 |
Collection:
| Collection ID: | CO001715 |
| Collection Summary: | Coral colonies were brought to the surface intact, and ~3 cm nubbins were clipped from actively growing branch tips. Nubbins were wrapped in aluminum foil and immediately frozen in liquid nitrogen. Nubbins were then ground down in an ice chilled mortar pastel in 10 mL of 2:1 Chloroform/Methanol solution. Supernatant was then transferred into a test tube labeled with sample I.D. and Organic and vortexed for 10 seconds. 2 mL of .9% NaCl was then added to each tube and vortexed for an additional 10 seconds. Samples were then allowed to separate for 15 minutes on ice. After the allotted time, the supernatant was separated and placed in a separate test tube labeled with sample I.D. and Aqueous. Both test tubes were then stored in a -80°C freezer until processing. |
| Sample Type: | Tissue and skeleton |
Treatment:
| Treatment ID: | TR001735 |
| Treatment Summary: | No treatment was applied; study was conducted on natural metabolomic variation among genotypes |
Sample Preparation:
| Sampleprep ID: | SP001728 |
| Sampleprep Summary: | Metabolomic analyses were performed at the Southeast Center for Integrated Metabolomics (SECIM) at the University of Florida. Dried powder of aqueous phase samples acquired from methanol/chloroform extraction were dissolved in 50mM sodium phosphate buffer with 0.5mM D6-deuterated sodium trimethylsilylpropanesulfonate (DSS-d6). NMR spectra were measured using the first slice of a NOESY pulse sequence (tnnoesy) using 14.1 T Bruker Avance II NMR system with a CP TXI CryoProbe. The acquisition parameters used in Lohr et al. (2019) and Myer et al. (2020) were utilized to acquire proton spectra. All spectra were processed and the integrated area was extracted using MestReNova 11.0-17609 (Mestrelab Research S.L.). Before Fourier transformation, baseline correction and phase correction were applied with a line-broadening factor of 0.22 Hz and spectra were normalized with respect to a DSS signal at 0.0 ppm. |
| Processing Method: | Lyophilization and Homogenization |
| Processing Storage Conditions: | -80℃ |
| Extraction Method: | Modified FOLCH extraction |
| Extract Storage: | -80℃ |
| Sample Resuspension: | In 50 mM phosphate buffer (pH 7.2) with 2 mM EDTA, 0.5 mM DSS and 0.2% sodium azide for aqueous phase samples. |
| Sample Spiking: | 0.5 mM of DSS for aqueous phase samples |
Analysis:
| Analysis ID: | AN002691 |
| Laboratory Name: | Matt |
| Analysis Type: | NMR |
| Acquisition Date: | 02/02/2018 |
| Software Version: | Bruker Topspin |
| Operator Name: | Ram Khattri |
| Detector Type: | Bruker |
| Data Format: | fid, 1r |
NMR:
| NMR ID: | NM000199 |
| Analysis ID: | AN002691 |
| Instrument Name: | Bruker Avance Neo 600 MHz/54mm console |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D-1H |
| Field Frequency Lock: | Deuterium |
| Standard Concentration: | 0.5 mM DSS |
| Spectrometer Frequency: | 600.2328273 MHz |
| NMR Probe: | CP TXI CryoProbe |
| NMR Solvent: | Phosphate buffer (pH 7.2) + 2 mM EDTA + 0.5 mM DSS + 0.2% of sodium azide in deuterated environment |
| NMR Tube Size: | 1.5 mm O.D. |
| Shimming Method: | Topshim |
| Pulse Sequence: | noesypr1d |
| Water Suppression: | presat |
| Pulse Width: | 90-degree |
| Receiver Gain: | 256 |
| Offset Frequency: | 2827.31 Hz |
| Chemical Shift Ref Cpd: | DSS (4,4-dimethyl-4-silapentane-1-sulfonic acid) |
| Temperature: | 25 o C |
| Number Of Scans: | 64 |
| Dummy Scans: | 4 |
| Acquisition Time: | 4 s |
| Relaxation Delay: | 1 s |
| Spectral Width: | 7211.54 |
| Num Data Points Acquired: | 57690 |
| Real Data Points: | 65536 |
| Line Broadening: | 0.22 Hz |
| Zero Filling: | 65,536 points |
| Apodization: | Exponential |
| Baseline Correction Method: | Spline |
| Chemical Shift Ref Std: | 0 ppm for DSS |
| Binned Increment: | 0.4ppm |
| Binned Data Excluded Range: | greater than 9.5 ppm and below 0.5 ppm including water regions |
