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.

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Study IDST001645
Study TitleVariability in metabolomic profiles among unique genotypes of Acropora cervicornis (part -III)
Study Typeintraspecific variability
Study SummaryThis project aims to identify differences in metabolomic profiles among seven known, unique genotypes of the threatened staghorn coral Acropora cervicornis.
Institute
University of Florida
DepartmentSECIM
Last NamePatterson
First NameJoshua
AddressFlorida Aquarium Center for Conservation, 529 Estuary Shore Lane, Apollo Beach, FL 33572
Emailjoshpatterson@ufl.edu
Phone(813) 419-4917
Submit Date2020-12-22
Num Groups7
Total Subjects41
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2021-06-22
Release Version1
Joshua Patterson Joshua Patterson
https://dx.doi.org/10.21228/M8469M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA151460K1_C1K1
SA151461K1_C2K1
SA151462K1_B2K1
SA151463K1_B1K1
SA151464K1_A2K1
SA151465K1_A1K1
SA151466K2_A2K2
SA151467K2_A1K2
SA151468K2_B1K2
SA151469K2_B2K2
SA151470K2_C1K2
SA151471K2_C2K2
SA151472K3_C1K3
SA151473K3_C2K3
SA151474K3_B2K3
SA151475K3_A2K3
SA151476K3_A1K3
SA151477K3_B1K3
SA151478U25_C2U25
SA151479U25_C1U25
SA151480U25_B2U25
SA151481U25_A1U25
SA151482U25_A2U25
SA151483U25_B1U25
SA151484U41_A2U41
SA151485U41_A1U41
SA151486U41_B2U41
SA151487U41_C1U41
SA151488U41_C2U41
SA151489U44_A2U44
SA151490U44_A1U44
SA151491U44_B1U44
SA151492U44_C2U44
SA151493U44_B2U44
SA151494U44_C1U44
SA151495U77_B1U77
SA151496U77_A2U77
SA151497U77_B2U77
SA151498U77_C2U77
SA151499U77_A1U77
SA151500U77_C1U77
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
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