Summary of study ST001163

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 IDST001163
Study TitleVariability in metabolomic profiles among unique genotypes of Acropora cervicornis (part-II)
Study SummaryWe hypothesized that each of the three genotypes tested would have unique metabolomic profiles. These data increase our basic knowledge of the coral metabolome and represent an important step toward linking genotype, phenotype, and metabolome in reef-building corals.
Institute
University of Florida
DepartmentFlorida Aquarium Center for Conservation
Last NamePatterson
First NameJoshua
Address529 Estuary Shore Lane, Apollo Beach, FL 33572
Emailjoshpatterson@ufl.edu
Phone813-419-4917
Submit Date2019-03-11
Num Groups3
Total Subjects16
Analysis Type DetailLC-MS
Release Date2020-03-11
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:SU001228
Subject Type:Other
Subject Species:Acropora cervicornis
Taxonomy ID:6130
Genotype Strain:U25, U41, U44

Factors:

Subject type: Other; Subject species: Acropora cervicornis (Factor headings shown in green)

mb_sample_id local_sample_id Genotype
SA080488U25_B_2bU25
SA080489U25_A_1bU25
SA080490U25_B_1bU25
SA080491U25_A_3bU25
SA080492U25_A_2bU25
SA080493U41_B_1bU41
SA080494U41_B_2bU41
SA080495U41_A_4bU41
SA080496U41_A_3bU41
SA080497U41_A_1bU41
SA080498U41_A_2bU41
SA080499U44_B_2bU44
SA080500U44_B_1bU44
SA080501U44_A_2bU44
SA080502U44_A_1bU44
SA080503U44_A_3bU44
Showing results 1 to 16 of 16

Collection:

Collection ID:CO001222
Collection Summary:Coral colonies were brought to the surface intact, and ~3 cm nubbins were clipped from actively growing branch tips. Nubbins were placed in 20 mL scintillation vials containing 10 mL of 100% methanol spiked with a 0.005 mM aminoanthracene standard and immedately placed on ice. Samples were stored in a -20°C freezer overnight, then transported back to the laboratory n ice and again stored in a 20°C freezer overnight prior to extraction. The next day, samples were agitated for 5 minutes, then allowed to settle for one hour in the -20°C freezer. One mL of the sample extract was transferred to clean 1.5 mL microcentrifuge tubes and centrifuged at 20,000 g for 5 minutes. The supernatant was then transferred to a new 1.5 mL microcentrifuge tube and stored in a -80°C freezer until processing.
Sample Type:Tissue and skeleton

Treatment:

Treatment ID:TR001243
Treatment Summary:No treatment was applied; study was conducted on natural metabolomic variation among genotypes

Sample Preparation:

Sampleprep ID:SP001236
Sampleprep Summary:Corol holobiont extract (in methonol) was added to double distilled water (1:2 v/v of sample to water), then flash freeze lyophilized (Labconco) until dry. Lyophilized dry powder was re-suspended in phosphate buffer in deuterium oxide at pH 7. The final volume for the 1H-NMR samples was 60 μL (in a 1.5 mm O.D. tube) with 90 % (v/v) of deuterated 50 mM sodium phosphate buffer (pH 7) with 2 mM of ethylene diamine tetra-acetic acid (EDTA). The remaining 10 % (v/v) was occupied by an internal standard [5 mM D6-4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS-D6) and 0.2% sodium azide in deuterated environment; Chenomx, Inc.].
Processing Method:Lyophilization
Processing Storage Conditions:-80℃
Extract Storage:-80℃

Combined analysis:

Analysis ID AN001923 AN001924
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column ACE Excel 2 C18-PFP (100 x 2.1mm, 2um) ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Exactive Plus Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Peak Height Peak Height

Chromatography:

Chromatography ID:CH001396
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
Chromatography Type:Reversed phase

MS:

MS ID:MS001779
Analysis ID:AN001923
Instrument Name:Thermo Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metaboanalyst for data processing
Ion Mode:POSITIVE
  
MS ID:MS001780
Analysis ID:AN001924
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Metaboanalyst for data processing
Ion Mode:NEGATIVE
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