Summary of Study ST002321

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 PR001487. The data can be accessed directly via it's Project DOI: 10.21228/M8HM7D 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 IDST002321
Study Title13C NMR metabolomics: integrating J-resolved STOCSY and INADEQUATE
Study SummaryRobust annotation of metabolites remains a challenging task in metabolomics. This study introduces an approach that uses 13C homonuclear J-resolved experiment (JRES), statistical total correlation spectroscopy (STOCSY), and 2D incredible natural abundance double-quantum experiment (INADEQUATE) complementarily, to obtain robust molecular structure information based on 13C NMR with less experiment time. This approach was tested using the endometabolome from a model marine phytoplankton strain, varying the settings of incubation temperature, nutrient condition, and the presence of co-culturing bacteria.
Institute
University of Georgia
Last NameUchimiya
First NameMario
Address315 Riverbend Rd, Athens, GA, 30602, USA
Emailmario.uchimiya@uga.edu
Phone‭(706) 542-8387‬
Submit Date2022-10-17
Raw Data AvailableYes
Raw Data File Type(s)ser
Analysis Type DetailNMR
Release Date2022-11-25
Release Version1
Mario Uchimiya Mario Uchimiya
https://dx.doi.org/10.21228/M8HM7D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001487
Project DOI:doi: 10.21228/M8HM7D
Project Title:13C NMR metabolomics: integrating J-resolved STOCSY and INADEQUATE
Project Summary:Robust annotation of metabolites remains a challenging task in metabolomics. This study introduces an approach that uses 13C homonuclear J-resolved experiment (JRES), statistical total correlation spectroscopy (STOCSY), and 2D incredible natural abundance double-quantum experiment (INADEQUATE) complementarily, to obtain robust molecular structure information based on 13C NMR with less experiment time. This approach was tested using the endometabolome from a model marine phytoplankton strain, varying the settings of incubation temperature, nutrient condition, and the presence of co-culturing bacteria.
Institute:University of Georgia
Last Name:Uchimiya
First Name:Mario
Address:315 Riverbend Rd, Athens, GA, 30602, USA
Email:mario.uchimiya@uga.edu
Phone:‭(706) 542-8387‬
Funding Source:NSF (grant numbers 1948104, OCE-2019589, and 1946970), NIH (5R01GM120151-04)
Contributors:Edison Lab, Moran Lab

Subject:

Subject ID:SU002407
Subject Type:Other organism
Subject Species:Thalassiosira pseudonana
Taxonomy ID:296543

Factors:

Subject type: Other organism; Subject species: Thalassiosira pseudonana (Factor headings shown in green)

mb_sample_id local_sample_id Factor_1 (temperature) Factor_2 (bacteria presence)
SA2273725414.0 0.0
SA2273735714.0 0.0
SA2273745114.0 0.0
SA2273754814.0 0.0
SA2273761214.0 1.0
SA227377914.0 1.0
SA227378614.0 1.0
SA2273791514.0 1.0
SA2273806620.0 0.0
SA2273816920.0 0.0
SA2273826320.0 0.0
SA2273836020.0 0.0
SA2273841820.0 1.0
SA2273852720.0 1.0
SA2273862420.0 1.0
SA2273872120.0 1.0
SA2273887228.0 0.0
SA2273897828.0 0.0
SA2273907528.0 0.0
SA2273918128.0 0.0
SA2273924528.0 1.0
SA2273933928.0 1.0
SA2273943028.0 1.0
SA2273954228.0 1.0
Showing results 1 to 24 of 24

Collection:

Collection ID:CO002400
Collection Summary:320 mL of diatom cells were collected by filtering the culture onto 2.0-µm-pore-size PCTE membrane filters (MilliporeSigma Isopore). Filters were kept in 50 mL tubes (Falcon) and stored at -80oC until processing.
Collection Protocol Filename:2_Collection protocol__UGA_phytoplankton_Oct2022.docx
Sample Type:Algae

Treatment:

Treatment ID:TR002419
Treatment Summary:Six treatments of a marine diatom strain Thalassiosira pseudonana CCMP1335 were prepared: treatments incubated axenically at either 14, 20, or 28 oC, and treatments co-cultured with a bacterial strain Ruegeria pomeroyi DSS-3 at the corresponding temperatures (four replicates for each). L1 media was used with NaH13CO3 as a source of bicarbonate. The diatom used for the co-cultured treatments was B12 stressed to emphasize the known co-existing system. The light cycle consisted of 16 h light (120 µmol photons m-2 s-1) and 8 h of dark.
Treatment Protocol Filename:3_Treatment protocol__UGA_phytoplankton_Oct2022.docx

Sample Preparation:

Sampleprep ID:SP002413
Sampleprep Summary:Phytoplankton cells were removed from filters using a sonicator SLPe (Branson) in ultra-pure water (Millipore), concentrated by a lyophilizer (Labconco), and kept -80oC until further processing. The samples were mixed with 600 µL of 30 mmol L-1 sodium phosphate buffer (18 mmol L-1 NaHPO4, 12 mmol L-1, pH 7.4) and an internal standard of 2,2-dimethyl-2-silapentane-5-sulfonate-d6 (DSS, 1 mmol L-1), vortexed at 4oC for 5 minutes, centrifuged at 20,800 rcf using an ultracentrifuge 5417C (Eppendorf) at 4oC for 10 minutes, and supernatants were transferred to 5-mm NMR tubes (NORELL).
Sampleprep Protocol Filename:4_Sample preparation protocol__UGA_phytoplankton_Oct2022.docx

Analysis:

Analysis ID:AN003788
Analysis Type:NMR
Results File:ST002321_AN003788_Results.txt
Units:Intensity

NMR:

NMR ID:NM000254
Analysis ID:AN003788
Instrument Name:Bruker NEO
Instrument Type:CW-NMR
NMR Experiment Type:Other
Spectrometer Frequency:600 MHz
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