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.
| Study ID | ST002321 |
| Study Title | 13C NMR metabolomics: integrating J-resolved STOCSY and INADEQUATE |
| Study 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 |
| mario.uchimiya@uga.edu | |
| Phone | (706) 542-8387 |
| Submit Date | 2022-10-17 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | ser |
| Analysis Type Detail | NMR |
| Release Date | 2022-11-25 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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) |
|---|---|---|---|
| SA227372 | 54 | 14.0 | 0.0 |
| SA227373 | 57 | 14.0 | 0.0 |
| SA227374 | 51 | 14.0 | 0.0 |
| SA227375 | 48 | 14.0 | 0.0 |
| SA227376 | 12 | 14.0 | 1.0 |
| SA227377 | 9 | 14.0 | 1.0 |
| SA227378 | 6 | 14.0 | 1.0 |
| SA227379 | 15 | 14.0 | 1.0 |
| SA227380 | 66 | 20.0 | 0.0 |
| SA227381 | 69 | 20.0 | 0.0 |
| SA227382 | 63 | 20.0 | 0.0 |
| SA227383 | 60 | 20.0 | 0.0 |
| SA227384 | 18 | 20.0 | 1.0 |
| SA227385 | 27 | 20.0 | 1.0 |
| SA227386 | 24 | 20.0 | 1.0 |
| SA227387 | 21 | 20.0 | 1.0 |
| SA227388 | 72 | 28.0 | 0.0 |
| SA227389 | 78 | 28.0 | 0.0 |
| SA227390 | 75 | 28.0 | 0.0 |
| SA227391 | 81 | 28.0 | 0.0 |
| SA227392 | 45 | 28.0 | 1.0 |
| SA227393 | 39 | 28.0 | 1.0 |
| SA227394 | 30 | 28.0 | 1.0 |
| SA227395 | 42 | 28.0 | 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 |
