Summary of Study ST000103
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 PR000095. The data can be accessed directly via it's Project DOI: 10.21228/M8S88T This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000103 |
| Study Title | 2D-INADEQUATE NMR study of C. elegans metabolome |
| Study Type | Heats Shock Worms |
| Study Summary | 2D INADEQUATE NMR datasets were collected from the endo and exo metabolome of heat shocked and control C. elegans |
| Institute | University of Florida |
| Department | Department of Biochemistry and Molecular Biology and Southeastern Center for Integrated Metabolomics (SECIM) |
| Laboratory | Arthur Edison |
| Last Name | Chaevien |
| First Name | Clendinen |
| Address | R3-226 Academic Research Building, Department of Biochemistry & Molecular Biology, PO Box 100245, Gainesville, FL 32610-0245 |
| csclendinen@ufl.edu | |
| Phone | 352-392-4535 |
| Submit Date | 2014-09-25 |
| Num Groups | 2 |
| Total Subjects | 4 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | fid |
| Uploaded File Size | 3.1 G |
| Analysis Type Detail | NMR |
| Release Date | 2016-06-18 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000095 |
| Project DOI: | doi: 10.21228/M8S88T |
| Project Title: | 13C Metabolomics using INADEQUATE |
| Project Summary: | Demonstrate a method using high-sensitivity NMR to identify an unknown metabolite from a fraction isolated from an IROA LC-MS experiment. |
| Institute: | University of Florida |
| Department: | Department of Biochemistry and Molecular Biology and Southeastern Center for Integrated Metabolomics (SECIM) |
| Laboratory: | Edison |
| Last Name: | Edison |
| First Name: | Arthur |
| Email: | aedison@ufl.edu |
| Phone: | 352-392-4535 |
Subject:
| Subject ID: | SU000122 |
| Subject Type: | Invertebrate |
| Subject Species: | Caenorhabditis elegans |
| Taxonomy ID: | 6239 |
| Genotype Strain: | Wild Type (N2) |
| Gender: | Hermaphrodites |
| Species Group: | Invertebrates |
Factors:
Subject type: Invertebrate; Subject species: Caenorhabditis elegans (Factor headings shown in green)
| mb_sample_id | local_sample_id | Incubation Temperature |
|---|---|---|
| SA005669 | Control_2 | 22 C |
| SA005670 | Control_3 | 22 C |
| SA005671 | Control_4 | 22 C |
| SA005672 | Control_1 | 22 C |
| SA005673 | HS_4 | 33 C |
| SA005674 | HS_2 | 33 C |
| SA005675 | HS_3 | 33 C |
| SA005676 | HS_1 | 33 C |
| Showing results 1 to 8 of 8 |
Collection:
| Collection ID: | CO000105 |
| Collection Summary: | Supernatant (exometabolome) and worm pellet (endometabolome) were collected from each flask via centrifugation. The supernatant was filtered using a 20 ?m nylon syringe filter and lyophilized. The worm pellets were homogenized using a Biospec Mini-Beadbeater 8 in 80% methanol and dried. |
| Sample Type: | Whole worm extract |
| Collection Location: | University of Florida |
| Storage Conditions: | -80 celsius |
Treatment:
| Treatment ID: | TR000123 |
| Treatment Summary: | Two generations of wild-type C. elegans (N2) were fed 99% labeled e. coli. Upon reaching the young adult stage, 4 replicates of 1 million worms each were designated as the experimental population and were treated to a 30 minute heat shock by incubating at 33 °C in the absence of food. After 30 minutes of heat shock, the experimental populations were incubated at room temperature (22 °C) for an additional 1.5 hours. In addition 4 additional replicates of 1 million worms each were designated as the control population and was incubated at room temperature (22 °C) 2 hours in the absence of food. |
Sample Preparation:
| Sampleprep ID: | SP000118 |
| Sampleprep Summary: | Exometabolome samples were resuspended in 50 ul of Dueterium Oxide (D2O) and the Endometabolome were resuspended in 50 ul of Deuterated Methanol (MeOD). |
| Processing Method: | Lyophilization |
| Extract Storage: | -80 celsius |
| Sample Resuspension: | 50 microliters of D2O or MeOD |
Analysis:
| Analysis ID: | AN000171 |
| Laboratory Name: | Arthur Edison |
| Analysis Type: | NMR |
| Analysis Comments: | Data was processed in NMRpipe |
| Software Version: | VNMRJ |
| Operator Name: | Chaevien Clendinen |
| Chromatography ID: | CH000117 |
| Num Factors: | 2 |
NMR:
| NMR ID: | NM000038 |
| Analysis ID: | AN000171 |
| Instrument Name: | Agilent VNMRS-600 |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 2D-INADEQUATE |
| Spectrometer Frequency: | 600 MHz |
| NMR Probe: | 1.5 mm HTS probe |
| NMR Solvent: | D2O and MeOD |
| NMR Tube Size: | 1.5 mm |
| Pulse Sequence: | INADEQUATEAD |
| Pulse Width: | 15.6 |
| Power Level: | 37 |
| Receiver Gain: | 60 |
| Temperature: | 23 |
| Number Of Scans: | 4 |
| Dummy Scans: | 32 |
| Acquisition Time: | 0.067 |
| Relaxation Delay: | 3 sec |
| Spectral Width: | 30487.8 Hz |
| Num Data Points Acquired: | 4096 |
| Real Data Points: | 2048 |
| Zero Filling: | 2x |
| Apodization: | Lorentz-to-Gaussian |
| Baseline Correction Method: | POLY |
