Summary of Study ST001183
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 PR000794. The data can be accessed directly via it's Project DOI: 10.21228/M8240W This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001183 |
| Study Title | Correlations between LC-MS/MS-detected Glycomics and NMR-detected Metabolomics in Caenorhabditis (part-II) elegans Development. |
| Study Summary | This study examines the relationship between glycans, metabolites, and development in C. elegans. Samples of N2 animals were synchronized and grown to five different time points that ranged from L1 to a mixed population of adults, gravid adults, and offspring. |
| Institute | University of Georgia |
| Department | Complex Carbohydrate Research Center |
| Laboratory | Edison and Wells |
| Last Name | Edison |
| First Name | Arthur |
| Address | 315 Riverbend Road Athens, Georgia 30602-4712 USA |
| aedison@uga.edu | |
| Phone | 706-542-8156 |
| Submit Date | 2019-05-14 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | fid |
| Analysis Type Detail | NMR |
| Release Date | 2019-07-17 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000794 |
| Project DOI: | doi: 10.21228/M8240W |
| Project Title: | Correlations between LC-MS/MS-detected Glycomics and NMR- detected Metabolomics in Caenorhabditis elegans Development. |
| Project Summary: | New approach to evaluate the relationship between Caenorhabditis elegans development, glycan abundance, and metabolites |
| Institute: | University of Georgia |
| Department: | Complex Carbohydrate Research Center |
| Laboratory: | Edison |
| Last Name: | Edison |
| First Name: | Arthur |
| Address: | 315 Riverbend Road, Athens, GA, 30602, USA |
| Email: | asedison@uga.edu |
| Phone: | 706-542-8156 |
Subject:
| Subject ID: | SU001249 |
| Subject Type: | Other |
| Subject Species: | Caenorhabditis elegans |
| Taxonomy ID: | 6239 |
Factors:
Subject type: Other; Subject species: Caenorhabditis elegans (Factor headings shown in green)
| mb_sample_id | local_sample_id | Time point |
|---|---|---|
| SA082048 | W_09_FVP_N2_L1s | 1 |
| SA082049 | W_09_FVP_N2_07_03 | 2 |
| SA082050 | W_09_FVP_N2_05_04 | 2 |
| SA082051 | W_09_FVP_N2_03_01 | 2 |
| SA082052 | W_09_FVP_N2_06_02 | 2 |
| SA082053 | W_09_FVP_N2_08_03 | 2 |
| SA082054 | W_09_FVP_N2_01_02 | 2 |
| SA082055 | W_09_FVP_N2_04_03 | 2 |
| SA082056 | W_09_FVP_N2_01_01 | 3 |
| SA082057 | W_09_FVP_N2_08_01 | 3 |
| SA082058 | W_09_FVP_N2_06_03 | 3 |
| SA082059 | W_09_FVP_N2_04_01 | 3 |
| SA082060 | W_09_FVP_N2_07_04 | 3 |
| SA082061 | W_09_FVP_N2_05_01 | 3 |
| SA082062 | W_09_FVP_N2_03_02 | 3 |
| SA082063 | W_09_FVP_N2_03_03 | 4 |
| SA082064 | W_09_FVP_N2_07_01 | 4 |
| SA082065 | W_09_FVP_N2_06_04 | 4 |
| SA082066 | W_09_FVP_N2_04_04 | 4 |
| SA082067 | W_09_FVP_N2_01_03 | 4 |
| SA082068 | W_09_FVP_N2_08_02 | 4 |
| SA082069 | W_09_FVP_N2_05_02 | 4 |
| SA082070 | W_09_FVP_N2_05_03 | 5 |
| SA082071 | W_09_FVP_N2_04_02 | 5 |
| SA082072 | W_09_FVP_N2_07_02 | 5 |
| SA082073 | W_09_FVP_N2_06_01 | 5 |
| SA082074 | W_09_FVP_N2_08_04 | 5 |
| SA082075 | W_09_FVP_N2_01_04 | 5 |
| SA082076 | W_09_FVP_N2_03_04 | 5 |
| Showing results 1 to 29 of 29 |
Collection:
| Collection ID: | CO001243 |
| Collection Summary: | This study used N2, the laboratory reference strain of C. elegans, which was obtained from the Caenorhabditis Genetics Center (CGC). We followed the general protocol published previously for obtaining liquid cultures of synchronized worms. This defines our biological replicate: A single L1 animal from a synchronized culture was placed onto an agar plate seeded with E. coli MG1655. This plate was grown until there were a large number of young gravid adult hermaphrodites (about 48 h at 24 °C. The plate was then washed into a 15 mL tube with M9 buffer, rinsed 3x with M9, and lysed with an alkaline hypochlorite solution until about 50% of the worms were dissolved (no more than 5 min). Then, M9 buffer was added to dilute the lysing solution, and the liquid was removed after gentle centrifugation at 580 g for 2 min to pellet the eggs without breaking them. This step was repeated 3x to completely remove the lysis solution. After the final rinse, eggs were resuspended in sterile water before a sucrose gradient to remove cellular debris and bacteria. An equal volume (5 mL) of 60% sucrose was added to the eggs in water and centrifuged at 350 g for 4 min. The eggs were rinsed to remove residual sucrose and once they hatched, approximately 200,000 animals were transferred to 20 mL of S-complete with 2 mL of 50% MG1655. This material was grown to the desired developmental stage and prepared as described below. The C. elegans cultures were synchronized, but they gradually lost synchrony over time. We collected samples at 5 different time points (T1-T5) in development. We report results using these time points rather than developmental larval stages, since they are not all pure stage cultures. The first time, T1, was collected immediately after hatching and was perfectly synchronized L1 animals, but as time progressed the cultures became more mixed. The other samples were collected at 22, 36, 49, and 90 hours (T2, T3, T4, and T5, respectively) after feeding the cultures. T5 was a mixture of adults, gravid adults, and offspring. Each of the five time points were replicated seven times. Stage-specific information can be recovered, even with samples that have lost synchrony. |
| Collection Protocol Filename: | CO_Celegans_sample_preparation_.pdf |
| Sample Type: | Worms |
Treatment:
| Treatment ID: | TR001264 |
| Treatment Summary: | N/A |
Sample Preparation:
| Sampleprep ID: | SP001257 |
| Sampleprep Summary: | The remaining 97.5% of the worm pellets after biosorting were bead homogenized with 80% methanol/20% water and remaining pellets after extraction used for glycomics. |
| Sampleprep Protocol Filename: | SP_NMR_sample_preparation.pdf MS-Glycomics-DataProcessingWorkflow.pdf SP_Biosorting.pdf |
Analysis:
| Analysis ID: | AN001961 |
| Laboratory Name: | Edison Lab/ The CCRC NMR spectroscopy facility |
| Analysis Type: | NMR |
| Analysis Protocol File: | CO_Celegans_sample_preparation_.pdf |
| Operator Name: | Fariba Tayyari |
| Num Factors: | 5 |
| Units: | N/A |
NMR:
| NMR ID: | NM000149 |
| Analysis ID: | AN001961 |
| Instrument Name: | Bruker AVIII-HD |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D-1H |
| NMR Comments: | 1D NMR for all the samples and 2D NMR on selected samples |
| Spectrometer Frequency: | 600 MHz |
| NMR Solvent: | D2O |
| NMR Tube Size: | 5mm x 7 in |
| Shimming Method: | topshim |
| Temperature: | 27 |
| Number Of Scans: | 128 |
| Dummy Scans: | 4 |
| Acquisition Time: | 2.7198913 |
| Spectral Width: | 20.0276 |
| Line Broadening: | 0.3 |
