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.

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Study IDST001183
Study TitleCorrelations between LC-MS/MS-detected Glycomics and NMR-detected Metabolomics in Caenorhabditis (part-II) elegans Development.
Study SummaryThis 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
DepartmentComplex Carbohydrate Research Center
LaboratoryEdison and Wells
Last NameEdison
First NameArthur
Address315 Riverbend Road Athens, Georgia 30602-4712 USA
Emailaedison@uga.edu
Phone706-542-8156
Submit Date2019-05-14
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2019-07-17
Release Version1
Arthur Edison Arthur Edison
https://dx.doi.org/10.21228/M8240W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA082048W_09_FVP_N2_L1s1
SA082049W_09_FVP_N2_07_032
SA082050W_09_FVP_N2_05_042
SA082051W_09_FVP_N2_03_012
SA082052W_09_FVP_N2_06_022
SA082053W_09_FVP_N2_08_032
SA082054W_09_FVP_N2_01_022
SA082055W_09_FVP_N2_04_032
SA082056W_09_FVP_N2_01_013
SA082057W_09_FVP_N2_08_013
SA082058W_09_FVP_N2_06_033
SA082059W_09_FVP_N2_04_013
SA082060W_09_FVP_N2_07_043
SA082061W_09_FVP_N2_05_013
SA082062W_09_FVP_N2_03_023
SA082063W_09_FVP_N2_03_034
SA082064W_09_FVP_N2_07_014
SA082065W_09_FVP_N2_06_044
SA082066W_09_FVP_N2_04_044
SA082067W_09_FVP_N2_01_034
SA082068W_09_FVP_N2_08_024
SA082069W_09_FVP_N2_05_024
SA082070W_09_FVP_N2_05_035
SA082071W_09_FVP_N2_04_025
SA082072W_09_FVP_N2_07_025
SA082073W_09_FVP_N2_06_015
SA082074W_09_FVP_N2_08_045
SA082075W_09_FVP_N2_01_045
SA082076W_09_FVP_N2_03_045
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
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