Summary of Study ST001182

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 IDST001182
Study TitleCorrelations between LC-MS/MS-detected Glycomics and NMR-detected Metabolomics in Caenorhabditis (part -I) 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/ 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
Analysis Type DetailLC-MS
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:SU001248
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
SA082019L1s_PMe1
SA0820207_03_PMe2
SA0820215_04_PMe2
SA0820223_01_PMe2
SA0820236_02_PMe2
SA0820248_03_PMe2
SA0820251_02_PMe2
SA0820264_03_PMe2
SA0820271_01_PMe3
SA0820288_01_PMe3
SA0820296_03_PMe3
SA0820304_01_PMe3
SA0820317_04_PMe3
SA0820325_01_PMe3
SA0820333_02_PMe3
SA0820343_03_PMe4
SA0820357_01_PMe4
SA0820366_04_PMe4
SA0820374_04_PMe4
SA0820381_03_PMe4
SA0820398_02_PMe4
SA0820405_02_PMe4
SA0820415_03_PMe5
SA0820424_02_PMe5
SA0820437_02_PMe5
SA0820446_01_PMe5
SA0820458_04_PMe5
SA0820461_04_PMe5
SA0820473_04_PMe5
Showing results 1 to 29 of 29

Collection:

Collection ID:CO001242
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:TR001263
Treatment Summary:N/A

Sample Preparation:

Sampleprep ID:SP001256
Sampleprep Summary:Preparation of released glycans followed by permethylation
Sampleprep Protocol Filename:SP_Glycomics_sample_preparation.pdf

Combined analysis:

Analysis ID AN001960
Analysis type MS
Chromatography type None (Direct infusion)
Chromatography system none
Column none
MS Type ESI
MS instrument type Ion trap
MS instrument name Thermo Velos Pro Linear Ion Trap
Ion Mode POSITIVE
Units peak area

Chromatography:

Chromatography ID:CH001421
Instrument Name:none
Column Name:none
Column Pressure:120 bar
Column Temperature:60°C
Flow Gradient:linear gradient from 30% to 70% LC-MS Buffer B
Flow Rate:300 nL/min
Injection Temperature:RT
Internal Standard:13C-Permethylated isomaltopentaose (DP5)
Sample Injection:5 µL
Solvent A:1 mM LiOAc and 0.02% acetic acid
Solvent B:1 mM LiOAc and 0.02% acetic acid, 80% Acetonitrile
Analytical Time:180 min
Oven Temperature:60 °C
Chromatography Type:None (Direct infusion)

MS:

MS ID:MS001815
Analysis ID:AN001960
Instrument Name:Thermo Velos Pro Linear Ion Trap
Instrument Type:Ion trap
MS Type:ESI
MS Comments:protocol added
Ion Mode:POSITIVE
Capillary Temperature:210 °C
Collision Energy:50%
Collision Gas:N2
Dry Gas Flow:N/A
Dry Gas Temp:N/A
Fragmentation Method:CID
Ion Spray Voltage:1.8 kV
Ionization:Nanospray
Mass Accuracy:0.1 Da
Analysis Protocol File:MS-Glycomics-DataProcessingWorkflow.pdf
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