Summary of Study ST002092
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 PR001328. The data can be accessed directly via it's Project DOI: 10.21228/M82978 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 | ST002092 |
| Study Title | Addressing batch effects in large-scale metabolomics with augmented experimental design and meta-analysis |
| Study Summary | Untargeted LC-MS study conducted using RP and HILIC chromatography on three groups of C. elegans: natural isolates, central metabolism mutants, and UDP-glucuronosyltransferase mutants. An augmented study design, rank transformation of the raw data, strict QA/QC followed by a meta-analysis was used for data analysis. |
| Institute | University of Georgia - Complex Carbohydrate Research Center |
| Laboratory | Edison Lab |
| Last Name | Garcia |
| First Name | Brianna |
| Address | 315 Riverbend Road |
| brianna.garcia@uga.edu | |
| Phone | 7065424401 |
| Submit Date | 2022-02-14 |
| Num Groups | 3 |
| Total Subjects | 119 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-04-04 |
| Release Version | 1 |
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Sample Preparation:
| Sampleprep ID: | SP002182 |
| Sampleprep Summary: | Frozen aliquots of 200,000 C. elegans worms were retrieved from -80°C and lyophilized in a VirTis® BenchTop™ “K” Series Freeze Dryer (SP Industries, Inc.). After lyophilization, each aliquot was weighed and stored at -80°C until homogenization. Aliquots were homogenized for three minutes in a Qiagen Tissuelyser 2, using glass beads. Homogenized worms were extracted with 1.5 mL of isopropanol (IPA) at -20°C overnight (approximately 12 hours), then pelleted and the supernatant transferred to separate 2 mL centrifuge tubes. Supernatants were then dried down to completion in a Labconco Centrivap and stored at -80°C for non-polar LC-MS analysis. The pellet was extracted a second time using 80:20 methanol:water (MeOH:H2O) (v:v) for 20 minutes at room temperature (RT) while shaking at 1500 rpm. Samples were again pelleted to separate proteins, and the supernatant was transferred to separate 2 mL centrifuge tubes, dried down to completion, and stored at -80°C for polar LC-MS analysis |
| Sampleprep Protocol Filename: | lcms_sequential_extraction_method.pdf |
| Processing Storage Conditions: | -80℃ |
| Extraction Method: | IPA for non-polar; 80/20 MeOH/H2O for polar |
| Extract Storage: | -80℃ |
| Sample Resuspension: | 75 µL of IPA containing isotopically labeled lipid standards; 75 µL of 80:20 MeOH: H2O containing isotopically labeled arginine, hypoxanthine, hippuric acid, and methionine |
