Summary of Study ST002095
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 | ST002095 |
Study Title | Addressing batch effects in large-scale metabolomics with augmented experimental design and meta-analysis (Part 1) |
Study Summary | Non-polar and polar sequential extracts were collected on three groups of C. elegans: natural isolates, central metabolism mutants, and UDP-glucuronosyltrasnferase mutants. Untargeted LC-MS (HILIC/RP - positive and negative mode) and NMR (CDCl3/H2O) studies were conducted using a Vanquish UHPLC coupled to an Orbitrap Elite MS and NEO 800 MHz Bruker NMR spectrometer, respectively. An augmented design, rank transformation of the raw data, strict feature filtering and QA/QC followed by a meta-analysis was performed on all datasets to demonstrate the benefits of this analysis approach and identify stable, significant features to prioritize for downstream compound identification efforts. |
Institute | University of Georgia - Complex Carbohydrate Research Center |
Laboratory | Edison Lab |
Last Name | Garcia |
First Name | Brianna |
Address | 315 Riverbend Road, Athens, GA, 30602, USA |
brianna.garcia@uga.edu | |
Phone | 7065424401 |
Submit Date | 2022-02-22 |
Num Groups | 3 |
Total Subjects | 116 |
Study Comments | Three study groups of C. elegans strains were used: central metabolism mutants (CMM), UDP-glucuronosyltransferase (UGT) mutants, and natural isolates. |
Raw Data Available | Yes |
Raw Data File Type(s) | fid |
Analysis Type Detail | NMR |
Release Date | 2022-04-04 |
Release Version | 1 |
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Sample Preparation:
Sampleprep ID: | SP002185 |
Sampleprep Summary: | Frozen lyophilized C. elegans aliquots were retrieved from -80°C. 200 μL of 1 mm zirconia beads were added to each sample and homogenized at 420 rcf for 90 seconds in a FastPrep-96 homogenizer and subsequently placed on dry ice for 90 seconds to avoid overheating, this step was repeated twice for a total of three rounds. Using the homogenized samples, 1 mL of 100% IPA chilled to -20°C was added to the lyophilized/homogenized sample powder and Zirconia beads in two increments of 500 μL. After each addition of 500 μL, samples were vortexed for 30 seconds – 1 minute and left at RT for 15 - 20 minutes. After RT incubation, samples were stored overnight (~12 hours) at -20°C. Samples were centrifuged for 30 minutes at 4°C (20,800 rcf). The supernatant was transferred to a new tube to use for analysis of non-polar molecules. 1 mL of pre-chilled 80:20 MeOH:H2O (4°C) was added to the remaining worm pellet to analyze polar molecules. The polar fraction shook at 4°C for 30 minutes. Samples were centrifuged at 20,800 rcf for 30 minutes at 4°C. The supernatant was transferred to a new tube to use for analysis of non-polar molecules. Both polar and non-polar samples were placed in a Labconco Centrivap at RT and monitored until completely dry. Once dry, polar and non-polar samples were reconstituted in D2O (99%, Cambridge Isotope Laboratories, Inc.) in a buffered solution with DSS (D6) and CDCl3 (99.96%, Cambridge Isotope Laboratories, Inc.) respectively. Samples were vortexed until fully soluble, and 45 μL of each sample were transferred into 1.7 mm NMR tubes (Bruker SampleJet) for acquisition. |
Processing Storage Conditions: | -80℃ |
Extraction Method: | Sequential extraction of (1) IPA for non-polar molecule followed by (2) 80/20 MeOH/H2O for polar |
Extract Storage: | -80℃ |
Sample Resuspension: | CDCl3 for non-polar; D2O (99%, Cambridge Isotope Laboratories, Inc.) in a buffered solution with DSS (D6) for polar |