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 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001328 |
| Project DOI: | doi: 10.21228/M82978 |
| Project Title: | Addressing batch effects in large-scale metabolomics with augmented experimental design and meta-analysis |
| Project 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, Athens, GA 30602 |
| Email: | brianna.garcia@uga.edu |
| Phone: | 7065424401 |
| Funding Source: | U2CES030167 |
| Contributors: | Amanda O. Shaver, Goncalo J. Gouveia, Alison M. Morse, Zihao Liu, Carter K. Asef, Ricardo M. Borges, Franklin E. Leach III, Erik C. Andersen, I. Jonathan Amster, Facundo M. Fernández, Arthur S. Edison, and Lauren M. McIntyre |
Subject:
| Subject ID: | SU002179 |
| Subject Type: | Invertebrate |
| Subject Species: | Caenorhabditis elegans |
| Taxonomy ID: | 6239 |
Factors:
Subject type: Invertebrate; Subject species: Caenorhabditis elegans (Factor headings shown in green)
| mb_sample_id | local_sample_id | set | batch | genotype |
|---|---|---|---|---|
| SA200948 | aos142_ga_ms2_7 | 1 | 1 | CB4856 |
| SA200949 | aos145_ga_ms2_8 | 1 | 1 | CB4856 |
| SA200950 | aos127_ga_ms2_5 | 1 | 1 | CX11314 |
| SA200951 | aos76_ga_ms2_21 | 1 | 1 | CX11314 |
| SA200952 | aos25_ga_ms2_10 | 1 | 1 | CX11314 |
| SA200953 | aos46_ga_ms2_14 | 1 | 1 | DL238 |
| SA200954 | aos65_ga_ms2_19 | 1 | 1 | DL238 |
| SA200955 | aos50_ga_ms2_16 | 1 | 1 | DL238 |
| SA200956 | aos67_ga_ms2_20 | 1 | 1 | N2 |
| SA200957 | aos48_ga_ms2_15 | 1 | 1 | N2 |
| SA200958 | aos58_ga_ms2_18 | 1 | 1 | N2 |
| SA200959 | aos43_ga_ms4_13 | 1 | 1 | PD1074 |
| SA200960 | aos27_ga_ms3_11 | 1 | 1 | PD1074 |
| SA200961 | aos129_ga_ms2_6 | 1 | 1 | PD1074 |
| SA200962 | aos149_ga_ms2_9 | 1 | 1 | PD1074 |
| SA200963 | aos78_ga_ms4_22 | 1 | 1 | PD1074 |
| SA200964 | aos32_ga_ms2_12 | 1 | 1 | RB2011 |
| SA200965 | aos122_ga_ms2_4 | 1 | 1 | RB2011 |
| SA200966 | solera_3 | 1 | 1 | solera |
| SA200967 | aos170_ga_ms2_32 | 1 | 2 | CB4856 |
| SA200968 | aos115_gt_ms1_29 | 1 | 2 | CB4856 |
| SA200969 | aos199_ga_ms2_38 | 1 | 2 | CX11314 |
| SA200970 | aos175_ga_ms2_35 | 1 | 2 | CX11314 |
| SA200971 | aos127_ga_ms3_24 | 1 | 2 | CX11314 |
| SA200972 | aos165_ga_ms2_30 | 1 | 2 | DL238 |
| SA200973 | aos192_ga_ms2_37 | 1 | 2 | DL238 |
| SA200974 | aos174_ga_ms2_34 | 1 | 2 | DL238 |
| SA200975 | aos106_co_ms2_25 | 1 | 2 | N2 |
| SA200976 | aos56_ga_ms2_41 | 1 | 2 | N2 |
| SA200977 | aos113_ga_ms1_28 | 1 | 2 | PD1074 |
| SA200978 | aos188_ga_ms3_36 | 1 | 2 | PD1074 |
| SA200979 | aos99_ga_ms2_26 | 1 | 2 | PD1074 |
| SA200980 | aos53_ga_ms2_40 | 1 | 2 | PD1074 |
| SA200981 | aos200_ga_ms2_39 | 1 | 2 | PD1074 |
| SA200982 | aos167_ga_ms3_31 | 1 | 2 | PD1074 |
| SA200985 | pooled_natural_isolate_42 | 1 | 2 | pooled_natural_isolate |
| SA200986 | pooled_pd1074_43 | 1 | 2 | pooled_pd1074 |
| SA200983 | aos173_ga_ms2_33 | 1 | 2 | RB2011 |
| SA200984 | aos108_ga_ms2_27 | 1 | 2 | RB2011 |
| SA200987 | solera_44 | 1 | 2 | solera |
| SA200988 | aos86_ga_ms2_65 | 2 | 3 | KJ550 |
| SA200989 | aos28_ga_ms2_53 | 2 | 3 | KJ550 |
| SA200990 | aos69_ga_ms1_64 | 2 | 3 | PD1074 |
| SA200991 | aos43_ga_bku_60 | 2 | 3 | PD1074 |
| SA200992 | aos90_ga_ms3_66 | 2 | 3 | PD1074 |
| SA200993 | aos27_ga_ms4_52 | 2 | 3 | PD1074 |
| SA200994 | aos99_ga_ms2_68 | 2 | 3 | PD1074 |
| SA200995 | aos38_ga_ms2_57 | 2 | 3 | PD1074 |
| SA200996 | aos185_ga_ms2_51 | 2 | 3 | PD1074 |
| SA200997 | aos37_ga_ms2_56 | 2 | 3 | RB2347 |
| SA200998 | aos74_ga_ms2_63 | 2 | 3 | RB2347 |
| SA200999 | aos36_ga_ms2_55 | 2 | 3 | RB2347 |
| SA201000 | aos35_ga_ms2_54 | 2 | 3 | RB2550 |
| SA201001 | aos40_ga_ms2_58 | 2 | 3 | RB2550 |
| SA201002 | aos71_ga_ms2_62 | 2 | 3 | RB2550 |
| SA201006 | solera_49 | 2 | 3 | solera |
| SA201003 | aos98_ga_ms2_67 | 2 | 3 | VC1265 |
| SA201004 | aos42_ga_ms2_59 | 2 | 3 | VC1265 |
| SA201005 | aos184_ga_ms2_50 | 2 | 3 | VC1265 |
| SA201007 | aos109_ga_ms2_81 | 2 | 4 | KJ550 |
| SA201008 | aos100_ga_ms2_73 | 2 | 4 | KJ550 |
| SA201009 | aos134_ga_ms2_86 | 2 | 4 | KJ550 |
| SA201010 | aos140_ga_ms3_87 | 2 | 4 | PD1074 |
| SA201011 | aos113_ga_ms1_84 | 2 | 4 | PD1074 |
| SA201012 | aos180_ga_ms2_89 | 2 | 4 | PD1074 |
| SA201013 | aos92_ga_ms2_77 | 2 | 4 | PD1074 |
| SA201014 | aos87_co_ms3_72 | 2 | 4 | PD1074 |
| SA201015 | aos107_ga_bku_80 | 2 | 4 | PD1074 |
| SA201027 | pooled_mutant_90 | 2 | 4 | pooled_mutant |
| SA201028 | pooled_pd1074_91 | 2 | 4 | pooled_pd1074 |
| SA201016 | aos95_ga_ms2_79 | 2 | 4 | RB2347 |
| SA201017 | aos116_ga_ms2_83 | 2 | 4 | RB2347 |
| SA201018 | aos171_ga_ms2_88 | 2 | 4 | RB2347 |
| SA201019 | aos82_ga_ms2_75 | 2 | 4 | RB2347 |
| SA201020 | aos81_ga_ms2_71 | 2 | 4 | RB2550 |
| SA201021 | aos111_ga_ms2_82 | 2 | 4 | RB2550 |
| SA201022 | aos96_ga_ms2_74 | 2 | 4 | RB2550 |
| SA201029 | solera_92 | 2 | 4 | solera |
| SA201023 | aos84_ga_ms2_76 | 2 | 4 | VC1265 |
| SA201024 | aos73_ga_ms2_70 | 2 | 4 | VC1265 |
| SA201025 | aos125_ga_ms2_85 | 2 | 4 | VC1265 |
| SA201026 | aos93_ga_ms2_78 | 2 | 4 | VC1265 |
| SA201030 | aos79_ga_ms2_116 | 3 | 5 | AUM2073 |
| SA201031 | aos51_ga_ms2_109 | 3 | 5 | AUM2073 |
| SA201032 | aos91_ga_ms2_119 | 3 | 5 | AUM2073 |
| SA201033 | aos75_ga_ms4_115 | 3 | 5 | PD1074 |
| SA201034 | aos41_ga_ms2_104 | 3 | 5 | PD1074 |
| SA201035 | aos44_ga_ms2_106 | 3 | 5 | PD1074 |
| SA201036 | aos69_ga_ms3_114 | 3 | 5 | PD1074 |
| SA201037 | aos87_ga_ms3_118 | 3 | 5 | PD1074 |
| SA201038 | aos196_ga_ms2_101 | 3 | 5 | PD1074 |
| SA201039 | aos181_ga_ms2_99 | 3 | 5 | PD1074 |
| SA201040 | aos83_ga_ms2_117 | 3 | 5 | RB2055 |
| SA201041 | aos26_ga_ms2_102 | 3 | 5 | RB2055 |
| SA201042 | aos45_ga_ms2_110 | 3 | 5 | RB2055 |
| SA201051 | solera_97 | 3 | 5 | solera |
| SA201043 | aos39_ga_ms2_103 | 3 | 5 | UGT49 |
| SA201044 | aos49_ga_ms2_108 | 3 | 5 | UGT49 |
| SA201045 | aos66_ga_ms2_112 | 3 | 5 | UGT60 |
| SA201046 | aos33_ga_ms2_105 | 3 | 5 | UGT60 |
Collection:
| Collection ID: | CO002172 |
| Collection Summary: | Escherichia coli (E. coli) IBAT (iterative batch average method) reference material and food source used throughout this experiment. Briefly, for each biological sample, a large-scale culture plate (LSCP) was used to generate a large mixed-stage population of worms (four to seven LSCP replicates per test strain). For each LSCP, worms were collected, population size estimated, and subsequently divided into at least 12 identical aliquots of 200,000 worms in ddH2O and flash-frozen in liquid nitrogen and stored at -80°C. As a quality control sample, C. elegans IBAT reference material was generated and saved in 200,000 worm aliquots. |
| Sample Type: | Worms |
| Volumeoramount Collected: | 200,000 worms |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002191 |
| Treatment Summary: | No treatments. |
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 |
Analysis:
| Analysis ID: | AN003423 |
| Laboratory Name: | Edison Lab – Complex Carbohydrate Research Center |
| Analysis Type: | NMR |
| Acquisition Date: | 2020-03-19 |
| Operator Name: | Amanda O. Shaver |
| Detector Type: | Bruker Neo 1.7 mm TCI Cryo Probe |
| Data Format: | ft |
| Num Factors: | 46 |
| Num Metabolites: | 16 |
| Units: | Meta-Analysis Effect Size |
NMR:
| NMR ID: | NM000232 |
| Analysis ID: | AN003423 |
| Instrument Name: | Bruker Neo 800 MHz |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D-1H |
| Spectrometer Frequency: | 800 |
| NMR Probe: | 1.7 mm TCI cryoprobe |
| NMR Solvent: | D2O |
| NMR Tube Size: | 1.7 mm |
| Shimming Method: | Automatic (“Topshim”) |
| Pulse Sequence: | noesypr1d |
| Water Suppression: | 3758.64 @ 4.7 ppm |
| Receiver Gain: | 65.1 |
| Temperature: | 6 |
| Number Of Scans: | 128 |
| Dummy Scans: | 2 |
| Acquisition Time: | 1.31 sec |
| Spectral Width: | 15 |
| Num Data Points Acquired: | 32,768 |
| Line Broadening: | 1.5 |
| Apodization: | exponential |
| Baseline Correction Method: | Polynomial Automatic fit |
| Chemical Shift Ref Std: | 0.00 |
