Summary of Study ST002096

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.

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Study ID	ST002096
Study Title	Addressing batch effects in large-scale metabolomics with augmented experimental design and meta-analysis (Part 2)
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
Email	brianna.garcia@uga.edu
Phone	7065424401
Submit Date	2022-03-04
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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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:	SU002180
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
SA201076	aos142_ga_ms2_7	1	1	CB4856
SA201077	aos145_ga_ms2_8	1	1	CB4856
SA201078	aos127_ga_ms2_5	1	1	CX11314
SA201079	aos76_ga_ms2_21	1	1	CX11314
SA201080	aos25_ga_ms2_10	1	1	CX11314
SA201081	aos46_ga_ms2_14	1	1	DL238
SA201082	aos65_ga_ms2_19	1	1	DL238
SA201083	aos50_ga_ms2_16	1	1	DL238
SA201084	aos67_ga_ms2_20	1	1	N2
SA201085	aos48_ga_ms2_15	1	1	N2
SA201086	aos58_ga_ms2_18	1	1	N2
SA201087	aos43_ga_ms4_13	1	1	PD1074
SA201088	aos27_ga_ms3_11	1	1	PD1074
SA201089	aos129_ga_ms2_6	1	1	PD1074
SA201090	aos149_ga_ms2_9	1	1	PD1074
SA201091	aos78_ga_ms4_22	1	1	PD1074
SA201092	aos32_ga_ms2_12	1	1	RB2011
SA201093	aos122_ga_ms2_4	1	1	RB2011
SA201094	solera_3	1	1	solera
SA201095	aos170_ga_ms2_32	1	2	CB4856
SA201096	aos115_gt_ms1_29	1	2	CB4856
SA201097	aos199_ga_ms2_38	1	2	CX11314
SA201098	aos175_ga_ms2_35	1	2	CX11314
SA201099	aos127_ga_ms3_24	1	2	CX11314
SA201100	aos165_ga_ms2_30	1	2	DL238
SA201101	aos192_ga_ms2_37	1	2	DL238
SA201102	aos174_ga_ms2_34	1	2	DL238
SA201103	aos106_co_ms2_25	1	2	N2
SA201104	aos56_ga_ms2_41	1	2	N2
SA201105	aos113_ga_ms1_28	1	2	PD1074
SA201106	aos188_ga_ms3_36	1	2	PD1074
SA201107	aos99_ga_ms2_26	1	2	PD1074
SA201108	aos53_ga_ms2_40	1	2	PD1074
SA201109	aos200_ga_ms2_39	1	2	PD1074
SA201110	aos167_ga_ms3_31	1	2	PD1074
SA201113	pooled_natural_isolate_42	1	2	pooled_natural_isolate
SA201114	pooled_pd1074_43	1	2	pooled_pd1074
SA201111	aos173_ga_ms2_33	1	2	RB2011
SA201112	aos108_ga_ms2_27	1	2	RB2011
SA201115	solera_44	1	2	solera
SA201116	aos86_ga_ms2_65	2	3	KJ550
SA201117	aos28_ga_ms2_53	2	3	KJ550
SA201118	aos69_ga_ms1_64	2	3	PD1074
SA201119	aos43_ga_bku_60	2	3	PD1074
SA201120	aos90_ga_ms3_66	2	3	PD1074
SA201121	aos27_ga_ms4_52	2	3	PD1074
SA201122	aos99_ga_ms2_68	2	3	PD1074
SA201123	aos38_ga_ms2_57	2	3	PD1074
SA201124	aos185_ga_ms2_51	2	3	PD1074
SA201125	aos37_ga_ms2_56	2	3	RB2347
SA201126	aos74_ga_ms2_63	2	3	RB2347
SA201127	aos36_ga_ms2_55	2	3	RB2347
SA201128	aos35_ga_ms2_54	2	3	RB2550
SA201129	aos40_ga_ms2_58	2	3	RB2550
SA201130	aos71_ga_ms2_62	2	3	RB2550
SA201134	solera_49	2	3	solera
SA201131	aos98_ga_ms2_67	2	3	VC1265
SA201132	aos42_ga_ms2_59	2	3	VC1265
SA201133	aos184_ga_ms2_50	2	3	VC1265
SA201135	aos109_ga_ms2_81	2	4	KJ550
SA201136	aos100_ga_ms2_73	2	4	KJ550
SA201137	aos134_ga_ms2_86	2	4	KJ550
SA201138	aos140_ga_ms3_87	2	4	PD1074
SA201139	aos113_ga_ms1_84	2	4	PD1074
SA201140	aos180_ga_ms2_89	2	4	PD1074
SA201141	aos92_ga_ms2_77	2	4	PD1074
SA201142	aos87_co_ms3_72	2	4	PD1074
SA201143	aos107_ga_bku_80	2	4	PD1074
SA201155	pooled_mutant_90	2	4	pooled_mutant
SA201156	pooled_pd1074_91	2	4	pooled_pd1074
SA201144	aos95_ga_ms2_79	2	4	RB2347
SA201145	aos116_ga_ms2_83	2	4	RB2347
SA201146	aos171_ga_ms2_88	2	4	RB2347
SA201147	aos82_ga_ms2_75	2	4	RB2347
SA201148	aos81_ga_ms2_71	2	4	RB2550
SA201149	aos111_ga_ms2_82	2	4	RB2550
SA201150	aos96_ga_ms2_74	2	4	RB2550
SA201157	solera_92	2	4	solera
SA201151	aos84_ga_ms2_76	2	4	VC1265
SA201152	aos73_ga_ms2_70	2	4	VC1265
SA201153	aos125_ga_ms2_85	2	4	VC1265
SA201154	aos93_ga_ms2_78	2	4	VC1265
SA201158	aos79_ga_ms2_116	3	5	AUM2073
SA201159	aos51_ga_ms2_109	3	5	AUM2073
SA201160	aos91_ga_ms2_119	3	5	AUM2073
SA201161	aos75_ga_ms4_115	3	5	PD1074
SA201162	aos41_ga_ms2_104	3	5	PD1074
SA201163	aos44_ga_ms2_106	3	5	PD1074
SA201164	aos69_ga_ms3_114	3	5	PD1074
SA201165	aos87_ga_ms3_118	3	5	PD1074
SA201166	aos196_ga_ms2_101	3	5	PD1074
SA201167	aos181_ga_ms2_99	3	5	PD1074
SA201168	aos83_ga_ms2_117	3	5	RB2055
SA201169	aos26_ga_ms2_102	3	5	RB2055
SA201170	aos45_ga_ms2_110	3	5	RB2055
SA201179	solera_97	3	5	solera
SA201171	aos39_ga_ms2_103	3	5	UGT49
SA201172	aos49_ga_ms2_108	3	5	UGT49
SA201173	aos66_ga_ms2_112	3	5	UGT60
SA201174	aos33_ga_ms2_105	3	5	UGT60

Showing page 1 of 2 Results: 1 2 Next Showing results 1 to 100 of 128

Collection:

Collection ID:	CO002173
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:	TR002192
Treatment Summary:	No treatments.

Sample Preparation:

Sampleprep ID:	SP002186
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:	AN003424
Laboratory Name:	Edison Lab – Complex Carbohydrate Research Center
Analysis Type:	NMR
Acquisition Date:	2020-03-30
Operator Name:	Amanda O. Shaver
Detector Type:	Bruker Neo 1.7 mm TCI Cryo Probe
Data Format:	ft
Results File:	ST002096_AN003424_Results.txt
Units:	Ranked Intensity

NMR:

NMR ID:	NM000233
Analysis ID:	AN003424
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:	CDCl3
NMR Tube Size:	1.7 mm
Shimming Method:	Automatic (“Topshim”)
Pulse Sequence:	zg
Water Suppression:	3758.64 @ 4.7 ppm
Receiver Gain:	65.1
Temperature:	6
Number Of Scans:	64
Dummy Scans:	4
Acquisition Time:	1.31 sec
Spectral Width:	20.2
Num Data Points Acquired:	65,536
Line Broadening:	1.5
Apodization:	exponential
Baseline Correction Method:	Polynomial Automatic fit
Chemical Shift Ref Std:	7.24