Summary of Study ST002252

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 PR001440. The data can be accessed directly via it's Project DOI: 10.21228/M8KQ6P 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	ST002252
Study Title	Lipidomics analysis on Arabidopsis autophagy mutants
Study Summary	Autophagy is an essential cellular process in eukaryotes that degrades and recycles macromolecules and organelles. Defects in autophagy is known to affect metabolism, including the lipidome. Genetic approaches have identified a series of AuTophaGy-related (ATG) genes in Arabidopsis. In this study we used WT (ecotype Col-0) and two Arabidopsis autophagy-defective mutants, atg7 and atg9 to perform a multi-omics study on the effect of nitrogen starvation treatment, which induces autophagy. Specifically, we have quantified ~100 lipids from leaf and root tissues of WT, atg7 and atg9 mutant plants, under either autophagy-inducing conditions (-N) or normal nitrogen conditions (+N). The lipid species we quantified include: DGDG, MGDG, LPC, LPE, PE, LPG, PC, PA, PG, PI, and PS. Our study sheds lights on the understanding of the relationships between autophagy and metabolism, especially lipid metabolism.
Institute	Iowa State University
Department	Biochemistry Biophysics, and Molecular Biology
Laboratory	Nikolau Lab
Last Name	Ding
First Name	Geng
Address	2252 Molecular Biology BLDG, Pammel Drive
Email	gengding@iastate.edu
Phone	515-294-0347
Submit Date	2022-02-21
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	MS(Dir. Inf.)
Release Date	2023-02-21
Release Version	1

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Sample Preparation:

Sampleprep ID:	SP002344
Sampleprep Summary:	Lipids were extracted using a modification of a standard protocol. The collected plant tissues (leaf or root) were transferred in to a 50 mL Teflon-lined screw-caped glass tube (Thermo Fisher Scientific) containing 3 mL preheated isopropanol (Thermo Fisher Scientific) containing 0.01 % (v/v) butylated hydroxytoluene (BHT) (MilliporeSigma) and 1 µM 1,2-didecanoyl-sn-glycero-3-phosphocholine (PC 20:0)(MilliporeSigma) as an internal standard. The tubes were incubated at 75 °C for 15 min to quench the action of any lipases. Following the addition of 1.5 mL chloroform and 0.6 mL water the mixture was vigorously shaken at room temperature for 1 h. The clear liquid extract was transferred to another 50 mL tube using glass Pasteur pipettes, and the remnant tissue was further extracted for 30-minutes with another 4 mL chloroform/methanol (2:1) that contained 0.01% BHT. The clear liquid from this second extraction was removed and combined with the initial liquid extract. This chloroform/methanol (2:1) extraction was repeated three times, and the last extraction being incubated overnight. The residue tissue remaining after lipid extraction was dried at 105 °C, and the dry weight of each sample determined; each leaf tissue sample weighed approximately 20 mg, and each root tissue sampled weighed approximately 10 mg. All extract aliquots from each biological sample were combined into a single screw capped tube and stored at -80 °C under a nitrogen gas atmosphere. The solvent from each extract removed by evaporation with the aid of a stream of N2 gas, and the lipid residue was dissolved in 1 mL chloroform and transferred to 2.0 mL clear glass vial with Teflon-lined screw cap (Thermo Fisher Scientific). The solvent was again evaporated with N2 gas, and the vials were shipped, overnight on dry ice to Kansas Lipidomics Research Center (https://www.k-state.edu/lipid/) for lipidomics analysis.

Sampleprep ID:

SP002344

Sampleprep Summary:

Lipids were extracted using a modification of a standard protocol. The collected plant tissues (leaf or root) were transferred in to a 50 mL Teflon-lined screw-caped glass tube (Thermo Fisher Scientific) containing 3 mL preheated isopropanol (Thermo Fisher Scientific) containing 0.01 % (v/v) butylated hydroxytoluene (BHT) (MilliporeSigma) and 1 µM 1,2-didecanoyl-sn-glycero-3-phosphocholine (PC 20:0)(MilliporeSigma) as an internal standard. The tubes were incubated at 75 °C for 15 min to quench the action of any lipases. Following the addition of 1.5 mL chloroform and 0.6 mL water the mixture was vigorously shaken at room temperature for 1 h. The clear liquid extract was transferred to another 50 mL tube using glass Pasteur pipettes, and the remnant tissue was further extracted for 30-minutes with another 4 mL chloroform/methanol (2:1) that contained 0.01% BHT. The clear liquid from this second extraction was removed and combined with the initial liquid extract. This chloroform/methanol (2:1) extraction was repeated three times, and the last extraction being incubated overnight. The residue tissue remaining after lipid extraction was dried at 105 °C, and the dry weight of each sample determined; each leaf tissue sample weighed approximately 20 mg, and each root tissue sampled weighed approximately 10 mg. All extract aliquots from each biological sample were combined into a single screw capped tube and stored at -80 °C under a nitrogen gas atmosphere. The solvent from each extract removed by evaporation with the aid of a stream of N2 gas, and the lipid residue was dissolved in 1 mL chloroform and transferred to 2.0 mL clear glass vial with Teflon-lined screw cap (Thermo Fisher Scientific). The solvent was again evaporated with N2 gas, and the vials were shipped, overnight on dry ice to Kansas Lipidomics Research Center (https://www.k-state.edu/lipid/) for lipidomics analysis.