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 |
| 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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Collection:
| Collection ID: | CO002331 |
| Collection Summary: | Leaf and root tissues of Arabidopsis seedlings were collected from plants growing in hydroponic conditions. |
| Sample Type: | Plant |
| Collection Method: | Seeds were sterilized with 70% ethanol, followed by a 10-min incubation in 0.1% (v/v) Tween 20 (Thermo Fisher Scientific, Waltham, MA) and 50% (v/v) bleach solution. The seeds were then washed with sterile water, at least three times. Subsequently, the suspended seeds were vernalized by incubating at 4ºC in darkness for 2 days. After vernalization, the seeds were suspended in sterile 0.1% (w/v) agarose (VWR, Radnor, PA), and sown on 3.5 cm x 4 cm autoclaved stainless steel growth mesh (14 Mesh T304 Woven Stainless 0.017" wire diameter, TWP Inc. Berkeley, California), which were laid on ½ strength Murashige and Skoog (MS) solid medium composed of 2.15 g/L Murashige and Skoog Basal Salt Mixture (MilliporeSigma, Burlington, MA), 0.05% (v/v) Murashige and Skoog Vitamin Solution (MilliporeSigma), 1% (w/v) sucrose (Thermo Fisher Scientific), 6g/L Phytoblend Agar (Caisson Labs, Smithfield, UT), and 2mM MES (MilliporeSigma) at pH 5.7. Each 10 cm x 10 cm square Petri dish, containing 4 growth meshes were placed in a growth room maintained at 22 ºC under continuous illumination (50 ± 10 μE m−2 s−1) for a period of 5 days. Subsequently, the growth mesh, carrying the germinated seedlings, were sterilely moved onto a sterile 7.5 cm x 8.5 cm stainless steel platform mesh (10 Mesh Woven Stainless 0.025" wire diameter, TWP Inc.), which was in 11.4 cm × 8.6 cm × 6.4 cm Phytatray dish (MilliporeSigma) that contained sterile liquid medium, composed of ½ strength MS liquid media, which contained 10 mM NH4NO3 and 9.4 mM KNO3 (+N media). The volume of the medium was adjusted so that the growth mesh that carried the seeds was in contact with the surface of the medium, and thus as seedlings grew the root system extended into the liquid medium. After 1 day incubation in the +N liquid medium, half the growth meshes from each Phytatray dish were moved into a Phytatray dish that contained nitrogen-deficient liquid medium (-N medium, which contains no nitrogen salts). This medium was composed of 5% (v/v) Murashige and Skoog Basal Salt Micronutrient Solution (MilliporeSigma), 0.05% (v/v) Murashige and Skoog Vitamin Solution, 1.5 mM CaCl2, 0.75 mM MgSO4, 0.625 mM KH2PO4, 2.5 mM KCl, 2 mM MES and 1% (w/v) sucrose. After an additional 3-day incubation, the seedlings from both the +N and -N media were harvested by cutting the hypocotyls that were extending below the growth mesh, and leaf and root tissues were collected separately. |
| Collection Tube Temp: | 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 (MilliporeSigma) as an internal standard. The tubes were incubated at 75 °C for 15 min to quench the action of any lipases. |
