Summary of Study ST002270

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 PR001452. The data can be accessed directly via it's Project DOI: 10.21228/M81Q5B This work is supported by NIH grant, U2C- DK119886.

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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 IDST002270
Study TitleXenopus tropicalis glycolysis and PPP inhibition
Study SummaryStage 41 tadpoles were injected with 4 nmol of the glycolysis inhibitor, 2-deoxyglucose (2DG), or a tracer control to evaluate consequences of inhibition on metabolites 24 hours after treatment began. Similarly, tadpoles were incubated in DMSO control or 1 of 2 G6PD inhibitors (Dehydroepiandrosterone and g6pdi), to similarly assess the consequences of inhibiting the pentose phosphate pathway. We find that inhibition of glucose metabolism with 2DG results in a decrease in downstream glycolytic intermediates, confirming a reduction in activity of this pathway. G6PD inhibition was not as clear as changes were less consistent across treatments and downstream metabolites did not behave in a coordinated way, though impacts on other metabolic processes by these inhibitors may be fruitful for exploring how they perturb metabolism in the tadpoles.
Institute
University of Washington
Last NamePatel
First NameJeet
Address1705 NE Pacific St., HSB J-Wing, J405, Seattle, Washington, 98195, USA
Emailpateljeet1224@gmail.com
Phone2065431748
Submit Date2022-08-03
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2022-10-25
Release Version1
Jeet Patel Jeet Patel
https://dx.doi.org/10.21228/M81Q5B
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001452
Project DOI:doi: 10.21228/M81Q5B
Project Title:Glucose metabolism during Xenopus Regeneration
Project Summary:Targeted metabolomics of Xenopus tropicalis to study glucose metabolism during regeneration
Institute:University of Washington
Department:Biochemistry
Laboratory:Wills Lab
Last Name:Patel
First Name:Jeet
Address:1705 NE Pacific St., HSB J-Wing, J405, Seattle, Washington, 98195, USA
Email:pateljeet1224@gmail.com
Phone:2065431748
Funding Source:Royalty Research Fund, 1R01NS099124 from NINDS

Subject:

Subject ID:SU002356
Subject Type:Other organism
Subject Species:Xenopus tropicalis
Age Or Age Range:Stage 41-43

Factors:

Subject type: Other organism; Subject species: Xenopus tropicalis (Factor headings shown in green)

mb_sample_id local_sample_id Condition
SA2177362DG22DG
SA2177372DG42DG
SA2177382DG32DG
SA2177392DG12DG
SA217740DHEA2DHEA
SA217741DHEA3DHEA
SA217742DHEA4DHEA
SA217743DHEA1DHEA
SA217744DMSO2DMSO
SA217745DMSO4DMSO
SA217746DMSO3DMSO
SA217747DMSO1DMSO
SA217752g6pdi1g6pdi
SA217753g6pdi2g6pdi
SA217754g6pdi3g6pdi
SA217755g6pdi4g6pdi
SA217748MR3MR
SA217749MR2MR
SA217750MR4MR
SA217751MR1MR
Showing results 1 to 20 of 20

Collection:

Collection ID:CO002349
Collection Summary:Tadpoles were anesthetized with 0.05% MS-222 in 1/9x MR and tested for response to touch prior to tissue collection. Injections of miniRuby or 4nmol of 2DG were performed or tadpoles were incubated in media with DMSO, DHEA, or g6pdi/ 10 whole animals were collected at 24 hours post treatment, media was removed, and samples were frozen on dry ice immediately.
Sample Type:Stage 43 tadpoles

Treatment:

Treatment ID:TR002368
Treatment Summary:Dihydroepiandrosterone (BioVision, 2172) was resuspended to a 1M stock in DMSO and g6pdi (Cayman Chemical Co., 31484) to a 10mM stock in DMSO. Tadples were reared with 0.1% DMSO, 25µM DHEA or 10µM g6pdi diluted in 1/9x MR until collection after a 24 treatment. For 2DG injections, wild type tadpoles at stage 41 were anesthetized with MS-222 and moved from culture dish to a thickly coasted agarose dish in one drop of media. Excess media was removed. Using a microinjector, a pulled needle containing vMO and labeled dextran tracer was inserted into the ventral tail vein and 2×2 nL of 1M 2DG (Sigma, D8375) were injected. Controls for 2DG experiments were injected with equal volumes of tracer. Embryos were returned to fresh media and screened for tracer fluorescence in the bloodstream. Injected animals were kept in 1/9x MR until collection after a 24 treatment.

Sample Preparation:

Sampleprep ID:SP002362
Sampleprep Summary:Aqueous metabolites for targeted LC-MS analysis were extracted using a protein precipitation method similar to the one described elsewhere (Mathon et al., 2019; Meador et al., 2020). Samples were first homogenized in 200 µL purified deionized water at 4 ˚C, and then 800 µL of methanol containing 6C13-glucose and 2C13-glutamate (reference internal standards) was added. Afterwards samples were vortexed, stored for 30 minutes at -20 ˚C, sonicated in an ice bath for 10 minutes, centrifuged for 15 min at 14,000 rpm and 4 ˚C, and then 600 µL of supernatant was collected from each sample. Lastly, recovered supernatants were dried on a SpeedVac and reconstituted in 1.0 mL of LC-matching solvent containing 2C13-tyrosine and 3C13-lactate (reference internal standards).
Sampleprep Protocol Filename:JPatel_LC-MS_Methods.pdf

Combined analysis:

Analysis ID AN003710 AN003711
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Shimadzu Nexera X2 Shimadzu Nexera X2
Column Waters XBridge BEH Amide XP Waters XBridge BEH Amide XP
MS Type ESI ESI
MS instrument type Triple quadrupole Triple quadrupole
MS instrument name ABI Sciex 6500+ QTrap ABI Sciex 6500+ QTrap
Ion Mode POSITIVE NEGATIVE
Units Peak Intensity Peak intensity

Chromatography:

Chromatography ID:CH002749
Instrument Name:Shimadzu Nexera X2
Column Name:Waters XBridge BEH Amide XP
Chromatography Type:HILIC

MS:

MS ID:MS003459
Analysis ID:AN003710
Instrument Name:ABI Sciex 6500+ QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:MS data acquisition was performed in multiple-reaction-monitoring (MRM) mode. LC-MS system was controlled using AB Sciex Analyst 1.6.3 software. Measured MS peaks were integrated using AB Sciex MultiQuant 3.0.3 software. The LC-MS assay was targeting 361 metabolites (plus 4 spiked reference internal standards).
Ion Mode:POSITIVE
Analysis Protocol File:JPatel_LC-MS_Methods.pdf
  
MS ID:MS003460
Analysis ID:AN003711
Instrument Name:ABI Sciex 6500+ QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:MS data acquisition was performed in multiple-reaction-monitoring (MRM) mode. LC-MS system was controlled using AB Sciex Analyst 1.6.3 software. Measured MS peaks were integrated using AB Sciex MultiQuant 3.0.3 software. The LC-MS assay was targeting 361 metabolites (plus 4 spiked reference internal standards).
Ion Mode:NEGATIVE
Analysis Protocol File:JPatel_LC-MS_Methods.pdf
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