Summary of Study ST002271

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 IDST002271
Study TitleXenopus tropicalis regeneration timecourse
Study SummaryTo identify changes in metabolites that correlate with progression of tail regeneration, we collected a timecourse of tissues containing 250 um of tissue anterior to the wound site as well as all regenerating tissue at 0, 3, and 24 hours post amputation. We also collected the posterior 500 um of the developing tail to represent the metabolic profile of uninjured tissues. Tissues from 25 individuals were collected and frozen in more than 5-8 minutes per replicate before processing as in the methods. 104 metabolites were identified in these samples and relative peak intensities were compared to identify changes in abundance corresponding to regeneration. 42 differentially abundant metabolites were found using MetaboAnalyst, the majority of which were increased 24 hours post amputation. Further investigation of these 24 hours post amputation enriched metabolites revealed that these metabolites were largely associated with increased growth and nucleotide metabolism. This finding is in line with the growth of new tissue seen at this timepoint and also suggests that generation of nucleotides are a major factor in sustaining this growth.
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:SU002357
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 Timepoint
SA2177560hpa_T0hpa
SA2177570hpa_S0hpa
SA2177580hpa_K0hpa
SA2177590hpa_O0hpa
SA2177600hpa_B0hpa
SA2177610hpa_M0hpa
SA2177620hpa_G0hpa
SA2177630hpa_L0hpa
SA2177640hpa_P0hpa
SA2177650hpa_R0hpa
SA21776624hpa_T24hpa
SA21776724hpa_K24hpa
SA21776824hpa_M24hpa
SA21776924hpa_O24hpa
SA21777024hpa_L24hpa
SA21777124hpa_P24hpa
SA21777224hpa_R24hpa
SA21777324hpa_S24hpa
SA2177743hpa_P3hpa
SA2177753hpa_L3hpa
SA2177763hpa_T3hpa
SA2177773hpa_S3hpa
SA2177783hpa_O3hpa
SA2177793hpa_M3hpa
SA2177803hpa_K3hpa
SA2177813hpa_R3hpa
SA2177823hpa_G3hpa
SA2177833hpa_B3hpa
SA217784Tips_PTips
SA217785Tips_MTips
SA217786Tips_TTips
SA217787Tips_STips
SA217788Tips_BTips
SA217789Tips_OTips
SA217790Tips_LTips
SA217791Tips_KTips
SA217792Tips_RTips
SA217793Tips_GTips
Showing results 1 to 38 of 38

Collection:

Collection ID:CO002350
Collection Summary:Tadpoles were anesthetized with 0.05% MS-222 in 1/9x MR and tested for response to touch prior to tissue collection. For uninjured tips (Tips), a sterilized scalpel was used to amputate 500µm of the posterior tip. For 0 hours post amputation (hpa) samples, the posterior third of the tail was amputated followed by collection of tail tissue 250µm anterior to the initial wound. For 3 and 24hpa, 250µm of tissue, including the regenerating tissue, was collected. 10 replicates of 25 tails (8 replicates for the 24hpa timepoint) were collected. For each sample, media was removed, and samples were frozen on dry ice within 5-8 minutes from the first amputation.
Sample Type:Tails

Treatment:

Treatment ID:TR002369
Treatment Summary:No applicable

Sample Preparation:

Sampleprep ID:SP002363
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 AN003712 AN003713
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:CH002750
Instrument Name:Shimadzu Nexera X2
Column Name:Waters XBridge BEH Amide XP
Chromatography Type:HILIC

MS:

MS ID:MS003461
Analysis ID:AN003712
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:MS003462
Analysis ID:AN003713
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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