Summary of Study ST000584

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 PR000427. The data can be accessed directly via it's Project DOI: 10.21228/M8VK5D 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.

Show all samples  |  Perform analysis on untargeted data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files
Study IDST000584
Study TitleFasting wildtype, tfeb -/- knockout, and lmna -/- knockout metabolite profiling of adult zebrafish
Study SummaryInhibition of mechanistic target of rapamycin (mTOR) activity exerts cardioprotective functions. We propose to assess the metabolite profile in zebrafish cardiomyopathy models to test the cardioprotective role of mTOR-TFEB-autophagy and mTOR-lmna- autophagy signaling in heart, liver, muscle, brain, and kidney tissue. In addition mTOR signaling among zebrafish 2 hour post feeding, 24 hour post feeding, and 48 hour post feeding will be profiled. These studes will be used as a baseline and for protocol development before we assess changes in DOX-induced cardiomyopathy.
Institute
Mayo Clinic
Last NameXu
First NameXiaolei
Address200 First Street SW, Rochester, MN 55905
EmailXu.Xiaolei@mayo.edu
Phone507-284-0685
Submit Date2017-03-10
Analysis Type DetailLC-MS
Release Date2019-05-15
Release Version1
Xiaolei Xu Xiaolei Xu
https://dx.doi.org/10.21228/M8VK5D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000427
Project DOI:doi: 10.21228/M8VK5D
Project Title:Mayo Metabolomics Pilot and Feasibility Award: Deciphering cardioprotective effects of mTOR inhibition via metabolite profiling
Project Summary:Cardiomyopathy is the most common cause for sudden death and heart failure with tremendous public health burden in the U.S. Accumulating evidence from both animal models and clinical studies in human transplant patients suggests that partial inhibition of mechanistic Taget of Rapamycin (mTOR) signaling is a viable avenue for therapeutic intervention. Specifically, we recently showed both compound (rapamycin) treatment and genetic manipulation using a mechanistic Target of Rapamycin (mTOR) haploinsufficient (mTOR+/-) mutant confers cardiac protection against cardiomyopathies of two different etiologies in zebrafish. Mechanistically, antihypertrophy, anti-apoptosis and proautophagy of mTOR inhibition play important roles in this cardioprotection process. Our central hypothesis is that this mTOR inhibition-mediated cardioprotection is conferred by transcription factor EB (TFEB)-regulated autophagy activation. To test this hypothesis, we propose to pursue a systematic metabolite profiling analysis in the heart upon DOX stress under fine-tuned mTOR inhibition. We expect to define metabolite signatures in different types of cardiomyopathy, metabolite signature for the cardioprotective effects of mTOR inhibition, as well as metabolite signatures for TFEB genetic manipulations. These data will be compared with transcriptome studies to prove functions of TFEB signaling in cardioprotective effects of mTOR inhibition, which shall provide a solid foundation for renewing our current RO1 grant aiming to develop mTOR-based therapy for heart failure.
Institute:Mayo Clinic
Last Name:Xu
First Name:Xiaolei
Address:200 First Street SW, Rochester, MN 55905
Email:Xu.Xiaolei@mayo.edu
Phone:507-284-0685

Subject:

Subject ID:SU000607
Subject Type:Zebrafish
Subject Species:Danio rerio
Taxonomy ID:7955
Species Group:Fish

Factors:

Subject type: Zebrafish; Subject species: Danio rerio (Factor headings shown in green)

mb_sample_id local_sample_id sex tissue timepoint genotype
SA030858nC18-20nov15-020-r001female heart tfeb-/- tfeb-/-
SA030859nC18-20nov15-018-r002female heart tfeb-/- tfeb-/-
SA030860nC18-20nov15-020-r002female heart tfeb-/- tfeb-/-
SA030861nC18-20nov15-018-r001female heart tfeb-/- tfeb-/-
SA030862nC18-20nov15-022-r001female heart tfeb-/- tfeb-/-
SA030863nC18-20nov15-025-r002female heart tfeb-/- tfeb-/-
SA030864nC18-20nov15-025-r001female heart tfeb-/- tfeb-/-
SA030865pC18-18nov15-025-r002female heart tfeb-/- tfeb-/-
SA030866nhilic-19nov15-025-r002female heart tfeb-/- tfeb-/-
SA030867nhilic-19nov15-025-r001female heart tfeb-/- tfeb-/-
SA030868nhilic-19nov15-020-r002female heart tfeb-/- tfeb-/-
SA030869nhilic-19nov15-020-r001female heart tfeb-/- tfeb-/-
SA030870nhilic-19nov15-018-r002female heart tfeb-/- tfeb-/-
SA030871nhilic-19nov15-022-r001female heart tfeb-/- tfeb-/-
SA030872nhilic-19nov15-022-r002female heart tfeb-/- tfeb-/-
SA030873nC18-20nov15-005-r002female heart tfeb-/- tfeb-/-
SA030874nC18-20nov15-005-r001female heart tfeb-/- tfeb-/-
SA030875philic-18nov15-005-r001female heart tfeb-/- tfeb-/-
SA030876philic-18nov15-005-r002female heart tfeb-/- tfeb-/-
SA030877pC18-18nov15-018-r002female heart tfeb-/- tfeb-/-
SA030878pC18-18nov15-018-r001female heart tfeb-/- tfeb-/-
SA030879pC18-18nov15-005-r002female heart tfeb-/- tfeb-/-
SA030880pC18-18nov15-020-r001female heart tfeb-/- tfeb-/-
SA030881pC18-18nov15-020-r002female heart tfeb-/- tfeb-/-
SA030882pC18-18nov15-025-r001female heart tfeb-/- tfeb-/-
SA030883pC18-18nov15-022-r002female heart tfeb-/- tfeb-/-
SA030884pC18-18nov15-022-r001female heart tfeb-/- tfeb-/-
SA030885pC18-18nov15-005-r001female heart tfeb-/- tfeb-/-
SA030886philic-18nov15-018-r001female heart tfeb-/- tfeb-/-
SA030887philic-18nov15-022-r002female heart tfeb-/- tfeb-/-
SA030888philic-18nov15-025-r001female heart tfeb-/- tfeb-/-
SA030889philic-18nov15-025-r002female heart tfeb-/- tfeb-/-
SA030890philic-18nov15-022-r001female heart tfeb-/- tfeb-/-
SA030891philic-18nov15-020-r002female heart tfeb-/- tfeb-/-
SA030892philic-18nov15-018-r002female heart tfeb-/- tfeb-/-
SA030893philic-18nov15-020-r001female heart tfeb-/- tfeb-/-
SA030894nhilic-19nov15-018-r001female heart tfeb-/- tfeb-/-
SA030895nC18-20nov15-022-r002female heart tfeb-/- tfeb-/-
SA030896nhilic-19nov15-005-r001female heart tfeb-/- tfeb-/-
SA030897nhilic-19nov15-005-r002female heart tfeb-/- tfeb-/-
SA030898nC18-26nov15-023-r002female kidney tfeb-/- tfeb-/-
SA030899nC18-26nov15-023-r001female kidney tfeb-/- tfeb-/-
SA030900philic-24nov15-005-r002female kidney tfeb-/- tfeb-/-
SA030901pC18-24nov15-023-r002_1female kidney tfeb-/- tfeb-/-
SA030902philic-24nov15-015-r001female kidney tfeb-/- tfeb-/-
SA030903philic-24nov15-017-r002female kidney tfeb-/- tfeb-/-
SA030904philic-24nov15-017-r001female kidney tfeb-/- tfeb-/-
SA030905philic-24nov15-015-r002female kidney tfeb-/- tfeb-/-
SA030906nhilic-25nov15-012-r001female kidney tfeb-/- tfeb-/-
SA030907nhilic-25nov15-012-r002female kidney tfeb-/- tfeb-/-
SA030908nhilic-25nov15-017-r002female kidney tfeb-/- tfeb-/-
SA030909nhilic-25nov15-017-r001female kidney tfeb-/- tfeb-/-
SA030910nhilic-25nov15-015-r002female kidney tfeb-/- tfeb-/-
SA030911nhilic-25nov15-023-r001female kidney tfeb-/- tfeb-/-
SA030912philic-24nov15-005-r001female kidney tfeb-/- tfeb-/-
SA030913philic-24nov15-023-r002female kidney tfeb-/- tfeb-/-
SA030914philic-24nov15-023-r001female kidney tfeb-/- tfeb-/-
SA030915nhilic-25nov15-023-r002female kidney tfeb-/- tfeb-/-
SA030916nhilic-25nov15-005-r002female kidney tfeb-/- tfeb-/-
SA030917pC18-24nov15-017-r002_1female kidney tfeb-/- tfeb-/-
SA030918nC18-26nov15-005-r001female kidney tfeb-/- tfeb-/-
SA030919nC18-26nov15-015-r001female kidney tfeb-/- tfeb-/-
SA030920nC18-26nov15-015-r002female kidney tfeb-/- tfeb-/-
SA030921nC18-26nov15-017-r001female kidney tfeb-/- tfeb-/-
SA030922nC18-26nov15-005-r002female kidney tfeb-/- tfeb-/-
SA030923pC18-24nov15-005-r002_1female kidney tfeb-/- tfeb-/-
SA030924nC18-26nov15-012-r001female kidney tfeb-/- tfeb-/-
SA030925nC18-26nov15-012-r002female kidney tfeb-/- tfeb-/-
SA030926pC18-24nov15-005-r001_1female kidney tfeb-/- tfeb-/-
SA030927pC18-24nov15-012-r001_1female kidney tfeb-/- tfeb-/-
SA030928nC18-26nov15-017-r002female kidney tfeb-/- tfeb-/-
SA030929philic-24nov15-012-r002female kidney tfeb-/- tfeb-/-
SA030930nhilic-25nov15-005-r001female kidney tfeb-/- tfeb-/-
SA030931nhilic-25nov15-015-r001female kidney tfeb-/- tfeb-/-
SA030932pC18-24nov15-017-r001_1female kidney tfeb-/- tfeb-/-
SA030933pC18-24nov15-015-r002_1female kidney tfeb-/- tfeb-/-
SA030934philic-24nov15-012-r001female kidney tfeb-/- tfeb-/-
SA030935pC18-24nov15-012-r002_1female kidney tfeb-/- tfeb-/-
SA030936pC18-24nov15-015-r001_1female kidney tfeb-/- tfeb-/-
SA030937pC18-24nov15-023-r001_1female kidney tfeb-/- tfeb-/-
SA030938pC18-11nov15-019-r001female muscle tfeb-/- tfeb-/-
SA030939pC18-11nov15-022-r002female muscle tfeb-/- tfeb-/-
SA030940nhilic-12nov15-015-r001female muscle tfeb-/- tfeb-/-
SA030941nhilic-12nov15-015-r002female muscle tfeb-/- tfeb-/-
SA030942pC18-11nov15-022-r001female muscle tfeb-/- tfeb-/-
SA030943pC18-11nov15-019-r002female muscle tfeb-/- tfeb-/-
SA030944pC18-11nov15-016-r001female muscle tfeb-/- tfeb-/-
SA030945pC18-11nov15-016-r002female muscle tfeb-/- tfeb-/-
SA030946pC18-11nov15-015-r002female muscle tfeb-/- tfeb-/-
SA030947pC18-11nov15-003-r002female muscle tfeb-/- tfeb-/-
SA030948philic-11nov15-016-r001female muscle tfeb-/- tfeb-/-
SA030949philic-11nov15-016-r002female muscle tfeb-/- tfeb-/-
SA030950philic-11nov15-015-r002female muscle tfeb-/- tfeb-/-
SA030951philic-11nov15-015-r001female muscle tfeb-/- tfeb-/-
SA030952philic-11nov15-003-r001female muscle tfeb-/- tfeb-/-
SA030953philic-11nov15-003-r002female muscle tfeb-/- tfeb-/-
SA030954philic-11nov15-019-r001female muscle tfeb-/- tfeb-/-
SA030955philic-11nov15-019-r002female muscle tfeb-/- tfeb-/-
SA030956nhilic-12nov15-003-r001female muscle tfeb-/- tfeb-/-
SA030957nhilic-12nov15-003-r002female muscle tfeb-/- tfeb-/-
Showing page 1 of 9     Results:    1  2  3  4  5  Next  Last     Showing results 1 to 100 of 836

Collection:

Collection ID:CO000601
Collection Summary:When testing the wildtype fasting fish, we only choose male fish. For each of the 3 time points, we scarifice 25 fish, put 5 tissue in one tube for 5 repeats. Because of tissue size, I adjusted heart sample at 2h and kidney sample at 2h to 3 repeats, liver sample at 2h to 4 repeats. For tfeb-/-fish, we collected heart, muscle, kidney with each of them 5 repeats. We collected both male and female. For lmna-/- we collected heart and muscle(only male) with each 3 repeats.
Sample Type:Blood

Treatment:

Treatment ID:TR000621
Treatment Summary:This is pre-test study for protocal development and baseline measures. Fish hearts are small, and more than 30 adult fish heart might need to be pooled to generated sufficient sample for a metabolic profiling experiments. Therefore, we will first test the condition using wild type fish at 3 months for this purpose. Tfeb -/- knockouts and lmna -/- knockouts are similarily being used for protocal development. After we optimize the protocol, we will assess changes in DOX-induced cardiomyopathy.

Sample Preparation:

Sampleprep ID:SP000614
Sampleprep Summary:Handling of tissue 1) Keep tubes on ice for 10 min. Spin down @ 1000 RCF for 30 sec 2) Add 20 ul PBS per sample and 3 ul 13C6-Phe 3) Sonicate on ice bath for 30 sec x 4 times 4) Add 250 ul ACN/MeOH mixture and incubate on ice for 30 min 5) Pool 20 ul sup from each sample and split 100 ul pool in 5 tubes 6) Split remaining sup in two 1 dram vials x 2 (100 ul per vial) 7) Dry under N2 stream

Combined analysis:

Analysis ID AN000896 AN000897 AN000898 AN000899
Analysis type MS MS MS MS
Chromatography type HILIC HILIC Reversed phase Reversed phase
Chromatography system Agilent 1290 Infinity Agilent 1290 Infinity Agilent 1290 Infinity Agilent 1290 Infinity
Column Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity HSS C18 (150 x 2.1mm,1.8um) Waters Acquity HSS C18 (150 x 2.1mm,1.8um)
MS Type ESI ESI ESI ESI
MS instrument type QTOF QTOF QTOF QTOF
MS instrument name Agilent 6550 QTOF Agilent 6550 QTOF Agilent 6550 QTOF Agilent 6550 QTOF
Ion Mode POSITIVE NEGATIVE POSITIVE NEGATIVE
Units unspecified unspecified unspecified unspecified

Chromatography:

Chromatography ID:CH000638
Instrument Name:Agilent 1290 Infinity
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Chromatography Type:HILIC
  
Chromatography ID:CH000639
Instrument Name:Agilent 1290 Infinity
Column Name:Waters Acquity HSS C18 (150 x 2.1mm,1.8um)
Chromatography Type:Reversed phase

MS:

MS ID:MS000798
Analysis ID:AN000896
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000799
Analysis ID:AN000897
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
  
MS ID:MS000800
Analysis ID:AN000898
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000801
Analysis ID:AN000899
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
  logo