Summary of study ST000365

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 PR000290. The data can be accessed directly via it's Project DOI: 10.21228/M8JW2K This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

Perform statistical analysis  |  Show all samples  |  Download all metabolite data  |  Download binned data  |  Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data (Contains raw data)
Study IDST000365
Study TitleZebrafish Metabolomics: Model for Environmental Metal Toxicity
Study SummaryThis metabolomics seed project will test the hypothesis that zebrafish can provide mechanistic insights into the human health effects of developmental exposure to Cd and Pb. We will use broad spectrum metabolomics of zebrafish larvae after exposure to Cd, Pb, and Cd and Pb compared to controls. Activity observed at 5 days post fertilization is will be used to determine if there is a correlation between biological pathways implicated by these metabolic profiles and cardiovascular, metabolic (obesity), and neurological phenotypes. The behavioral phenotypes have been quantified in zebrafish previously and have been measured in the Newborn Epigenetic STudy (NEST), a NIH-funded project that is investigating how environmental exposures and nutrition, in the womb and during childhood, affect how genes work and how these exposures developed into obesity and other diseases, disorders, and conditions. The results from this study will demonstrate the power of using zebrafish as a model for mechanism discovery in exposure using metabolomics to advance understanding of early life exposure to Cd and Pb and serve as preliminary data for opportunities.
Institute
University of North Carolina
DepartmentDiscovery Sciences
LaboratorySumner Lab
Last NameSumner
First NameSusan
AddressEastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081
Emailsusan_sumner @unc.edu
Phone704-250-5066
Submit Date2016-03-09
Raw Data AvailableYes
Raw Data File Type(s)pdata, scon2, shimvalues, .par, acqu, acqus
Analysis Type DetailNMR
Release Date2017-10-03
Release Version1
Susan Sumner Susan Sumner
https://dx.doi.org/10.21228/M8JW2K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000290
Project DOI:doi: 10.21228/M8JW2K
Project Title:Zebrafish Metabolomics: Model for Environmental Metal Toxicity
Project Summary:This metabolomics seed project will test the hypothesis that zebrafish can provide mechanistic insights into the human health effects of developmental exposure to Cd and Pb. We will use broad spectrum metabolomics of zebrafish larvae after exposure to Cd, Pb, and Cd and Pb compared to controls. Activity observed at 5 days post fertilization is will be used to determine if there is a correlation between biological pathways implicated by these metabolic profiles and cardiovascular, metabolic (obesity), and neurological phenotypes. The behavioral phenotypes have been quantified in zebrafish previously and have been measured in the Newborn Epigenetic STudy (NEST), a NIH-funded project that is investigating how environmental exposures and nutrition, in the womb and during childhood, affect how genes work and how these exposures developed into obesity and other diseases, disorders, and conditions. The results from this study will demonstrate the power of using zebrafish as a model for mechanism discovery in exposure using metabolomics to advance understanding of early life exposure to Cd and Pb and serve as preliminary data for opportunities.
Institute:North Carolina State University
Last Name:Mattingly
First Name:Carolyn
Address:142 David Clark Labs, Raleigh, NC 27695-7617
Email:cjmattin@ncsu.edu
Phone:919-515-2024

Subject:

Subject ID:SU000386
Subject Type:Zebrafish
Subject Species:Danio rerio
Species Group:Fish

Factors:

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

mb_sample_id local_sample_id Metal Exposure Exposure Level
SA016457CM_CdPool_1Cd -
SA016458CM_CdPool_2Cd -
SA016459CM_CdPool_3Cd -
SA016460CM_Cdhigh_1Cd high (1000 ppb)
SA016461CM_Cdhigh_3Cd high (1000 ppb)
SA016462CM_Cdhigh_2Cd high (1000 ppb)
SA016463CM_Cdlow_1Cd low (10 ppb)
SA016464CM_Cdlow_3Cd low (10 ppb)
SA016465CM_Cdlow_2Cd low (10 ppb)
SA016466CM_Cdmid_1Cd mid (100 ppb)
SA016467CM_Cdmid_3Cd mid (100 ppb)
SA016468CM_Cdmid_2Cd mid (100 ppb)
SA016445CM_CdPbPool_2Cd+Pb -
SA016446CM_CdPbPool_3-RCd+Pb -
SA016447CM_CdPbPool_1Cd+Pb -
SA016442CM_TotalPool_3CD+Pb -
SA016443CM_TotalPool_2CD+Pb -
SA016444CM_TotalPool_1CD+Pb -
SA016448CM_CdPbhigh_1Cd+Pb high (1000 ppb Cd and 1000 ppb Pb)
SA016449CM_CdPbhigh_3Cd+Pb high (1000 ppb Cd and 1000 ppb Pb)
SA016450CM_CdPbhigh_2Cd+Pb high (1000 ppb Cd and 1000 ppb Pb)
SA016451CM_CdPblow_1Cd+Pb low (10 ppb Cd and 10 ppb Pb)
SA016452CM_CdPblow_2Cd+Pb low (10 ppb Cd and 10 ppb Pb)
SA016453CM_CdPblow_3Cd+Pb low (10 ppb Cd and 10 ppb Pb)
SA016454CM_CdPBmid_2Cd+Pb mid (100 ppb Cd and 100 ppb Pb)
SA016455CM_CdPBmid_3Cd+Pb mid (100 ppb Cd and 100 ppb Pb)
SA016456CM_CdPBmid_1Cd+Pb mid (100 ppb Cd and 100 ppb Pb)
SA016481CM_NoExpPool_1control -
SA016482CM_NoExpPool_3control -
SA016483CM_NoExpPool_2control -
SA016484CM_NoExp_2control No
SA016485CM_NoExp_3control No
SA016486CM_NoExp_1control No
SA016469CM_PbPool_2Pb -
SA016470CM_PbPool_1Pb -
SA016471CM_PbPool_3-RPb -
SA016472CM_Pbhigh_2Pb high (1000 ppb)
SA016473CM_Pbhigh_3Pb high (1000 ppb)
SA016474CM_Pbhigh_1Pb high (1000 ppb)
SA016475CM_Pblow_2Pb low (10 ppb)
SA016476CM_Pblow_1Pb low (10 ppb)
SA016477CM_Pblow_3Pb low (10 ppb)
SA016478CM_Pbmid_3Pb mid (100 ppb)
SA016479CM_Pbmid_1Pb mid (100 ppb)
SA016480CM_Pbmid_2Pb mid (100 ppb)
Showing results 1 to 45 of 45

Collection:

Collection ID:CO000380
Collection Summary:The larvae were collected at 48 hours post fertilization (hpf).
Sample Type:Fish larvae

Treatment:

Treatment ID:TR000400
Treatment Summary:Zebrafish larvae were exposured to Cd (10, 100, and 1000 ppb), Pb (10, 100, and 1000 ppb), and Cd and Pb (10 ppb Cd and 10 ppb Pb, 100 ppb Cd and 100 ppb Pb, and 1000 ppb Cd and 1000 ppb Pb) and compared to controls. The exposure period was between 6-48 hours post fertilization (hpf). The larvae were collected at 48 hpf.

Sample Preparation:

Sampleprep ID:SP000393
Sampleprep Summary:Pools with 40 larvae each were washed and snap frozen before being shipped to the NIH RTI-RCMRC on dry ice and immediately stored at -80 °C after being logged in for metabolomics analysis. A total of 30 study samples were lyophilized overnight for sample preparation. Each sample was mixed with 750 μl of methanol, vortexed, and centrifuged. 300 μl of the supernatant were used for the study samples, phenotypic pools were created using 350 μl of each phenotype and a total study pool was created by mixing 35 μl from each sample. Three aliquots were created from each pool for a total of 15 pooled samples. All samples were dried in vacuum overnight. Each sample was reconstituted with 250 μl of 0.5 mM phosphate buffer (pH 7.5) and 25 μl of d-DSS/Chenomx as an internal standard. The tubes were vortexed for 2 min on a multi-tube vortexer and centrifuged at 16,000 rcf for 10 min. A 200 µl aliquot of the supernatant was transferred into pre-labeled 3 mm (4”) NMR tubes for data acquisition on a 700 MHz spectrometer. 1H NMR spectra of zebrafish extraction samples were acquired on a Bruker 700 MHz NMR spectrometer (located at David H. Murdock Research Institute, Kannapolis, NC, USA) using a 5 mm cryogenically cooled ATMA inverse probe and ambient temperature of 25 ℃. A 1D NOESY presaturation pulse sequence (noesypr1d, [recycle delay (RD)-90°-t1-90°-tm-90°-acquire free induction decay (FID) was used for data acquisition. For each sample 32 transients were collected into 65k data points using a spectral width of 17.17 ppm, 2 s relaxation delay, 100 ms mixing time, and an acquisition time of 3.9 s per FID. The water resonance was suppressed using resonance irradiation during the relaxation delay and mixing time. NMR spectra were processed using TopSpin 3.2 software (Bruker-Biospin, Germany). Spectra were zero filled, and Fourier transformed after exponential multiplication with line broadening factor of 0.5. Phase and baseline of the spectra were manually corrected for each spectrum. Spectra were referenced internally to the DSS-d6 signal. The quality of each NMR spectrum was assessed for the level of noise and alignment of identified markers. Spectra were assessed for missing data and underwent quality checks.

Analysis:

Analysis ID:AN000598
Analysis Type:NMR
Num Factors:15

NMR:

NMR ID:NM000065
Analysis ID:AN000598
Instrument Name:Bruker Avance III
Instrument Type:FT-NMR
NMR Experiment Type:1D 1H
Spectrometer Frequency:700 MHz
  logo