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

Study ID	ST000365
Study Title	Zebrafish Metabolomics: Model for Environmental Metal Toxicity
Study 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	University of North Carolina
Department	Discovery Sciences
Laboratory	Sumner Lab
Last Name	Sumner
First Name	Susan
Address	Eastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081
Email	susan_sumner @unc.edu
Phone	704-250-5066
Submit Date	2016-03-09
Raw Data Available	Yes
Raw Data File Type(s)	1r
Analysis Type Detail	NMR
Release Date	2017-10-03
Release Version	1

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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
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	Metal Exposure	Exposure Level
SA016457	CM_CdPool_1	Cd	-
SA016458	CM_CdPool_2	Cd	-
SA016459	CM_CdPool_3	Cd	-
SA016460	CM_Cdhigh_1	Cd	high (1000 ppb)
SA016461	CM_Cdhigh_3	Cd	high (1000 ppb)
SA016462	CM_Cdhigh_2	Cd	high (1000 ppb)
SA016463	CM_Cdlow_1	Cd	low (10 ppb)
SA016464	CM_Cdlow_3	Cd	low (10 ppb)
SA016465	CM_Cdlow_2	Cd	low (10 ppb)
SA016466	CM_Cdmid_1	Cd	mid (100 ppb)
SA016467	CM_Cdmid_3	Cd	mid (100 ppb)
SA016468	CM_Cdmid_2	Cd	mid (100 ppb)
SA016445	CM_CdPbPool_2	Cd+Pb	-
SA016446	CM_CdPbPool_3-R	Cd+Pb	-
SA016447	CM_CdPbPool_1	Cd+Pb	-
SA016442	CM_TotalPool_3	CD+Pb	-
SA016443	CM_TotalPool_2	CD+Pb	-
SA016444	CM_TotalPool_1	CD+Pb	-
SA016448	CM_CdPbhigh_1	Cd+Pb	high (1000 ppb Cd and 1000 ppb Pb)
SA016449	CM_CdPbhigh_3	Cd+Pb	high (1000 ppb Cd and 1000 ppb Pb)
SA016450	CM_CdPbhigh_2	Cd+Pb	high (1000 ppb Cd and 1000 ppb Pb)
SA016451	CM_CdPblow_1	Cd+Pb	low (10 ppb Cd and 10 ppb Pb)
SA016452	CM_CdPblow_2	Cd+Pb	low (10 ppb Cd and 10 ppb Pb)
SA016453	CM_CdPblow_3	Cd+Pb	low (10 ppb Cd and 10 ppb Pb)
SA016454	CM_CdPBmid_2	Cd+Pb	mid (100 ppb Cd and 100 ppb Pb)
SA016455	CM_CdPBmid_3	Cd+Pb	mid (100 ppb Cd and 100 ppb Pb)
SA016456	CM_CdPBmid_1	Cd+Pb	mid (100 ppb Cd and 100 ppb Pb)
SA016481	CM_NoExpPool_1	control	-
SA016482	CM_NoExpPool_3	control	-
SA016483	CM_NoExpPool_2	control	-
SA016484	CM_NoExp_2	control	No
SA016485	CM_NoExp_3	control	No
SA016486	CM_NoExp_1	control	No
SA016469	CM_PbPool_2	Pb	-
SA016470	CM_PbPool_1	Pb	-
SA016471	CM_PbPool_3-R	Pb	-
SA016472	CM_Pbhigh_2	Pb	high (1000 ppb)
SA016473	CM_Pbhigh_3	Pb	high (1000 ppb)
SA016474	CM_Pbhigh_1	Pb	high (1000 ppb)
SA016475	CM_Pblow_2	Pb	low (10 ppb)
SA016476	CM_Pblow_1	Pb	low (10 ppb)
SA016477	CM_Pblow_3	Pb	low (10 ppb)
SA016478	CM_Pbmid_3	Pb	mid (100 ppb)
SA016479	CM_Pbmid_1	Pb	mid (100 ppb)
SA016480	CM_Pbmid_2	Pb	mid (100 ppb)

Showing results 1 to 45 of 45

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.

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