Summary of Study ST000305

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 PR000245. The data can be accessed directly via it's Project DOI: 10.21228/M8401H This work is supported by NIH grant, U2C- DK119886.

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Study ID	ST000305
Study Title	Pig Athersclerosis Model
Study Type	Metabolomics
Study Summary	Insulin-resistant subjects develop more severe and diffuse coronary artery atherosclerosis than insulin sensitive control but the mechanisms that mediate the atherosclerosis phenotype are unknown. The objective of this study is to investigate whether the severity of atherosclerosis is associated not only with lipoprotein concentrations, weight, blood pressure, biomarkers of inflammation and IR in an animal model but also changes in parameters that measure protein glycation. The experimental approach was to study normocholestrolemic pigs fed a high fat diet that also contained increased NaCl. The choice of pigs was driven by the fact that, like humans, they develop coronary artery and aortic atherosclerosis and insulin resistance. In addition, pigs have been used in many studies to define the mechanisms that mediate increased atherosclerosis in diabetes.
Institute	University of North Carolina
Department	Systems and Translational 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	2015-12-31
Total Subjects	90
Raw Data Available	Yes
Raw Data File Type(s)	fid
Analysis Type Detail	NMR
Release Date	2016-12-31
Release Version	1

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Project:

Project ID:	PR000245
Project DOI:	doi: 10.21228/M8401H
Project Title:	Pig Athersclerosis Model
Project Summary:	Insulin-resistant subjects develop more severe and diffuse coronary artery atherosclerosis than insulin sensitive control but the mechanisms that mediate the atherosclerosis phenotype are unknown. The objective of this study is to investigate whether the severity of atherosclerosis is associated not only with lipoprotein concentrations, weight, blood pressure, biomarkers of inflammation and IR in an animal model but also changes in parameters that measure protein glycation. The experimental approach was to study normocholestrolemic pigs fed a high fat diet that also contained increased NaCl. The choice of pigs was driven by the fact that, like humans, they develop coronary artery and aortic atherosclerosis and insulin resistance. In addition, pigs have been used in many studies to define the mechanisms that mediate increased atherosclerosis in diabetes.
Institute:	University of North Carolina at Chapel Hill
Department:	Department of Pathology and Laboratory Medicine
Last Name:	Nichols
First Name:	Timothy
Address:	-
Email:	tnichols@med.unc.edu
Phone:	-

Subject:

Subject ID:	SU000325
Subject Type:	Animal
Subject Species:	Sus scrofa
Taxonomy ID:	9823
Species Group:	Mammal

Factors:

Subject type: Animal; Subject species: Sus scrofa (Factor headings shown in green)

mb_sample_id	local_sample_id	atherosclerosis	diet	phenotype	sex
SA013757	FN_46L	Little to None	Control	CH/FH	female
SA013758	FN_22I	Little to None	Control	CH/FH	female
SA013759	BN_46L	Little to None	Control	CH/FH	female
SA013760	BN_22I	Little to None	Control	CH/FH	female
SA013761	BN_05K	Little to None	Control	CH/FH	male
SA013762	FN_05K	Little to None	Control	CH/FH	male
SA013763	FN_18K	Little to None	Control	CH	female
SA013764	BN_18K	Little to None	Control	CH	female
SA013765	BN_16K	Little to None	Control	CH	male
SA013766	FN_16K	Little to None	Control	CH	male
SA013767	BM_08K	Moderate	High fat and salt	CH/FH	female
SA013768	FM_08K	Moderate	High fat and salt	CH/FH	female
SA013769	FM_01F	Moderate	High fat and salt	CH/FH	male
SA013770	BM_69G	Moderate	High fat and salt	CH/FH	male
SA013771	BM_21J	Moderate	High fat and salt	CH/FH	male
SA013772	BM_14K	Moderate	High fat and salt	CH/FH	male
SA013773	FM_02F	Moderate	High fat and salt	CH/FH	male
SA013774	FM_05I	Moderate	High fat and salt	CH/FH	male
SA013775	FM_20J	Moderate	High fat and salt	CH/FH	male
SA013776	FM_14K	Moderate	High fat and salt	CH/FH	male
SA013777	FM_69G	Moderate	High fat and salt	CH/FH	male
SA013778	FM_21J	Moderate	High fat and salt	CH/FH	male
SA013779	BM_20J	Moderate	High fat and salt	CH/FH	male
SA013780	BM_01F	Moderate	High fat and salt	CH/FH	male
SA013781	BM_06I	Moderate	High fat and salt	CH/FH	male
SA013782	BM_02F	Moderate	High fat and salt	CH/FH	male
SA013783	BM_05I	Moderate	High fat and salt	CH/FH	male
SA013784	FM_11G	Moderate	High fat and salt	CH	female
SA013785	BM_11G	Moderate	High fat and salt	CH	female
SA013786	FM_69F	Moderate	High fat and salt	CH	male
SA013787	FM_62F	Moderate	High fat and salt	CH	male
SA013788	FM_45L	Moderate	High fat and salt	CH	male
SA013789	FM_15K	Moderate	High fat and salt	CH	male
SA013790	FM_68F	Moderate	High fat and salt	CH	male
SA013791	FM_02C	Moderate	High fat and salt	CH	male
SA013792	BM_62F	Moderate	High fat and salt	CH	male
SA013793	BM_45L	Moderate	High fat and salt	CH	male
SA013794	BM_15K	Moderate	High fat and salt	CH	male
SA013795	BM_02C	Moderate	High fat and salt	CH	male
SA013796	BM_69F	Moderate	High fat and salt	CH	male
SA013797	Mod_FU_Pool2	Moderate	Pool
SA013798	Mod_Base_Pool1	Moderate	Pool
SA013799	Mod_Base_Pool2	Moderate	Pool
SA013800	Mod_FU_Pool1	Moderate	Pool
SA013801	Total_FU_Pool3	Pool	Pool
SA013802	Total_Base_Pool5	Pool	Pool
SA013803	FS_10K	Severe & Diffuse	High fat and salt	CH/FH	female
SA013804	FS_18J	Severe & Diffuse	High fat and salt	CH/FH	female
SA013805	FS_17K	Severe & Diffuse	High fat and salt	CH/FH	female
SA013806	FS_24I	Severe & Diffuse	High fat and salt	CH/FH	female
SA013807	FS_07K	Severe & Diffuse	High fat and salt	CH/FH	female
SA013808	BS_49L	Severe & Diffuse	High fat and salt	CH/FH	female
SA013809	FS_02I	Severe & Diffuse	High fat and salt	CH/FH	female
SA013810	FS_03I	Severe & Diffuse	High fat and salt	CH/FH	female
SA013811	FS_06F	Severe & Diffuse	High fat and salt	CH/FH	female
SA013812	FS_09K	Severe & Diffuse	High fat and salt	CH/FH	female
SA013813	BS_10K	Severe & Diffuse	High fat and salt	CH/FH	female
SA013814	BS_24I	Severe & Diffuse	High fat and salt	CH/FH	female
SA013815	BS_07K	Severe & Diffuse	High fat and salt	CH/FH	female
SA013816	BS_09K	Severe & Diffuse	High fat and salt	CH/FH	female
SA013817	BS_18J	Severe & Diffuse	High fat and salt	CH/FH	female
SA013818	BS_03I	Severe & Diffuse	High fat and salt	CH/FH	female
SA013819	BS_02I	Severe & Diffuse	High fat and salt	CH/FH	female
SA013820	FS_49L	Severe & Diffuse	High fat and salt	CH/FH	female
SA013821	BS_17K	Severe & Diffuse	High fat and salt	CH/FH	female
SA013822	FS_21I	Severe & Diffuse	High fat and salt	CH/FH	male
SA013823	FS_02K	Severe & Diffuse	High fat and salt	CH/FH	male
SA013824	BS_02K	Severe & Diffuse	High fat and salt	CH/FH	male
SA013825	BS_21I	Severe & Diffuse	High fat and salt	CH/FH	male
SA013826	FS_48L	Severe & Diffuse	High fat and salt	CH	female
SA013827	FS_47L	Severe & Diffuse	High fat and salt	CH	female
SA013828	BS_47L	Severe & Diffuse	High fat and salt	CH	female
SA013829	FS_05B	Severe & Diffuse	High fat and salt	CH	female
SA013830	FS_35G	Severe & Diffuse	High fat and salt	CH	female
SA013831	BS_35G	Severe & Diffuse	High fat and salt	CH	female
SA013832	BS_48L	Severe & Diffuse	High fat and salt	CH	female
SA013833	BS_05B	Severe & Diffuse	High fat and salt	CH	female
SA013834	BS_33G	Severe & Diffuse	High fat and salt	CH	male
SA013835	BS_44L	Severe & Diffuse	High fat and salt	CH	male
SA013836	FS_44L	Severe & Diffuse	High fat and salt	CH	male
SA013837	BS_34G	Severe & Diffuse	High fat and salt	CH	male
SA013838	FS_33G	Severe & Diffuse	High fat and salt	CH	male
SA013839	FS_34G	Severe & Diffuse	High fat and salt	CH	male
SA013840	BS_20I	Severe & Diffuse	High fat and salt	CH	male
SA013841	Sev_Base_Pool1	Severe & Diffuse	Pool
SA013842	Sev_FU_Pool2	Severe & Diffuse	Pool
SA013843	Sev_FU_Pool1	Severe & Diffuse	Pool
SA013844	Sev_Base_Pool3	Severe & Diffuse	Pool
SA013845	Sev_Base_Pool2	Severe & Diffuse	Pool
SA013846	Sev_FU_Pool3	Severe & Diffuse	Pool

Showing results 1 to 90 of 90

Showing results 1 to 90 of 90

Collection:

Collection ID:	CO000319
Collection Summary:	-
Sample Type:	Serum
Storage Conditions:	-80C

Treatment:

Treatment ID:	TR000339
Treatment Summary:	-

Sample Preparation:

Sampleprep ID:	SP000333
Sampleprep Summary:	Serum samples were transferred to labeled tubes. A total of 112 study samples were thawed on ice for sample preparation 350 uL of serum sample were thawed and transferred to labeled tubes on ice where they were prepared and eventually mixed with 700uL master mix containing 630 uL of phosphate buffer and 70 uL of Chenomx ISTD (5mM DSS, 6mM Imidazole, and 0.02% NaN3). Analytical quality control (QC) phenotypic pooled samples were generated by transferring a 75 µL of each sample of each respective phenotypical experimental sample into different 15 mL tubes. Whole study (total) pools were generated by transferring 200 uL of serum from each Pool sample into a 15 mL tube. The tubes were vortexed for 4 min on a multi-tube vortexer and centrifuged at 16,000 rcf for 4 min. A 600 µl aliquot of the supernatant was transferred into pre-labeled 5mm (4 inch) NMR tubes for data acquisition on a 700 MHz spectrometer..
Sampleprep Protocol Filename:	Pig_Athersclerosis_Model_Procedures.docx

Analysis:

Analysis ID:	AN000484
Analysis Type:	NMR
Num Factors:	15

NMR:

NMR ID:	NM000060
Analysis ID:	AN000484
Instrument Name:	Bruker
Instrument Type:	FT-NMR
NMR Experiment Type:	Other
Field Frequency Lock:	Deuterium
Standard Concentration:	0.5 mM
Spectrometer Frequency:	700 MHz
NMR Probe:	5 mm ATMA Cryoprobe
NMR Solvent:	D2O
NMR Tube Size:	5 mm
Shimming Method:	Topshim
Pulse Sequence:	noesypr1d
Water Suppression:	yes
Receiver Gain:	4.5
Offset Frequency:	3299.5
Chemical Shift Ref Cpd:	DSS
Temperature:	298.1 K
Number Of Scans:	128
Dummy Scans:	4
Acquisition Time:	3.893
Spectral Width:	12.0227 ppm, 8.417 Hz
Num Data Points Acquired:	65536
Real Data Points:	65536
Line Broadening:	0.5 Hz
Zero Filling:	yes
Apodization:	Lorentzian
Baseline Correction Method:	Polynomial
Chemical Shift Ref Std:	DSS-D6
Binned Increment:	0.04
Binned Data Excluded Range:	water (4.68 – 5.2 ppm) methanol (3.33 - 3.36 ppm) imidazole (7.27 - 7.40 ppm)