Summary of Study ST001935

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 PR001224. The data can be accessed directly via it's Project DOI: 10.21228/M8H12N 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.

Study ID	ST001935
Study Title	Metabolomic profiling of spontaneous macaque model for diabetes mellitus
Study Summary	The prevalence of diabetes mellitus has been increasing for decades worldwide. To develop safe and potent therapeutics, insights into the mechanisms underlying its pathogenesis are urgently needed. We reported the multi-omics profiling of the liver and sera of both peripheral blood and hepatic portal vein blood from Macaca fascicularis with spontaneous diabetes mellitus with a chow diet. The other two groups of the monkeys fed with chow diet and high-sugar high-fat (HSHF) diet, respectively, were included for comparison. These multi-omics datasets can provide a comprehensive picture of the molecular changes caused by diabetes in primates. Analyses of various omics datasets revealed the alterations of high consistency. Correlation between transcripts and proteins derived from the same genes was observed across individuals for most genes, especially the ones of differential expression. As a result, we found that distinct patterns of the metabolome, proteome, and transcriptome between spontaneous diabetes and HSHF diet-induced diabetes compared with healthy individuals.
Institute	Xiamen University
Last Name	Yang
First Name	Zhu
Address	OEW901, Oen Hall Building West Wing,, Ho Sin Hang Campus, Hong Kong Baptist University
Email	yangzhu@gmail.com
Phone	(+852)34115162
Submit Date	2021-09-18
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	GC-MS
Release Date	2022-02-19
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001224
Project DOI:	doi: 10.21228/M8H12N
Project Title:	Metabolomic, transcriptomic, and proteomic profiling of spontaneous macaque model for diabetes mellitus
Project Summary:	The prevalence of diabetes mellitus has been increasing for decades worldwide. To develop safe and potent therapeutics, insights into the mechanisms underlying its pathogenesis are urgently needed. We reported the multi-omics profiling of the liver and sera of both peripheral blood and hepatic portal vein blood from Macaca fascicularis with spontaneous diabetes mellitus with a chow diet. The other two groups of the monkeys fed with chow diet and high-sugar high-fat (HSHF) diet, respectively, were included for comparison. These multi-omics datasets can provide a comprehensive picture of the molecular changes caused by diabetes in primates. Analyses of various omics datasets revealed the alterations of high consistency. Correlation between transcripts and proteins derived from the same genes was observed across individuals for most genes, especially the ones of differential expression. As a result, we found that distinct patterns of the metabolome, proteome, and transcriptome between spontaneous diabetes and HSHF diet-induced diabetes compared with healthy individuals.
Institute:	Hong Kong Baptist University
Last Name:	Yang
First Name:	Zhu
Address:	OEW901, Oen Hall Building West Wing,, Ho Sin Hang Campus, Hong Kong Baptist University
Email:	yangzhu@gmail.com
Phone:	(+852)34115162

Subject:

Subject ID:	SU002013
Subject Type:	Mammal
Subject Species:	Macaca fascicularis
Taxonomy ID:	9541
Age Or Age Range:	16.3 - 18.8 yo
Weight Or Weight Range:	5.73 - 10.56 kg
Gender:	Male
Animal Animal Supplier:	Guangzhou Huazhen Biosciences Co., Ltd, Guangzhou
Animal Housing:	Guangzhou Huazhen Biosciences Co., Ltd, Guangzhou
Animal Light Cycle:	12-h/12-h light-dark cycle
Animal Feed:	normal food (19.26 % protein, 5% fat, no sugar, and no cholesterol), or high-fat and high-sugar (HFHS) food (≥ 30% sugar, ≥ 15% fat, ≥ 10.5% protein, and ≥ 0.5% cholesterol)
Animal Inclusion Criteria:	spontaneous diabetes mellitus and HFHS food-fed

Factors:

Subject type: Mammal; Subject species: Macaca fascicularis (Factor headings shown in green)

mb_sample_id	local_sample_id	Condition	Tissue
SA181877	HFD-HPVB-1	HFHS	HPVB
SA181878	HFD-HPVB-3	HFHS	HPVB
SA181879	HFD-HPVB-2	HFHS	HPVB
SA181880	HFD-Liver-2	HFHS	Liver
SA181881	HFD-Liver-3	HFHS	Liver
SA181882	HFD-Liver-1	HFHS	Liver
SA181883	HFD-PB1	HFHS	PB
SA181884	HFD-PB3	HFHS	PB
SA181885	HFD-PB2	HFHS	PB
SA181886	Nomal-HPVB-1	NC	HPVB
SA181887	Nomal-HPVB-3	NC	HPVB
SA181888	Nomal-HPVB-2	NC	HPVB
SA181889	Normal-Liver-2	NC	Liver
SA181890	Normal-Liver-3	NC	Liver
SA181891	Normal-Liver-1	NC	Liver
SA181892	Nomal-PB-1	NC	PB
SA181893	Nomal-PB-3	NC	PB
SA181894	Nomal-PB-2	NC	PB
SA181895	Diabetes-HPVB-3	sDM	HPVB
SA181896	Diabetes-HPVB-1	sDM	HPVB
SA181897	Diabetes-HPVB-2	sDM	HPVB
SA181898	Diabetes-Liver-3	sDM	Liver
SA181899	Diabetes-Liver-1	sDM	Liver
SA181900	Diabetes-Liver-2	sDM	Liver
SA181901	Diabetes-PB1	sDM	PB
SA181902	Diabetes-PB3	sDM	PB
SA181903	Diabetes-PB2	sDM	PB

Showing results 1 to 27 of 27

Showing results 1 to 27 of 27

Collection:

Collection ID:	CO002006
Collection Summary:	All macaques were sacrificed at about 18 years old, and the liver, PB, and HPVB samples were collected. Both blood samples were centrifuged at 3,000 rpm for 10 min at 4°C immediately to separate sera. All samples were frozen in liquid nitrogen and stored at -80°C until use. The study protocol received prior approval from the Institutional Animal Care and Use Committee of Huazhen Biosciences.
Sample Type:	Blood (serum) and Liver

Treatment:

Treatment ID:	TR002025
Treatment Summary:	Male Macaca fascicularis of about 18 years old were bought from Huazhen Biosciences (Guangzhou, China). All macaques were born from 16th August 2001 to 11th February 2004 (Supplemental Table S1) and housed in the animal rooms maintained at 16 ~ 26 °C and 40% ~ 70% room humidity on a 12-h/12-h light-dark cycle. All macaques of both NC and sDM groups were fed with the normal food (19.26 % protein, 5% fat, no sugar, and no cholesterol), whereas the HFHS monkeys were grown up on the same diet until switching to the high-fat and high-sugar (HFHS) food (≥ 30% sugar, ≥ 15% fat, ≥ 10.5% protein, and ≥ 0.5% cholesterol) on 1st March 2019 (Fig. 1a). After one year of food change, blood and urine samples were collected.

Treatment ID:

TR002025

Treatment Summary:

Male Macaca fascicularis of about 18 years old were bought from Huazhen Biosciences (Guangzhou, China). All macaques were born from 16th August 2001 to 11th February 2004 (Supplemental Table S1) and housed in the animal rooms maintained at 16 ~ 26 °C and 40% ~ 70% room humidity on a 12-h/12-h light-dark cycle. All macaques of both NC and sDM groups were fed with the normal food (19.26 % protein, 5% fat, no sugar, and no cholesterol), whereas the HFHS monkeys were grown up on the same diet until switching to the high-fat and high-sugar (HFHS) food (≥ 30% sugar, ≥ 15% fat, ≥ 10.5% protein, and ≥ 0.5% cholesterol) on 1st March 2019 (Fig. 1a). After one year of food change, blood and urine samples were collected.

Sample Preparation:

Sampleprep ID:	SP002019
Sampleprep Summary:	The hydrophilic and hydrophobic compounds were extracted using methanol/water and MTBE/methanol/water solvent systems, respectively. Samples were first thawed on ice. To extract hydrophilic metabolites from the tissue samples, 1 ml of methanol/water (7:3, v/v) was added to 50 mg of the liver, and homogenized with steel balls for 3 min at 30 Hz, followed by 1 min of a vortex. The homogenate was then centrifuged at 12,000 rpm for 10 min at 4°C to collect the supernatant. Hydrophobic compounds were extracted from another 50 mg using a slightly modified protocol. Homogenization was done with 1 ml of MTBE/methanol (10:3, v/v) and 100 µl of water was mixed with the homogenate to extract before centrifugation. For the sera of PB and HPVB, 3 volumes (v/v) of methanol and a mixture of MTBE and methanol (10:3, v/v) were whirled with the serum samples for 3 min, followed by centrifugation at 12,000 rpm for 10 min at 4°C. All collected supernatants were dried and store at -80°C until LC-MS/MS analysis. Internal standards were dissolved in the solvents before extraction.

Sampleprep ID:

SP002019

Sampleprep Summary:

The hydrophilic and hydrophobic compounds were extracted using methanol/water and MTBE/methanol/water solvent systems, respectively. Samples were first thawed on ice. To extract hydrophilic metabolites from the tissue samples, 1 ml of methanol/water (7:3, v/v) was added to 50 mg of the liver, and homogenized with steel balls for 3 min at 30 Hz, followed by 1 min of a vortex. The homogenate was then centrifuged at 12,000 rpm for 10 min at 4°C to collect the supernatant. Hydrophobic compounds were extracted from another 50 mg using a slightly modified protocol. Homogenization was done with 1 ml of MTBE/methanol (10:3, v/v) and 100 µl of water was mixed with the homogenate to extract before centrifugation. For the sera of PB and HPVB, 3 volumes (v/v) of methanol and a mixture of MTBE and methanol (10:3, v/v) were whirled with the serum samples for 3 min, followed by centrifugation at 12,000 rpm for 10 min at 4°C. All collected supernatants were dried and store at -80°C until LC-MS/MS analysis. Internal standards were dissolved in the solvents before extraction.

Combined analysis:

Analysis ID	AN003145	AN003146	AN003147	AN003148
Analysis type	MS	MS	MS	MS
Chromatography type	Reversed phase	Reversed phase	Reversed phase	Reversed phase
Chromatography system	Shim-pack UFLC SHIMADZU CBM A system	Shim-pack UFLC SHIMADZU CBM A system	Shim-pack UFLC SHIMADZU CBM A system	Shim-pack UFLC SHIMADZU CBM A system
Column	Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)	Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)	Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)	Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
MS Type	ESI	ESI	ESI	ESI
MS instrument type	Triple quadrupole	Triple quadrupole	Triple quadrupole	Triple quadrupole
MS instrument name	ABI Sciex 6500 QTrap	ABI Sciex 6500 QTrap	ABI Sciex 6500 QTrap	ABI Sciex 6500 QTrap
Ion Mode	POSITIVE	NEGATIVE	POSITIVE	NEGATIVE
Units	Peak area	Peak area	Peak area	Peak area

Chromatography:

Chromatography ID:	CH002327
Chromatography Summary:	The analysis of hydrophilic metabolites used 0.1% formic acid (in water) and acetonitrile with 0.1% formic acid as mobile phases, with a gradient (V/V) as following: 95:5 at 0 min, 10:90 at 11.0 min, 10:90 at 12.0 min, 95:5 at 12.1 min, and 95:5 at 14.0 min.
Instrument Name:	Shim-pack UFLC SHIMADZU CBM A system
Column Name:	Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
Flow Gradient:	95:5 at 0 min, 10:90 at 11.0 min, 10:90 at 12.0 min, 95:5 at 12.1 min, and 95:5 at 14.0 min.
Solvent A:	100% water; 0.1% formic acid
Solvent B:	100% acetonitrile; 0.1% formic acid
Chromatography Type:	Reversed phase

Chromatography ID:	CH002328
Chromatography Summary:	The two mobile phases for hydrophobic compounds were 0.04% acetic acid and acetonitrile with 0.04% acetic acid, and the gradient (V/V) program was 95:5 at 0 min, 5:95 at 11.0 min, 5:95 at 12.0 min, 95:5 at 12.1 min and 95:5 at 14.0 min.
Instrument Name:	Shim-pack UFLC SHIMADZU CBM A system
Column Name:	Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
Flow Gradient:	95:5 at 0 min, 5:95 at 11.0 min, 5:95 at 12.0 min, 95:5 at 12.1 min and 95:5 at 14.0 min.
Solvent A:	100% water; 0.04% acetic acid
Solvent B:	100% acetonitrile; 0.04% acetic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS002925
Analysis ID:	AN003145
Instrument Name:	ABI Sciex 6500 QTrap
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	LIT and triple quadrupole (QQQ) scans were acquired in both positive and negative ion modes under the control of Analyst 1.6.3 software (Sciex, Washington, USA). The ion spray voltage (IS) of the ESI source was 5500 and -4500 V for positive and negative modes, respectively. Source temperature was set at 500 C, ion source gas I (GSI), gas II (GSII), curtain gas (CUR) at 55, 60, and 25.0 psi, respectively, and collision gas (CAD) high. Instrument tuning and mass calibration in QQQ and LIT modes were performed with 10 and 100 μmol/L polypropylene glycol solutions, respectively. Specific sets of multiple reaction monitoring (MRM) transitions of various periods of retention time were monitored according to an in-house library of metabolites.
Ion Mode:	POSITIVE

MS ID:	MS002926
Analysis ID:	AN003146
Instrument Name:	ABI Sciex 6500 QTrap
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	LIT and triple quadrupole (QQQ) scans were acquired in both positive and negative ion modes under the control of Analyst 1.6.3 software (Sciex, Washington, USA). The ion spray voltage (IS) of the ESI source was 5500 and -4500 V for positive and negative modes, respectively. Source temperature was set at 500 C, ion source gas I (GSI), gas II (GSII), curtain gas (CUR) at 55, 60, and 25.0 psi, respectively, and collision gas (CAD) high. Instrument tuning and mass calibration in QQQ and LIT modes were performed with 10 and 100 μmol/L polypropylene glycol solutions, respectively. Specific sets of multiple reaction monitoring (MRM) transitions of various periods of retention time were monitored according to an in-house library of metabolites.
Ion Mode:	NEGATIVE

MS ID:	MS002927
Analysis ID:	AN003147
Instrument Name:	ABI Sciex 6500 QTrap
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	LIT and triple quadrupole (QQQ) scans were acquired in both positive and negative ion modes under the control of Analyst 1.6.3 software (Sciex, Washington, USA). The ion spray voltage (IS) of the ESI source was 5500 and -4500 V for positive and negative modes, respectively. Source temperature was set at 500 C, ion source gas I (GSI), gas II (GSII), curtain gas (CUR) at 55, 60, and 25.0 psi, respectively, and collision gas (CAD) high. Instrument tuning and mass calibration in QQQ and LIT modes were performed with 10 and 100 μmol/L polypropylene glycol solutions, respectively. Specific sets of multiple reaction monitoring (MRM) transitions of various periods of retention time were monitored according to an in-house library of metabolites.
Ion Mode:	POSITIVE

MS ID:	MS002928
Analysis ID:	AN003148
Instrument Name:	ABI Sciex 6500 QTrap
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	LIT and triple quadrupole (QQQ) scans were acquired in both positive and negative ion modes under the control of Analyst 1.6.3 software (Sciex, Washington, USA). The ion spray voltage (IS) of the ESI source was 5500 and -4500 V for positive and negative modes, respectively. Source temperature was set at 500 C, ion source gas I (GSI), gas II (GSII), curtain gas (CUR) at 55, 60, and 25.0 psi, respectively, and collision gas (CAD) high. Instrument tuning and mass calibration in QQQ and LIT modes were performed with 10 and 100 μmol/L polypropylene glycol solutions, respectively. Specific sets of multiple reaction monitoring (MRM) transitions of various periods of retention time were monitored according to an in-house library of metabolites.
Ion Mode:	NEGATIVE