Summary of Study ST000558

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 PR000409. The data can be accessed directly via it's Project DOI: 10.21228/M8602H This work is supported by NIH grant, U2C- DK119886.

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

Show all samples | Perform analysis on untargeted data
Download mwTab file (text) | Download mwTab file(JSON) | Download data files (Contains raw data)

Study ID	ST000558
Study Title	Plasma metabolomic profiling of diabetic nephropathy in the steptozotocin induced type-1 diabetes mouse model
Study Summary	This metabolomics study evaluated plasma from wild-type and meprin β knockout mice after induction of diabetes with streptozotocin or treatment with sodium citrate control to understand how these factors influence the metabotype.
Institute	RTI International
Last Name	Sumner
First Name	Susan
Address	3040 E. Cornwallis Road, Research Triangle Park, NC 27709
Email	susan_sumner@unc.edu
Phone	704-250-5000
Submit Date	2017-02-17
Raw Data Available	Yes
Raw Data File Type(s)	raw(Waters)
Analysis Type Detail	LC-MS
Release Date	2018-04-10
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR000409
Project DOI:	doi: 10.21228/M8602H
Project Title:	Plasma metabolomic profiling of diabetic nephropathy in the steptozotocin induced type-1 diabetes mouse model
Project Summary:	Diabetic nephropathy (DN) is the leading cause of end stage renal disease, and is associated with high morbidity and mortality rates. The pathophysiology of DN includes both glomerular and tubulointerstitial damage. Meprins are metalloproteinases which are most abundantly expressed in the brush border membranes of proximal kidney tubules. Meprins are also expressed in leukocytes (monocytes and macrophages) and podocytes. Meprins have been implicated in the pathology of acute and chronic kidney injury. Single nucleotide polymorphisms (SNPs) in the meprin β gene were associated in human DN in the Pima Indians, suggesting a role for meprins in the pathophysiology of DN. The current study was done to determine the mechanisms by which meprins modulate the progression of DN in mice.
Institute:	North Carolina A&T State University
Last Name:	Ongeri
First Name:	Elimelda Moige
Address:	1601 E Market Street, Greensboro, NC 27411
Email:	eongeri@ncat.edu
Phone:	336-285-2182
Funding Source:	NIH/NIGMS Grant # SC3102049 To Elimelda Moige Ongeri; NIH Center Grant # U24DK097193 to Susan Sumner; NIH/NCATS award # UL1TR001111 to John Buse, UNC-CH, PI, Sumner- Director, Metabolomics core; and NIH/NIGMS Grant # K01GM109320 to Jessica Gooding.

Subject:

Subject ID:	SU000580
Subject Type:	Animal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Genotype Strain:	C57BL/6
Gender:	Male
Animal Animal Supplier:	KO: bred and housed at the laboratory animal resource unit (LARU) of North Carolina A&T State University; WT: Charles River Laboratories
Animal Housing:	group cages of up to 5 mice per cage
Animal Light Cycle:	12:12h light:dark cycle
Animal Feed:	rat chow
Animal Water:	water ad libitum
Species Group:	Mammals

Factors:

Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatment	Genotype	Week
SA028783	Total Pool_6	-	-	-
SA028784	Total Pool_5	-	-	-
SA028785	Total Pool_2	-	-	-
SA028786	Equilibrium_6	-	-	-
SA028787	Total Pool_3	-	-	-
SA028788	Total Pool_4	-	-	-
SA028789	399-4	NaC	Meprin bKO	4
SA028790	383-4	NaC	Meprin bKO	4
SA028791	387-4	NaC	Meprin bKO	4
SA028792	398-4	NaC	Meprin bKO	4
SA028793	390-4	NaC	Meprin bKO	4
SA028794	391-4	NaC	Meprin bKO	4
SA028795	383-8	NaC	Meprin bKO	8
SA028796	399-8	NaC	Meprin bKO	8
SA028797	390-8	NaC	Meprin bKO	8
SA028798	387-8	NaC	Meprin bKO	8
SA028799	391-8	NaC	Meprin bKO	8
SA028800	398-8	NaC	Meprin bKO	8
SA028801	521-4	NaC	wild-type	4
SA028802	523-4	NaC	wild-type	4
SA028803	519-4	NaC	wild-type	4
SA028804	522-4	NaC	wild-type	4
SA028805	520-4	NaC	wild-type	4
SA028806	520-8	NaC	wild-type	8
SA028807	521-8	NaC	wild-type	8
SA028808	523-8	NaC	wild-type	8
SA028809	519-8	NaC	wild-type	8
SA028810	522-8	NaC	wild-type	8
SA028811	396-4	STZ	Meprin bKO	4
SA028812	516-4	STZ	Meprin bKO	4
SA028813	397-4	STZ	Meprin bKO	4
SA028814	400-4	STZ	Meprin bKO	4
SA028815	514-4	STZ	Meprin bKO	4
SA028816	395-4	STZ	Meprin bKO	4
SA028817	518-4	STZ	Meprin bKO	4
SA028818	515-4	STZ	Meprin bKO	4
SA028819	514-8	STZ	Meprin bKO	8
SA028820	397-8	STZ	Meprin bKO	8
SA028821	518-8	STZ	Meprin bKO	8
SA028822	396-8	STZ	Meprin bKO	8
SA028823	400-8	STZ	Meprin bKO	8
SA028824	515-8	STZ	Meprin bKO	8
SA028825	516-8	STZ	Meprin bKO	8
SA028826	395-8	STZ	Meprin bKO	8
SA028827	532-4	STZ	wild-type	4
SA028828	533-4	STZ	wild-type	4
SA028829	531-4	STZ	wild-type	4
SA028830	527-4	STZ	wild-type	4
SA028831	526-4	STZ	wild-type	4
SA028832	525-4	STZ	wild-type	4
SA028833	528-4	STZ	wild-type	4
SA028834	529-4	STZ	wild-type	4
SA028835	530-4	STZ	wild-type	4
SA028836	525-8	STZ	wild-type	8
SA028837	531-8	STZ	wild-type	8
SA028838	526-8	STZ	wild-type	8
SA028839	532-8	STZ	wild-type	8
SA028840	533-8	STZ	wild-type	8
SA028841	530-8	STZ	wild-type	8
SA028842	528-8	STZ	wild-type	8
SA028843	529-8	STZ	wild-type	8

Showing results 1 to 61 of 61

Showing results 1 to 61 of 61

Collection:

Collection ID:	CO000574
Collection Summary:	Blood samples were collected at 4 and 8 weeks post-STZ injection. Blood was obtained by tail nicking at week 4 and cardiac puncture at week 8, collected into heparin tubes, centrifuged to obtain plasma, and stored at -80oC until used.
Sample Type:	Blood
Storage Conditions:	-80 C
Additives:	Heparin
Blood Serum Or Plasma:	Plasma

Treatment:

Treatment ID:	TR000594
Treatment Summary:	Type 1 diabetes was induced at age 8 weeks. The mice were fasted for 6 hours prior to being injected with low dose STZ (50 mg/kg body weight) in sodium citrate buffer (10 mmol/L, pH 4.5) daily for 5 days following the protocols described by Tesch and Allen and recommended by the Animal Models of Diabetic Complications Consortium (AMDCC; amdcc.org)1. Control mice were injected with equivalent volumes of the sodium citrate buffer. Diabetes was confirmed by measuring fasting blood glucose levels using a standard glucose meter at 10 days post-STZ injection. Mice with a fasting glucose level ≥280 mg/dL were considered diabetic. STZ-injected mice with a fasting blood glucose of <280 mg/dL (15mmol/L) were culled and eliminated from the study.
Treatment Compound:	streptozotocin
Treatment Dose:	50 mg/kg body weight
Treatment Doseduration:	daily; 5 days
Treatment Vehicle:	sodium citrate
Animal Endp Tissue Coll List:	plasma, urine, kidney tissue

Sample Preparation:

Sampleprep ID:	SP000587
Sampleprep Summary:	Plasma samples were thawed on ice for 30–60 min and vortexed on a multi-tube vortexer for 4 min at 5,000 rpm, followed by centrifugation at room temperature at 16,000 rcf for 4 min. An aliquot of the supernatant was transferred to pre-labeled 1.5 mL low protein-binding microcentrifuge tube to make the individual study sample (40 µL). Another aliquot of supernatant (11 µL) was combined with those from all other plasma samples in a 1.5 mL low protein-binding microcentrifuge tube to make the total pool quality control sample. The total pool quality control sample was aliquoted (40 µL) to make 6 Total Pool Samples and 4 Column Equilibration samples. 132 µL of the total pool quality control sample was added to the total study sample pool to make a pool of kidney, urine, and plasma samples. The total study pool sample was used to prepare 9 Total Study Samples (40 µL) to aid in alignment of the three studies. Of these, 3 total study samples were included in the plasma analysis. Methanol containing the internal standard Tryptophan-d5 (320 µL; 0.0125 mg/ml) was added to all samples, and samples were vortexed on a multiple tube vortexer for 2 min at 5000 rpm followed by centrifugation at 16,000 rcf for 4 min. The supernatants (290 µL) were transferred into new, pre-labeled 2.0 mL low protein-binding microcentrifuge tubes and capped with disposable rubber stoppers. Samples were placed at -80 °C for 1 h and lyophilized for 18 h. Acetonitrile:Water (125 µL; 95:5) was added to each tube and vortex mixed for 10 min at 5000 rpm, followed by centrifugation at room temperature at 16,000 rcf for 4 min. The supernatants were transferred to pre-labeled autosampler vials and 3 µL was injected into SYNAPT G2-Si.

Sampleprep ID:

SP000587

Sampleprep Summary:

Plasma samples were thawed on ice for 30–60 min and vortexed on a multi-tube vortexer for 4 min at 5,000 rpm, followed by centrifugation at room temperature at 16,000 rcf for 4 min. An aliquot of the supernatant was transferred to pre-labeled 1.5 mL low protein-binding microcentrifuge tube to make the individual study sample (40 µL). Another aliquot of supernatant (11 µL) was combined with those from all other plasma samples in a 1.5 mL low protein-binding microcentrifuge tube to make the total pool quality control sample. The total pool quality control sample was aliquoted (40 µL) to make 6 Total Pool Samples and 4 Column Equilibration samples. 132 µL of the total pool quality control sample was added to the total study sample pool to make a pool of kidney, urine, and plasma samples. The total study pool sample was used to prepare 9 Total Study Samples (40 µL) to aid in alignment of the three studies. Of these, 3 total study samples were included in the plasma analysis. Methanol containing the internal standard Tryptophan-d5 (320 µL; 0.0125 mg/ml) was added to all samples, and samples were vortexed on a multiple tube vortexer for 2 min at 5000 rpm followed by centrifugation at 16,000 rcf for 4 min. The supernatants (290 µL) were transferred into new, pre-labeled 2.0 mL low protein-binding microcentrifuge tubes and capped with disposable rubber stoppers. Samples were placed at -80 °C for 1 h and lyophilized for 18 h. Acetonitrile:Water (125 µL; 95:5) was added to each tube and vortex mixed for 10 min at 5000 rpm, followed by centrifugation at room temperature at 16,000 rcf for 4 min. The supernatants were transferred to pre-labeled autosampler vials and 3 µL was injected into SYNAPT G2-Si.

Combined analysis:

Analysis ID	AN000856	AN000857
Analysis type	MS	MS
Chromatography type	HILIC	HILIC
Chromatography system	Waters Acquity I-Class	Waters Acquity I-Class
Column	Waters Acquity BEH Amide (150 x 2.1mm,1.7um)	Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
MS Type	ESI	ESI
MS instrument type	QTOF	QTOF
MS instrument name	Waters Synapt-G2-Si	Waters Synapt-G2-Si
Ion Mode	POSITIVE	NEGATIVE
Units	normalized ion counts	normalized ion counts

Chromatography:

Chromatography ID:	CH000610
Chromatography Summary:	Hydrophilic Interaction Liquid Chromatography (HILIC) Gradient Seperation
Instrument Name:	Waters Acquity I-Class
Column Name:	Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Chromatography Type:	HILIC

MS:

MS ID:	MS000757
Analysis ID:	AN000856
Instrument Name:	Waters Synapt-G2-Si
Instrument Type:	QTOF
MS Type:	ESI
Ion Mode:	POSITIVE

MS ID:	MS000758
Analysis ID:	AN000857
Instrument Name:	Waters Synapt-G2-Si
Instrument Type:	QTOF
MS Type:	ESI
Ion Mode:	NEGATIVE