Summary of Study ST000559

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 PR000410. The data can be accessed directly via it's Project DOI: 10.21228/M82889 This work is supported by NIH grant, U2C- DK119886.

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Study ID	ST000559
Study Title	Urine metabolomic profiling of diabetic nephropathy in the steptozotocin induced type-1 diabetes mouse model.
Study Summary	This metabolomics study evaluated urine 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
Laboratory	NIH Eastern Regional Comphrehensive Metabolomics Resource Core at UNC Chapel Hill (ERCMRC)
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:	PR000410
Project DOI:	doi: 10.21228/M82889
Project Title:	Urine 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
Department:	Department of Biology
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:	SU000581
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
SA028844	Total Pool_5	-	-	-
SA028845	Total Pool_4	-	-	-
SA028846	Total Pool_1	-	-	-
SA028847	Equilibrium_6	-	-	-
SA028848	Total Pool_3	-	-	-
SA028849	Total Pool_2	-	-	-
SA028850	387-4	NaC	Meprin bKO	4
SA028851	383-4	NaC	Meprin bKO	4
SA028852	391-4	NaC	Meprin bKO	4
SA028853	391-8	NaC	Meprin bKO	8
SA028854	399-8	NaC	Meprin bKO	8
SA028855	383-8	NaC	Meprin bKO	8
SA028856	390-8	NaC	Meprin bKO	8
SA028857	387-8	NaC	Meprin bKO	8
SA028858	520-4	NaC	wild-type	4
SA028859	521-4	NaC	wild-type	4
SA028860	523-4	NaC	wild-type	4
SA028861	519-4	NaC	wild-type	4
SA028862	520-8	NaC	wild-type	8
SA028863	522-8	NaC	wild-type	8
SA028864	523-8	NaC	wild-type	8
SA028865	519-8	NaC	wild-type	8
SA028866	521-8	NaC	wild-type	8
SA028867	514-4	STZ	Meprin bKO	4
SA028868	400-4	STZ	Meprin bKO	4
SA028869	396-4	STZ	Meprin bKO	4
SA028870	397-4	STZ	Meprin bKO	4
SA028871	515-4	STZ	Meprin bKO	4
SA028872	395-4	STZ	Meprin bKO	4
SA028873	516-4	STZ	Meprin bKO	4
SA028874	518-4	STZ	Meprin bKO	4
SA028875	516-8	STZ	Meprin bKO	8
SA028876	518-8	STZ	Meprin bKO	8
SA028877	515-8	STZ	Meprin bKO	8
SA028878	400-8	STZ	Meprin bKO	8
SA028879	395-8	STZ	Meprin bKO	8
SA028880	396-8	STZ	Meprin bKO	8
SA028881	531-4	STZ	wild-type	4
SA028882	533-4	STZ	wild-type	4
SA028883	532-4	STZ	wild-type	4
SA028884	527-4	STZ	wild-type	4
SA028885	525-4	STZ	wild-type	4
SA028886	526-4	STZ	wild-type	4
SA028887	528-4	STZ	wild-type	4
SA028888	529-4	STZ	wild-type	4
SA028889	530-4	STZ	wild-type	4
SA028890	529-8	STZ	wild-type	8
SA028891	526-8	STZ	wild-type	8
SA028892	525-8	STZ	wild-type	8
SA028893	528-8	STZ	wild-type	8
SA028894	530-8	STZ	wild-type	8
SA028895	532-8	STZ	wild-type	8
SA028896	531-8	STZ	wild-type	8
SA028897	533-8	STZ	wild-type	8

Showing results 1 to 54 of 54

Showing results 1 to 54 of 54

Collection:

Collection ID:	CO000575
Collection Summary:	Urine samples were collected at 4 and 8 weeks post-STZ injection. Urine samples were obtained by bladder massage unto sterile petri dishes and stored at -80oC until used.
Sample Type:	Urine
Storage Conditions:	-80 C

Treatment:

Treatment ID:	TR000595
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:	SP000588
Sampleprep Summary:	Urine samples were thawed on ice for 30–60 min and vortexed on a multi-tube vortexer for 2 mins 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 urine 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 5 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 urine analysis. Acetonitrile containing the internal standard Tryptophan-d5 (120 µL; 0.0167 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 (420 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 1.5 h and lyophilized for 18 h. Acetonitrile:Water (150 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 new, pre-labeled autosampler vials and 3 uL was injected into SYNAPT G2-Si.

Sampleprep ID:

SP000588

Sampleprep Summary:

Urine samples were thawed on ice for 30–60 min and vortexed on a multi-tube vortexer for 2 mins 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 urine 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 5 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 urine analysis. Acetonitrile containing the internal standard Tryptophan-d5 (120 µL; 0.0167 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 (420 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 1.5 h and lyophilized for 18 h. Acetonitrile:Water (150 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 new, pre-labeled autosampler vials and 3 uL was injected into SYNAPT G2-Si.

Combined analysis:

Analysis ID	AN000858	AN000859
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:	CH000611
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:	MS000759
Analysis ID:	AN000858
Instrument Name:	Waters Synapt-G2-Si
Instrument Type:	QTOF
MS Type:	ESI
Ion Mode:	POSITIVE

MS ID:	MS000760
Analysis ID:	AN000859
Instrument Name:	Waters Synapt-G2-Si
Instrument Type:	QTOF
MS Type:	ESI
Ion Mode:	NEGATIVE