Summary of Study ST000540

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 PR000395. The data can be accessed directly via it's Project DOI: 10.21228/M80G60 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	ST000540
Study Title	Kidney tissue metabolomic profiling of diabetic nephropathy in the steptozotocin induced type-1 diabetes mouse model.
Study Type	Metabolomics
Study Summary	This metabolomics study evaluated kidney tissue 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
Department	Discovery-Science-Technology
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	2017-01-20
Raw Data Available	Yes
Raw Data File Type(s)	raw(Waters)
Analysis Type Detail	LC-MS
Release Date	2018-02-07
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR000395
Project DOI:	doi: 10.21228/M80G60
Project Title:	Kidney tissue 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; NIH Center Grant # U24DK097193; NIH/NCATS award # UL1TR001111; NIH/NIGMS Grant # K01GM109320

Subject:

Subject ID:	SU000562
Subject Type:	mice
Subject Species:	Mus musculus
Taxonomy ID:	10090
Genotype Strain:	C57BL/6
Gender:	Male
Species Group:	Mammal

Factors:

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

mb_sample_id	local_sample_id	Treatment	Genotype
SA027963	Total Pool_4	-	-
SA027964	Total Pool_2	-	-
SA027965	Total Pool_3	-	-
SA027966	Total Pool_1	-	-
SA027967	Equilibrium_6	-	-
SA027968	383	NaC	Meprin bKO
SA027969	399	NaC	Meprin bKO
SA027970	398	NaC	Meprin bKO
SA027971	387	NaC	Meprin bKO
SA027972	390	NaC	Meprin bKO
SA027973	391	NaC	Meprin bKO
SA027974	522	NaC	wild-type
SA027975	523	NaC	wild-type
SA027976	520	NaC	wild-type
SA027977	521	NaC	wild-type
SA027978	519	NaC	wild-type
SA027979	400	STZ	Meprin bKO
SA027980	514	STZ	Meprin bKO
SA027981	397	STZ	Meprin bKO
SA027982	515	STZ	Meprin bKO
SA027983	396	STZ	Meprin bKO
SA027984	518	STZ	Meprin bKO
SA027985	516	STZ	Meprin bKO
SA027986	395	STZ	Meprin bKO
SA027987	533	STZ	wild-type
SA027988	531	STZ	wild-type
SA027989	526	STZ	wild-type
SA027990	525	STZ	wild-type
SA027991	528	STZ	wild-type
SA027992	529	STZ	wild-type
SA027993	530	STZ	wild-type
SA027994	532	STZ	wild-type

Showing results 1 to 32 of 32

Showing results 1 to 32 of 32

Collection:

Collection ID:	CO000556
Collection Summary:	Kidneys were harvested at 8-weeks post STZ-injection. The mice were sacrificed by CO2 asphyxiation. The kidneys were excised, decapsulated and individually weighed, snap-frozen in liquid nitrogen, and stored at -80oC until used.
Sample Type:	Kidney Tissue
Storage Conditions:	-80C

Treatment:

Treatment ID:	TR000576
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:	SP000569
Sampleprep Summary:	Frozen kidney tissue samples on dry ice were transferred to pre-chilled, pre-labeled tubes, and their weights recorded. For every 1 mg of tissue sample, 2 µL of 50:50 Acetonitrile:Water was added to the tube. Ceramic beads (2.3 mm; ~15-20 prewashed & dried) were added to the tubes, and the samples were homogenized on the MagNA Lyser system using a 30 s pulse at 4,000 rpm. The samples were centrifuged at room temperature at 16,000 rcf for 4 min. An aliquot of the supernatant was transferred to pre-labeled 2.0 mL low protein-binding microcentrifuge tube to make the individual study sample (40 µL). Another aliquot of supernatant (18 µL) was combined with those from all other kidney tissue 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 4 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 kidney tissue analysis. Acetonitrile containing the internal standard Tryptophan-d5 (460 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 (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 pre-labeled autosampler vials and 3 µL was injected into SYNAPT G2 Si.

Sampleprep ID:

SP000569

Sampleprep Summary:

Frozen kidney tissue samples on dry ice were transferred to pre-chilled, pre-labeled tubes, and their weights recorded. For every 1 mg of tissue sample, 2 µL of 50:50 Acetonitrile:Water was added to the tube. Ceramic beads (2.3 mm; ~15-20 prewashed & dried) were added to the tubes, and the samples were homogenized on the MagNA Lyser system using a 30 s pulse at 4,000 rpm. The samples were centrifuged at room temperature at 16,000 rcf for 4 min. An aliquot of the supernatant was transferred to pre-labeled 2.0 mL low protein-binding microcentrifuge tube to make the individual study sample (40 µL). Another aliquot of supernatant (18 µL) was combined with those from all other kidney tissue 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 4 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 kidney tissue analysis. Acetonitrile containing the internal standard Tryptophan-d5 (460 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 (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 pre-labeled autosampler vials and 3 µL was injected into SYNAPT G2 Si.

Combined analysis:

Analysis ID	AN000820	AN000821
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	m/z	m/z

Chromatography:

Chromatography ID:	CH000586
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:	MS000721
Analysis ID:	AN000820
Instrument Name:	Waters Synapt-G2-Si
Instrument Type:	QTOF
MS Type:	ESI
Ion Mode:	POSITIVE

MS ID:	MS000722
Analysis ID:	AN000821
Instrument Name:	Waters Synapt-G2-Si
Instrument Type:	QTOF
MS Type:	ESI
Ion Mode:	NEGATIVE