Summary of Study ST003380

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 PR002096. The data can be accessed directly via it's Project DOI: 10.21228/M8PJ8N 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.

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Study ID	ST003380
Study Title	Deletion of Kcnj16 altered transcriptomic and metabolomic profiles of Dahl salt-sensitive rats
Study Type	Untargeted metabolomis
Study Summary	The inwardly rectifying K+ Channel Kir5.1 (Kcnj16) is essential in renal salt handling and blood pressure control. However, the underlying mechanisms are not fully understood. Here, we integrated transcriptomics and metabolomics to comprehensively profile the changes in genes and metabolites in the Dahl salt-sensitive (SS) rat lacking Kcnj16 to identify potential mechanisms. Consistent with the phenotype of knock-out (KO) rats, the transcriptomic profile predicted reduced blood pressure, kidney damage, and increased ion transport. Canonical pathway analysis suggested activation of metabolic-related while suppression of immune responses-related pathways in KO rats. Untargeted metabolomic analysis revealed different metabolic profiles between WT and KO rats. Integration of transcriptomic and metabolomic profiles suggested altered tricarboxylic acid (TCA) cycle, amino acid, and reactive oxygen species (ROS) metabolism that are related to SS hypertension. In conclusion, besides increased ion transport, our data suggest suppressed immune responses-related and altered metabolic-related pathways of SS rats lacking Kir5.1.
Institute	University of South Florida
Department	Molecular Pharmacology and Physiology
Laboratory	Alexander Staruschenko
Last Name	Xu
First Name	Biyang
Address	560 channelside drive Tampa FL 33602
Email	bxu@usf.edu
Phone	3322014356
Submit Date	2024-07-31
Num Groups	2
Total Subjects	11
Num Males	11
Raw Data Available	Yes
Raw Data File Type(s)	d
Analysis Type Detail	LC-MS
Release Date	2024-08-08
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002096
Project DOI:	doi: 10.21228/M8PJ8N
Project Title:	Deletion of Kcnj16 altered transcriptomic and metabolomic profiles of Dahl salt-sensitive rats
Project Type:	Untargeted metabolomic analysis
Project Summary:	The objective of the project was to compare the metabolomic profiles in the kidney, urine and plasma of SSWT and SSKcnj16-/- rats. Untargeted metabolomic analysis revealed different metabolic profiles between SSWT and SSKcnj16-/- rats, with 219, 790, and 31 differentially expressed metabolites in plasma, urine, and kidney in SSKcnj16-/- rats compared to SSWT rats.
Institute:	University of South Florida
Department:	Molecular Pharmacology and Physiology
Laboratory:	Alexander Staruschenko
Last Name:	Xu
First Name:	Biyang
Address:	560 channelside drive, Tampa, FLORIDA, 33602, USA
Email:	bxu@usf.edu
Phone:	(332) 201-4356

Subject:

Subject ID:	SU003501
Subject Type:	Mammal
Subject Species:	Rattus norvegicus
Taxonomy ID:	10116
Gender:	Male

Factors:

Subject type: Mammal; Subject species: Rattus norvegicus (Factor headings shown in green)

mb_sample_id	local_sample_id	Sample source	Genotype
SA367303	s.9052.24	kidney cortex	control
SA367304	s.9052.26	kidney cortex	control
SA367305	s.9052.27	kidney cortex	control
SA367306	s.9052.31	kidney cortex	control
SA367307	s.9052.32	kidney cortex	control
SA367297	s.9052.25	kidney cortex	KO
SA367298	s.9052.33	kidney cortex	KO
SA367299	s.9052.30	kidney cortex	KO
SA367300	s.9052.29	kidney cortex	KO
SA367301	s.9052.28	kidney cortex	KO
SA367302	s.9052.23	kidney cortex	KO
SA367314	s.9052.06	plasma	control
SA367315	s.9052.03	plasma	control
SA367316	s.9052.07	plasma	control
SA367317	s.9052.10	plasma	control
SA367318	s.9052.01	plasma	control
SA367308	s.9052.05	plasma	KO
SA367309	s.9052.04	plasma	KO
SA367310	s.9052.11	plasma	KO
SA367311	s.9052.02	plasma	KO
SA367312	s.9052.08	plasma	KO
SA367313	s.9052.09	plasma	KO
SA367292	s.9052.22	Urine	control
SA367293	s.9052.21	Urine	control
SA367294	s.9052.15	Urine	control
SA367295	s.9052.18	Urine	control
SA367296	s.9052.12	Urine	control
SA367286	s.9052.13	Urine	KO
SA367287	s.9052.20	Urine	KO
SA367288	s.9052.19	Urine	KO
SA367289	s.9052.17	Urine	KO
SA367290	s.9052.16	Urine	KO
SA367291	s.9052.14	Urine	KO

Showing results 1 to 33 of 33

Showing results 1 to 33 of 33

Collection:

Collection ID:	CO003494
Collection Summary:	Flash frozen kidney tissue, urine and plasma from arterial blood were collected
Sample Type:	urine, plasma, kidney cortex

Treatment:

Treatment ID:	TR003510
Treatment Summary:	NA

Sample Preparation:

Sampleprep ID:	SP003508
Sampleprep Summary:	Kidney: 10 uL/mg 1X PBS was added to the pulverized kidney tissue followed by vortexing to form homogenous mixture. 50 uL of homogenate was used. 500 ng Ring 13C6-Phe IS (internal standard) were added to all samples and sonicated in ice bath for 30 seconds x 4 times. 300 uL 50x50 MeOH: ACN mixture were then added and incubated on ice for 30 min with occasional vortexing (every 10 min). The mixture were then centrifuged at 18,000 g for 20 min at 4oC, and dry under N2 stream on cold blocks. Urine: 50 uL urine sample was used. 500 ng Ring 13C6-Phe IS (internal standard) were added to all samples and sonicated in ice bath for 30 seconds x 4 times. 300 uL 50x50 MeOH: ACN mixture were then added and incubated on ice for 30 min with occasional vortexing (every 10 min). The mixture were then centrifuged at 18,000 g for 20 min at 4oC, and dry under N2 stream on cold blocks. Plasma: 25 uL of plasma was used. 500 ng Ring 13C6-Phe IS (internal standard) were added to all samples and sonicated in ice bath for 30 seconds x 4 times. 150 uL 50x50 MeOH: ACN mixture were then added and incubated on ice for 30 min with occasional vortexing (every 10 min). The mixture were then centrifuged at 18,000 g for 20 min at 4oC, and dry under N2 stream on cold blocks.

Sampleprep ID:

SP003508

Sampleprep Summary:

Kidney: 10 uL/mg 1X PBS was added to the pulverized kidney tissue followed by vortexing to form homogenous mixture. 50 uL of homogenate was used. 500 ng Ring 13C6-Phe IS (internal standard) were added to all samples and sonicated in ice bath for 30 seconds x 4 times. 300 uL 50x50 MeOH: ACN mixture were then added and incubated on ice for 30 min with occasional vortexing (every 10 min). The mixture were then centrifuged at 18,000 g for 20 min at 4oC, and dry under N2 stream on cold blocks. Urine: 50 uL urine sample was used. 500 ng Ring 13C6-Phe IS (internal standard) were added to all samples and sonicated in ice bath for 30 seconds x 4 times. 300 uL 50x50 MeOH: ACN mixture were then added and incubated on ice for 30 min with occasional vortexing (every 10 min). The mixture were then centrifuged at 18,000 g for 20 min at 4oC, and dry under N2 stream on cold blocks. Plasma: 25 uL of plasma was used. 500 ng Ring 13C6-Phe IS (internal standard) were added to all samples and sonicated in ice bath for 30 seconds x 4 times. 150 uL 50x50 MeOH: ACN mixture were then added and incubated on ice for 30 min with occasional vortexing (every 10 min). The mixture were then centrifuged at 18,000 g for 20 min at 4oC, and dry under N2 stream on cold blocks.

Combined analysis:

Analysis ID	AN005535	AN005536	AN005537	AN005538
Analysis type	MS	MS	MS	MS
Chromatography type	HILIC	HILIC	Reversed phase	Reversed phase
Chromatography system	Agilent 1290 Infinity	Agilent 1290 Infinity	Agilent 1290	Agilent 1290
Column	Waters ACQUITY UPLC BEH HILIC (150 x 2.1mm,1.7um)	Waters ACQUITY UPLC BEH HILIC (150 x 2.1mm,1.7um)	Waters ACQUITY UPLC BEH C18 (150 x 2.1mm, 1.8um)	Waters ACQUITY UPLC BEH C18 (150 x 2.1mm, 1.8um)
MS Type	ESI	ESI	ESI	ESI
MS instrument type	QTOF	QTOF	QTOF	QTOF
MS instrument name	Agilent 6550 QTOF	Agilent 6550 QTOF	Agilent 6550 QTOF	Agilent 6550 QTOF
Ion Mode	POSITIVE	NEGATIVE	POSITIVE	NEGATIVE
Units	peak area	peak area	peak area	peak area

Chromatography:

Chromatography ID:	CH004209
Instrument Name:	Agilent 1290 Infinity
Column Name:	Waters ACQUITY UPLC BEH HILIC (150 x 2.1mm,1.7um)
Column Temperature:	50
Flow Gradient:	0 min, 100% B; 1 min, 100% B; 5 min, 90% B; 13.0 min, 0% B; 16 min, 0% B; 16.5 min, 100% B; and 20 min, 100% B
Flow Rate:	400 uL/min
Solvent A:	Water with 1% acetonitrile, 5mM ammonium acetate & 0.1% formic acid
Solvent B:	Water with 95% acetonitrile, 5mM ammonium acetate & 0.1% formic acid
Chromatography Type:	HILIC

Chromatography ID:	CH004210
Instrument Name:	Agilent 1290
Column Name:	Waters ACQUITY UPLC BEH C18 (150 x 2.1mm, 1.8um)
Column Temperature:	50
Flow Gradient:	0 min, 0% B; 1 min, 0% B; 3 min, 5% B; 13.0 min, 100% B; 16 min, 100% B; 16.5 min, 0% B; and 20 min, 0% B
Flow Rate:	400 uL/min
Solvent A:	Water with 1% acetonitrile, 5mM ammonium acetate & 0.1% formic acid
Solvent B:	Water with 95% acetonitrile, 5mM ammonium acetate & 0.1% formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS005260
Analysis ID:	AN005535
Instrument Name:	Agilent 6550 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	For each column, the run time is 20 min using a flow rate of 400 μL/min. A total of four samples per run was performed to give maximum coverage of metabolites. Samples were injected in duplicate or triplicate, and a quality control sample, made up of a subset of samples from the study was injected several times during a run. All raw data files obtained were converted to compound exchange file format using Masshunter DA reprocessor software (Agilent, USA). Mass Profile Professional (Agilent, USA) was used for data alignment and to convert each metabolite feature (m/z x intensity x time) into a matrix of detected peaks for compound identification. Components that were matched were further examined by comparison to a purchased reference standard of the proposed compound. Mass accuracy of the Q-TOF method was <5ppm with retention time precision better than 0.2%. A 1.2x fold change can be detected with a precision of 4%.
Ion Mode:	POSITIVE

MS ID:	MS005261
Analysis ID:	AN005536
Instrument Name:	Agilent 6550 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	For each column, the run time is 20 min using a flow rate of 400 μL/min. A total of four samples per run was performed to give maximum coverage of metabolites. Samples were injected in duplicate or triplicate, and a quality control sample, made up of a subset of samples from the study was injected several times during a run. All raw data files obtained were converted to compound exchange file format using Masshunter DA reprocessor software (Agilent, USA). Mass Profile Professional (Agilent, USA) was used for data alignment and to convert each metabolite feature (m/z x intensity x time) into a matrix of detected peaks for compound identification. Components that were matched were further examined by comparison to a purchased reference standard of the proposed compound. Mass accuracy of the Q-TOF method was <5ppm with retention time precision better than 0.2%. A 1.2x fold change can be detected with a precision of 4%.
Ion Mode:	NEGATIVE

MS ID:	MS005262
Analysis ID:	AN005537
Instrument Name:	Agilent 6550 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	For each column, the run time is 20 min using a flow rate of 400 μL/min. A total of four samples per run was performed to give maximum coverage of metabolites. Samples were injected in duplicate or triplicate, and a quality control sample, made up of a subset of samples from the study was injected several times during a run. All raw data files obtained were converted to compound exchange file format using Masshunter DA reprocessor software (Agilent, USA). Mass Profile Professional (Agilent, USA) was used for data alignment and to convert each metabolite feature (m/z x intensity x time) into a matrix of detected peaks for compound identification. Components that were matched were further examined by comparison to a purchased reference standard of the proposed compound. Mass accuracy of the Q-TOF method was <5ppm with retention time precision better than 0.2%. A 1.2x fold change can be detected with a precision of 4%.
Ion Mode:	POSITIVE

MS ID:	MS005263
Analysis ID:	AN005538
Instrument Name:	Agilent 6550 QTOF
Instrument Type:	QTOF
MS Type:	ESI
MS Comments:	For each column, the run time is 20 min using a flow rate of 400 μL/min. A total of four samples per run was performed to give maximum coverage of metabolites. Samples were injected in duplicate or triplicate, and a quality control sample, made up of a subset of samples from the study was injected several times during a run. All raw data files obtained were converted to compound exchange file format using Masshunter DA reprocessor software (Agilent, USA). Mass Profile Professional (Agilent, USA) was used for data alignment and to convert each metabolite feature (m/z x intensity x time) into a matrix of detected peaks for compound identification. Components that were matched were further examined by comparison to a purchased reference standard of the proposed compound. Mass accuracy of the Q-TOF method was <5ppm with retention time precision better than 0.2%. A 1.2x fold change can be detected with a precision of 4%.
Ion Mode:	NEGATIVE