Summary of Study ST002760

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 PR001719. The data can be accessed directly via it's Project DOI: 10.21228/M8HF01 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 IDST002760
Study TitleMetabolic responses of normal rat kidneys to a high salt intake (Kidney outer medulla)
Study TypeTime-course metabolomics experiment
Study SummaryIn this study, novel methods were developed which allowed continuous (24/7) measurement of arterial blood pressure and renal blood flow in freely moving rats and the intermittent collection of arterial and renal venous blood to estimate kidney metabolic fluxes of O2 and metabolites. Specifically, the study determined the effects of a high salt (HS; 4.0% NaCl) diet upon whole kidney O2 consumption and arterial and renal venous plasma metabolomic profiles of normal Sprague-Dawley rats. A separate group of rats was studied to determine changes in the cortex and outer medulla tissue metabolomic profiles before and following the switch from a 0.4% to 4.0% NaCl diet.
Institute
Medical College of Wisconsin
DepartmentPhysiology
LaboratoryDr. Allen W. Cowley
Last NameCowley
First NameAllen
Address8701 W. Watertown Plank Rd, Milwaukee, WI 53226
Emailcowley@mcw.edu
Phone4149558277
Submit Date2023-06-26
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2023-07-02
Release Version1
Allen Cowley Allen Cowley
https://dx.doi.org/10.21228/M8HF01
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001719
Project DOI:doi: 10.21228/M8HF01
Project Title:SD Rat Metabolomics in Response to Salt
Project Type:Untargeted Four-Mode Metabolomics
Project Summary:This study analyzed the effects of a high salt (HS; 4.0% NaCl) diet upon the kidney, arterial plasma, and renal venous plasma metabolomic profiles of normal Sprague-Dawley rats.
Institute:Medical College of Wisconsin
Department:Physiology
Laboratory:Dr. Allen W. Cowley
Last Name:Cowley
First Name:Allen
Address:8701 W. Watertown Plank Rd, Milwaukee, WI 53226
Email:cowley@mcw.edu
Phone:414-955-8277
Funding Source:NHLBI
Contributors:Satoshi Shimada, Brian R. Hoffmann, Chun Yang, Theresa Kurth, Andrew S. Greene, Mingyu Liang, Ranjan K. Dash, Allen W. Cowley Jr

Subject:

Subject ID:SU002867
Subject Type:Mammal
Subject Species:Rattus norvegicus
Taxonomy ID:10116

Factors:

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

mb_sample_id local_sample_id Treatment Source CF
SA29081720220110_Cowley3_OM_2_22-391_C18posHS14 OM OM
SA29081820220111_Cowley3_OM_13_24-402_C18neg_repHS14 OM OM
SA29081920220113_Cowley3_OM_4_28-406_HILICpos_repHS14 OM OM
SA29082020220113_Cowley3_OM_5_30-413_HILICpos_repHS14 OM OM
SA29082120220113_Cowley3_OM_11_24-402_HILICposHS14 OM OM
SA29082220220111_Cowley3_OM_13_24-402_C18negHS14 OM OM
SA29082320220113_Cowley3_OM_5_30-413_HILICposHS14 OM OM
SA29082420220111_Cowley3_OM_9_26-405_C18negHS14 OM OM
SA29082520220111_Cowley3_OM_6_22-391_C18negHS14 OM OM
SA29082620220111_Cowley3_OM_1_30-413_C18neg_repHS14 OM OM
SA29082720220111_Cowley3_OM_6_22-391_C18neg_repHS14 OM OM
SA29082820220111_Cowley3_OM_8_28-406_C18negHS14 OM OM
SA29082920220113_Cowley3_OM_11_24-402_HILICpos_repHS14 OM OM
SA29083020220111_Cowley3_OM_8_28-406_C18neg_repHS14 OM OM
SA29083120220111_Cowley3_OM_9_26-405_C18neg_repHS14 OM OM
SA29083220220113_Cowley3_OM_13_26-405_HILICposHS14 OM OM
SA29083320220119_Cowley3_OM_13_24-402_HILICneg_repHS14 OM OM
SA29083420220119_Cowley3_OM_13_24-402_HILICnegHS14 OM OM
SA29083520220119_Cowley3_OM_14_28-406_HILICnegHS14 OM OM
SA29083620220119_Cowley3_OM_14_28-406_HILICneg_repHS14 OM OM
SA29083720220119_Cowley3_OM_15_22-391_HILICneg_repHS14 OM OM
SA29083820220119_Cowley3_OM_15_22-391_HILICnegHS14 OM OM
SA29083920220119_Cowley3_OM_10_26-405_HILICneg_repHS14 OM OM
SA29084020220119_Cowley3_OM_10_26-405_HILICnegHS14 OM OM
SA29084120220113_Cowley3_OM_15_22-391_HILICposHS14 OM OM
SA29084220220113_Cowley3_OM_13_26-405_HILICpos_repHS14 OM OM
SA29084320220113_Cowley3_OM_15_22-391_HILICpos_repHS14 OM OM
SA29084420220119_Cowley3_OM_2_30-413_HILICnegHS14 OM OM
SA29084520220119_Cowley3_OM_2_30-413_HILICneg_repHS14 OM OM
SA29084620220111_Cowley3_OM_1_30-413_C18negHS14 OM OM
SA29084720220113_Cowley3_OM_4_28-406_HILICposHS14 OM OM
SA29084820220110_Cowley3_OM_8_28-406_C18posHS14 OM OM
SA29084920220110_Cowley3_OM_6_24-402_C18pos_repHS14 OM OM
SA29085020220110_Cowley3_OM_8_28-406_C18pos_repHS14 OM OM
SA29085120220110_Cowley3_OM_9_30-413_C18posHS14 OM OM
SA29085220220110_Cowley3_OM_15_26-405_C18pos_repHS14 OM OM
SA29085320220110_Cowley3_OM_9_30-413_C18pos_repHS14 OM OM
SA29085420220110_Cowley3_OM_6_24-402_C18posHS14 OM OM
SA29085520220110_Cowley3_OM_15_26-405_C18posHS14 OM OM
SA29085620220110_Cowley3_OM_2_22-391_C18pos_repHS14 OM OM
SA29085720220113_Cowley3_OM_1_18-434_HILICposHS21 OM OM
SA29085820220113_Cowley3_OM_1_12-417_HILICpos_repHS21 OM OM
SA29085920220113_Cowley3_OM_1_18-434_HILICpos_repHS21 OM OM
SA29086020220113_Cowley3_OM_7_14-421_HILICpos_repHS21 OM OM
SA29086120220113_Cowley3_OM_7_14-421_HILICposHS21 OM OM
SA29086220220113_Cowley3_OM_1_12-417_HILICposHS21 OM OM
SA29086320220110_Cowley3_OM_4_18-434_C18posHS21 OM OM
SA29086420220110_Cowley3_OM_13_12-417_C18pos_repHS21 OM OM
SA29086520220110_Cowley3_OM_14_14-421_C18posHS21 OM OM
SA29086620220110_Cowley3_OM_13_12-417_C18posHS21 OM OM
SA29086720220110_Cowley3_OM_12_20-463_C18pos_repHS21 OM OM
SA29086820220110_Cowley3_OM_4_18-434_C18pos_repHS21 OM OM
SA29086920220110_Cowley3_OM_12_20-463_C18posHS21 OM OM
SA29087020220113_Cowley3_OM_8_20-463_HILICpos_repHS21 OM OM
SA29087120220113_Cowley3_OM_12_16-429_HILICpos_repHS21 OM OM
SA29087220220119_Cowley3_OM_7_12-417_HILICneg_repHS21 OM OM
SA29087320220119_Cowley3_OM_11_16-429_HILICnegHS21 OM OM
SA29087420220119_Cowley3_OM_7_12-417_HILICnegHS21 OM OM
SA29087520220119_Cowley3_OM_4_20-463_HILICnegHS21 OM OM
SA29087620220119_Cowley3_OM_5_14-421_HILICnegHS21 OM OM
SA29087720220119_Cowley3_OM_4_20-463_HILICneg_repHS21 OM OM
SA29087820220119_Cowley3_OM_11_16-429_HILICneg_repHS21 OM OM
SA29087920220119_Cowley3_OM_12_18-434_HILICnegHS21 OM OM
SA29088020220110_Cowley3_OM_1_16-429_C18pos_repHS21 OM OM
SA29088120220119_Cowley3_OM_5_14-421_HILICneg_repHS21 OM OM
SA29088220220110_Cowley3_OM_1_16-429_C18posHS21 OM OM
SA29088320220110_Cowley3_OM_14_14-421_C18pos_repHS21 OM OM
SA29088420220119_Cowley3_OM_12_18-434_HILICneg_repHS21 OM OM
SA29088520220113_Cowley3_OM_12_16-429_HILICposHS21 OM OM
SA29088620220113_Cowley3_OM_8_20-463_HILICposHS21 OM OM
SA29088720220111_Cowley3_OM_4_20-463_C18neg_repHS21 OM OM
SA29088820220111_Cowley3_OM_4_20-463_C18negHS21 OM OM
SA29088920220111_Cowley3_OM_1_18-434_C18neg_repHS21 OM OM
SA29089020220111_Cowley3_OM_7_16-429_C18negHS21 OM OM
SA29089120220111_Cowley3_OM_14_12-417_C18neg_repHS21 OM OM
SA29089220220111_Cowley3_OM_11_14-421_C18negHS21 OM OM
SA29089320220111_Cowley3_OM_11_14-421_C18neg_repHS21 OM OM
SA29089420220111_Cowley3_OM_14_12-417_C18negHS21 OM OM
SA29089520220111_Cowley3_OM_1_18-434_C18negHS21 OM OM
SA29089620220111_Cowley3_OM_7_16-429_C18neg_repHS21 OM OM
SA29089720220110_Cowley3_OM_11_4-467_C18posLS OM OM
SA29089820220110_Cowley3_OM_10_8-469_C18pos_repLS OM OM
SA29089920220119_Cowley3_OM_6_2-466_HILICneg_repLS OM OM
SA29090020220110_Cowley3_OM_11_4-467_C18pos_repLS OM OM
SA29090120220113_Cowley3_OM_14_2-466_HILICpos_repLS OM OM
SA29090220220113_Cowley3_OM_10_10-470_HILICposLS OM OM
SA29090320220113_Cowley3_OM_10_10-470_HILICpos_repLS OM OM
SA29090420220113_Cowley3_OM_14_2-466_HILICposLS OM OM
SA29090520220110_Cowley3_OM_10_8-469_C18posLS OM OM
SA29090620220119_Cowley3_OM_6_2-466_HILICnegLS OM OM
SA29090720220110_Cowley3_OM_7_6-468_C18pos_repLS OM OM
SA29090820220110_Cowley3_OM_7_6-468_C18posLS OM OM
SA29090920220110_Cowley3_OM_5_2-466_C18pos_repLS OM OM
SA29091020220113_Cowley3_OM_9_4-467_HILICpos_repLS OM OM
SA29091120220119_Cowley3_OM_1_10-470_HILICnegLS OM OM
SA29091220220119_Cowley3_OM_3_4-467_HILICneg_repLS OM OM
SA29091320220119_Cowley3_OM_3_4-467_HILICnegLS OM OM
SA29091420220119_Cowley3_OM_1_10-470_HILICneg_repLS OM OM
SA29091520220110_Cowley3_OM_5_2-466_C18posLS OM OM
SA29091620220113_Cowley3_OM_6_6-468_HILICpos_repLS OM OM
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Collection:

Collection ID:CO002860
Collection Summary:Plasma was collected through an arterial and renal venous catheter throughout the study (200 µL of arterial and renal venous blood were sampled at the day 7, 14, and 21). Overnight urine (18 hours) from the day before the blood draw was collected on ice. The kidneys were collected either at 14 days of HS (HS14) or 21 days of HS (HS21). The kidneys of only LS fed SD rats were also collected for comparison. The collected kidneys (n=5 for each group for metabolomics) were dissected to cortex and outer medulla and snap frozen with liquid nitrogen. Plasma, urine and tissue were stored in -80°C until further analysis.
Sample Type:Kidney outer medulla
Storage Conditions:-80?

Treatment:

Treatment ID:TR002876
Treatment Summary:Rats (n=7, 10-11 weeks of age) were performed renal blood flow (RBF) probe implantation and femoral arterial catheterization5. Briefly, rats were anesthetized with isoflurane and arterial catheter was inserted. Following an abdominal incision, RBF probe was implanted on left renal artery and the cable was exposed at nape of the neck via the subcutaneous route. In addition to the RBF probe implantation, renal venous catheter was inserted through the femoral vein and placed in the left renal vein and secured to the luminal wall with 10-0 nylon. RBF and BP via arterial line were measured by conscious freely moving rats and recorded on average of every minute for 24 h/day. After 7-10 days of recovery period, 200 µL of arterial and renal venous blood were sampled and that blood was replaced from donor rats before and following 7, 14 and 21 days after the switch in diet from 0.4% (LS) to 4.0% (HS) salt diet (Dyets Inc, Bethlehem, PA). Overnight urine (18 hours) from the day before the blood draw was collected on ice. The kidneys were collected either at 14 days of HS (HS14) or 21 days of HS (HS21). The kidneys of only LS fed SD rats were also collected for comparison. The collected kidneys (n=5 for each group for metabolomics and mRNAseq analysis) were dissected to cortex and outer medulla and snap frozen with liquid nitrogen. Plasma, urine and tissue were stored in -80°C until further analysis.

Sample Preparation:

Sampleprep ID:SP002873
Sampleprep Summary:Plasma/Urine Metabolite Extraction. Metabolites were extracted from 20 µL of plasma and 20 µL of urine from each SD rat in the study according to standard operating procedures in the Mass Spectrometry and Protein Chemistry Service at The Jackson Laboratory34. Metabolites were extracted using 500 µL of an ice cold 2:2:1 methanol:acetonitrile:water (MeOH:ACN:H2O) buffer; the sample was part of the water fraction. Caffeine, 1-napthylamine, and 9-anthracene carboxylic acid were all added at 0.5 ng/ µL in the extraction buffer as internal standards. Each sample was then vortexed for 30 seconds on the highest setting, subject to one minute of mixing with the Tissue Lyser II in pre-chilled cassettes, and then sonicated at 30 Hz for 5 minutes of 30 seconds on 30 seconds off in an ice water bath. Samples were then placed in the -20°C freezer overnight (16 hours) for extraction. Following the extraction, samples were centrifuged at 21,000 x g at 4°C and supernatant from each metabolite extract was equally divided into five 2 mL microcentrifuge tubes. Each sample supernatant was divided into five equal volume aliquots, one for each of the four modes and the rest to create equal representation pools of all samples, one for each mode. Each aliquot was then dried down using a vacuum centrifuge for storage at -80°C until further use. Tissue Metabolite Extraction. Metabolites were extracted from 20 mg of kidney cortex and medulla from each SD rat in the study according to standard operating procedures in the Mass Spectrometry and Protein Chemistry Service at The Jackson Laboratory34 as described for the plasma and urine samples with slight modification. Metabolites were extracted using 1000 µL of an ice cold 2:2:1 methanol:acetonitrile:water (MeOH:ACN:H2O) buffer containing internal standards as above per 20 mg of sample to ensure the extraction equivalents were normalized. Each sample had a 5 mm stainless steel bead added, then were pulverized in extraction buffer for two minutes usingTissue Lyser II. Samples were then placed in the -20°C freezer overnight (16 hours) for extraction and the supernatant was collected as with the urine/plasma samples. Each sample supernatant was divided into five equal volume aliquots, one for each of the four modes and the rest to create equal representation pools of all samples, one for each mode. Each aliquot was then dried down using a vacuum centrifuge for storage at -80°C until further use.

Combined analysis:

Analysis ID AN004483 AN004484 AN004485 AN004486
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase HILIC HILIC
Chromatography system Thermo Vanquish Thermo Vanquish Thermo Vanquish Thermo Vanquish
Column Agilent InfinityLab Poroshell 120 EC-C18 (2.1 x 50 mm; 2.7-Micron) Agilent InfinityLab Poroshell 120 HILIC-Z (2.1 x 50 mm; 2.7 micron; #689775-924) Agilent InfinityLab Poroshell 120 HILIC-Z (2.1 x 50 mm; 2.7 micron; #689775-924) Agilent InfiinityLab Poroshell 120 HILIC-Z (2.1 x 50 mm; 2.7 micron; #689775-924)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE POSITIVE NEGATIVE
Units Area Area Area Area

Chromatography:

Chromatography ID:CH003368
Chromatography Summary:This chromatography method was utilized for all C18 positive polarity runs in this study.
Instrument Name:Thermo Vanquish
Column Name:Agilent InfinityLab Poroshell 120 EC-C18 (2.1 x 50 mm; 2.7-Micron)
Column Temperature:25C
Flow Gradient:0-1 minutes at 98% A1/2% B1, 1-13 minutes from 98% A1/2% B1 to 10% A1/90% B1, 13-15 minutes at 10% A1/90% B1, 15-16 minutes from 10% A1/90% B1 to 98% A1/2% B1, and was re-equilibrated from 16-25 minutes at 98% A1/2% B1
Flow Rate:0.1 mL/minute
Internal Standard:Caffeine, 1-napthylamine, and 9-anthracene carboxylic acid were all added at 0.5 ng/ µL in the extraction buffer as internal standards
Solvent A:100% water, 0.2% acetic acid
Solvent B:100% acetonitrile, 0.2% acetic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH003369
Chromatography Summary:This chromatography method was utilized for all C18 negative polarity runs in this study.
Instrument Name:Thermo Vanquish
Column Name:Agilent InfinityLab Poroshell 120 HILIC-Z (2.1 x 50 mm; 2.7 micron; #689775-924)
Column Temperature:25C
Flow Gradient:0-1 minutes at 2% A/98% B, 1-11 minutes from 2% A/98% B to 30% A/70% B, 11-12 minutes from 30% A/70% B to 40% A/60% B, 12-16 minutes from 40% A/60% B to 95% A/5% B, was held at 95% A/5% B from 16-18 minutes, 18-20 minutes from 95% A/5% B to 2% A/98% B, and was re-equilibrated from 20-25 minutes at 2% A/98% B
Flow Rate:0.1 mL/minute
Internal Standard:Caffeine, 1-napthylamine, and 9-anthracene carboxylic acid were all added at 0.5 ng/ µL in the extraction buffer as internal standards
Solvent A:100% water, 0.2% acetic acid
Solvent B:100% acetonitrile, 0.2% acetic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH003370
Chromatography Summary:This chromatography method was utilized for all HILIC positive polarity runs in this study.
Instrument Name:Thermo Vanquish
Column Name:Agilent InfinityLab Poroshell 120 HILIC-Z (2.1 x 50 mm; 2.7 micron; #689775-924)
Column Temperature:25C
Flow Gradient:0-1 minutes at 2% A/98% B, 1-11 minutes from 2% A/98% B to 30% A/70% B, 11-12 minutes from 30% A/70% B to 40% A/60% B, 12-16 minutes from 40% A/60% B to 95% A/5% B, was held at 95% A/5% B from 16-18 minutes, 18-20 minutes from 95% A/5% B to 2% A/98% B, and was re-equilibrated from 20-25 minutes at 2% A/98% B
Flow Rate:0.1 mL/minute
Internal Standard:Caffeine, 1-napthylamine, and 9-anthracene carboxylic acid were all added at 0.5 ng/ µL in the extraction buffer as internal standards
Solvent A:10 mM ammonium formate in H2O with 0.1% formic acid (Solvent A2)
Solvent B:90% ACN with 10 mM ammonium formate in H2O with 0.1% formic acid (Solvent B2)
Chromatography Type:HILIC
  
Chromatography ID:CH003371
Chromatography Summary:This chromatography method was utilized for all HILIC negative polarity runs in this study.
Instrument Name:Thermo Vanquish
Column Name:Agilent InfiinityLab Poroshell 120 HILIC-Z (2.1 x 50 mm; 2.7 micron; #689775-924)
Column Temperature:25C
Flow Gradient:0-1 minutes at 2% A/98% B, 1-11 minutes from 2% A/98% B to 30% A/70% B, 11-12 minutes from 30% A/70% B to 40% A/60% B, 12-16 minutes from 40% A/60% B to 95% A/5% B, was held at 95% A/5% B from 16-18 minutes, 18-20 minutes from 95% A/5% B to 2% A/98% B, and was re-equilibrated from 20-25 minutes at 2% A/98% B
Flow Rate:0.1 mL/minute
Internal Standard:Caffeine, 1-napthylamine, and 9-anthracene carboxylic acid were all added at 0.5 ng/ µL in the extraction buffer as internal standards
Solvent A:10 mM ammonium acetate in H2O, pH 9.0 with 0.1% AffinityLab Deactivator Inhibitor (Agilent, #5191-3940; Solvent A3)
Solvent B:85% ACN with 10 mM ammonium acetate in H2O with 0.1% AffinityLab Deactivator Inhibitor (Solvent B3)
Chromatography Type:HILIC

MS:

MS ID:MS004230
Analysis ID:AN004483
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:C18 positive kidney outer medulla data: The tandem mass spectrometry RAW data files (consisting of MS1 and MS2 spectra collected) were analyzed using Thermo Compound Discoverer (v3.2.0.421). The MS1 and MS2 data was searched against the Thermo mzCloud database, ChemSpider database, Metabolika Pathways, and mzLogic predicted composition in the Compound Discoverer workflow.
Ion Mode:POSITIVE
  
MS ID:MS004231
Analysis ID:AN004484
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:C18 negative kidney outer medulla data: The tandem mass spectrometry RAW data files (consisting of MS1 and MS2 spectra collected) were analyzed using Thermo Compound Discoverer (v3.2.0.421). The MS1 and MS2 data was searched against the Thermo mzCloud database, ChemSpider database, Metabolika Pathways, and mzLogic predicted composition in the Compound Discoverer workflow.
Ion Mode:NEGATIVE
  
MS ID:MS004232
Analysis ID:AN004485
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:HILIC positive kidney outer medulla data: The tandem mass spectrometry RAW data files (consisting of MS1 and MS2 spectra collected) were analyzed using Thermo Compound Discoverer (v3.2.0.421). The MS1 and MS2 data was searched against the Thermo mzCloud database, ChemSpider database, Metabolika Pathways, and mzLogic predicted composition in the Compound Discoverer workflow.
Ion Mode:POSITIVE
  
MS ID:MS004233
Analysis ID:AN004486
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:HILIC negative kidney outer medulla data: The tandem mass spectrometry RAW data files (consisting of MS1 and MS2 spectra collected) were analyzed using Thermo Compound Discoverer (v3.2.0.421). The MS1 and MS2 data was searched against the Thermo mzCloud database, ChemSpider database, Metabolika Pathways, and mzLogic predicted composition in the Compound Discoverer workflow.
Ion Mode:NEGATIVE
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