Summary of study ST000342

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 PR000274. The data can be accessed directly via it's Project DOI: 10.21228/M8CC84 This work is supported by NIH grant, U2C- DK119886.

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

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  |  Download all metabolite data  |  Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data (Contains raw data)
Study IDST000342
Study TitleRenal metabolic pathways indicating ischemic or inflammatory changes
Study SummaryTissues were acquired from kidkeys that were deemed unsuitable for transplant and were then analyzed by the lab through normothermic machine perfusion. They were perfused with either whole blood perfusate or with packed red blood cell perfusate. These tissues' metabolic pathways were then analyzed for markers of ischemic or inflammatory responses in the renal tissue
Institute
University of California, Davis
DepartmentGenome and Biomedical Sciences Facility
LaboratoryWCMC Metabolomics Core
Last NameFiehn
First NameOliver
Address1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Emailofiehn@ucdavis.edu
Phone(530) 754-8258
Submit Date2016-02-04
Num Groups6
Total Subjects34
Raw Data AvailableYes
Raw Data File Type(s).bin,.cg,.cd,.xml
Analysis Type DetailLC-MS
Release Date2016-03-03
Release Version1
Oliver Fiehn Oliver Fiehn
https://dx.doi.org/10.21228/M8CC84
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000274
Project DOI:doi: 10.21228/M8CC84
Project Title:Renal metabolic pathways indicating ischemic or inflammatory changes
Project Summary:Tissues were acquired from kidkeys that were deemed unsuitable for transplant and were then analyzed by the lab through normothermic machine perfusion. They were perfused with either whole blood perfusate or with packed red blood cell perfusate. These tissues' metabolic pathways were then analyzed for markers of ischemic or inflammatory responses in the renal tissue
Institute:University of California, San Diego
Last Name:Fiehn
First Name:Oliver
Address:1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Email:ofiehn@ucdavis.edu
Phone:(530) 754-8258
Funding Source:NIH U24DK097154

Subject:

Subject ID:SU000362
Subject Type:Animal
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Human

Factors:

Subject type: Animal; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Organ Treatment
SA015195Biorec03_PalmaPlasma Quality Control
SA015196Biorec02_PalmaPlasma Quality Control
SA015197Biorec04_PalmaPlasma Quality Control
SA015198Palm26 _8B_T1_003Renal Tissue PRBC
SA015199Palm21 _9B_T1_007Renal Tissue PRBC
SA015200Palm16 _8B_T2_004Renal Tissue PRBC
SA015201Palm22 _9B_T2_008Renal Tissue PRBC
SA015202Palm34 _10B_T1_011Renal Tissue PRBC
SA015203Palm27 _11B_T2_016Renal Tissue PRBC
SA015204Palm32 _11B_T1_015Renal Tissue PRBC
SA015205Palm33 _10B_T2_012Renal Tissue PRBC
SA015210Palm30 _28B_T4_025Renal Tissue PRBC-FST
SA015211Palm12 _28B_T0_023Renal Tissue PRBC-FST
SA015212Palm23 _28B_T6_026Renal Tissue PRBC-FST
SA015213Palm35 _28B_T2_024Renal Tissue PRBC-FST
SA015206Palm19 _28A_T6_022Renal Tissue PRBC+FST
SA015207Palm29 _28A_T2_020Renal Tissue PRBC+FST
SA015208Palm24 _28A_T4_021Renal Tissue PRBC+FST
SA015209Palm15 _28A_T0_019Renal Tissue PRBC+FST
SA015214Palm07 _Pool_50_150Renal Tissue Quality Control
SA015215Palm08 _Pool_150_300Renal Tissue Quality Control
SA015216Palm10 _Pool_500_1600Renal Tissue Quality Control
SA015217Palm09 _Pool_300_500Renal Tissue Quality Control
SA015218Palm20 _10A_T2_010Renal Tissue WB
SA015219Palm11 _9A_T1_005Renal Tissue WB
SA015220Palm28 _8A_T2_002Renal Tissue WB
SA015221Palm25 _8A_T1_001Renal Tissue WB
SA015222Palm17 _9A_T2_006Renal Tissue WB
SA015223Palm13 _10A_T1_009Renal Tissue WB
SA015224Palm31 _29_T0_017Renal Tissue WB
SA015225Palm18 _11A_T2_014Renal Tissue WB
SA015226Palm36 _11A_T1_013Renal Tissue WB
SA015227Palm14 _29_T6_018Renal Tissue WB
Showing results 1 to 33 of 33

Collection:

Collection ID:CO000356
Collection Summary:Samples are renal tissues samples. These are from kidneys that were deemed unsuitable for transplantation and discarded. After being discarded these kidneys were brought to our lab where we conducted normothermic machine perfusion on them, where they were perfused with a blood based perfusate to analyze function. The samples are core needle biopsies taken by a surgical instrument. The samples were then snap frozen in liquid nitrogen and stored in -80C till analysis.
Collection Protocol Filename:StudyDesign_IvonnePalma_090815.pdf
Sample Type:Renal Tissue

Treatment:

Treatment ID:TR000376
Treatment Summary:Human 8A/B, 9A/B, 10A/B, 11A/B were perfused with either a Whole Blood perfusate or a Packed Red Blood Cells. We had previously sent samples from this group but we want to analyze other time points from this group. Group A was perfused with a whole blood perfusate while Group B was perfused with a packed red blood cell perfusate. Human 29 was perfused with a whole blood perfusate and this is from a pediatric patient. We are trying to compare young and old donors and we had previously submitted other pediatric patients. Huma 28A and B were perfused with a packed red blood perfusate. 28A was given Furosemide (a diuretic) to test urine output with acute kidney injury, Human 28B was not given the Furosemide since it is a control.
Treatment Protocol Filename:StudyDesign_IvonnePalma_090815.pdf

Sample Preparation:

Sampleprep ID:SP000369
Sampleprep Summary:None
Sampleprep Protocol Filename:Sample_Prep_Ivonne_Palma_mx_234649.pdf

Combined analysis:

Analysis ID AN000554
Analysis type MS
Chromatography type Reversed phase
Chromatography system Agilent 6530
Column Waters Acquity CSH C18 (100 x 2.1mm, 1.7um)
MS Type ESI
MS instrument type QTOF
MS instrument name Agilent 6550 QTOF
Ion Mode NEGATIVE
Units Peak height

Chromatography:

Chromatography ID:CH000391
Chromatography Summary:UPLC
Methods Filename:Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf
Instrument Name:Agilent 6530
Column Name:Waters Acquity CSH C18 (100 x 2.1mm, 1.7um)
Column Pressure:450-850 bar
Column Temperature:65 C
Flow Gradient:15% B to 99% B
Flow Rate:0.6 mL/min
Sample Injection:1.67 uL
Solvent A:60:40 Acetonitrile:Water +10mM Ammonium Formate +10mM Formic Acid
Solvent B:9:1 Isopropanol:Acetonitrile +10mM Ammonium Formate +10mM Formic Acid
Analytical Time:13 min
Capillary Voltage:3500
Time Program:15 min
Weak Wash Solvent Name:Isopropanol
Weak Wash Volume:5 seconds
Strong Wash Solvent Name:Same
Target Sample Temperature:Autosampler temp 4 C
Randomization Order:Excel
Chromatography Type:Reversed phase

MS:

MS ID:MS000490
Analysis ID:AN000554
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Lipidomics runs are MS1 data; Identifications made from pooled MS/MS runs Lipidomics runs are performed in negative and positve mode (two filenames)
Ion Mode:NEGATIVE
Capillary Voltage:3500
Collision Gas:Nitrogen
Dry Gas Flow:8 l/min
Dry Gas Temp:325
Fragment Voltage:175
Fragmentation Method:Auto MS/MS
Ion Source Temperature:200
Ion Spray Voltage:1000
Ionization:Neg
Precursor Type:Intact Molecule
Reagent Gas:Nitrogen
Source Temperature:325 C
Dataformat:.d
Desolvation Gas Flow:11 l/min
Desolvation Temperature:350 C
Nebulizer:35 psig
Octpole Voltage:750
Scan Range Moverz:60-1700 Da
Scanning Cycle:2 Hz
Scanning Range:60-1700 Da
Skimmer Voltage:65
  logo