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
Study ID | ST000342 |
Study Title | Renal metabolic pathways indicating ischemic or inflammatory changes |
Study 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, Davis |
Department | Genome and Biomedical Sciences Facility |
Laboratory | WCMC Metabolomics Core |
Last Name | Fiehn |
First Name | Oliver |
Address | 1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616 |
ofiehn@ucdavis.edu | |
Phone | (530) 754-8258 |
Submit Date | 2016-02-04 |
Num Groups | 6 |
Total Subjects | 34 |
Raw Data Available | Yes |
Raw Data File Type(s) | d |
Analysis Type Detail | LC-MS |
Release Date | 2016-03-03 |
Release Version | 1 |
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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: | Mammals |
Factors:
Subject type: Animal; Subject species: Homo sapiens (Factor headings shown in green)
mb_sample_id | local_sample_id | Organ | Treatment |
---|---|---|---|
SA015195 | Biorec03_Palma | Plasma | Quality Control |
SA015196 | Biorec02_Palma | Plasma | Quality Control |
SA015197 | Biorec04_Palma | Plasma | Quality Control |
SA015198 | Palm26 _8B_T1_003 | Renal Tissue | PRBC |
SA015199 | Palm21 _9B_T1_007 | Renal Tissue | PRBC |
SA015200 | Palm16 _8B_T2_004 | Renal Tissue | PRBC |
SA015201 | Palm22 _9B_T2_008 | Renal Tissue | PRBC |
SA015202 | Palm34 _10B_T1_011 | Renal Tissue | PRBC |
SA015203 | Palm27 _11B_T2_016 | Renal Tissue | PRBC |
SA015204 | Palm32 _11B_T1_015 | Renal Tissue | PRBC |
SA015205 | Palm33 _10B_T2_012 | Renal Tissue | PRBC |
SA015206 | Palm19 _28A_T6_022 | Renal Tissue | PRBC+FST |
SA015207 | Palm29 _28A_T2_020 | Renal Tissue | PRBC+FST |
SA015208 | Palm24 _28A_T4_021 | Renal Tissue | PRBC+FST |
SA015209 | Palm15 _28A_T0_019 | Renal Tissue | PRBC+FST |
SA015210 | Palm30 _28B_T4_025 | Renal Tissue | PRBC-FST |
SA015211 | Palm12 _28B_T0_023 | Renal Tissue | PRBC-FST |
SA015212 | Palm23 _28B_T6_026 | Renal Tissue | PRBC-FST |
SA015213 | Palm35 _28B_T2_024 | Renal Tissue | PRBC-FST |
SA015214 | Palm07 _Pool_50_150 | Renal Tissue | Quality Control |
SA015215 | Palm08 _Pool_150_300 | Renal Tissue | Quality Control |
SA015216 | Palm10 _Pool_500_1600 | Renal Tissue | Quality Control |
SA015217 | Palm09 _Pool_300_500 | Renal Tissue | Quality Control |
SA015218 | Palm20 _10A_T2_010 | Renal Tissue | WB |
SA015219 | Palm11 _9A_T1_005 | Renal Tissue | WB |
SA015220 | Palm28 _8A_T2_002 | Renal Tissue | WB |
SA015221 | Palm25 _8A_T1_001 | Renal Tissue | WB |
SA015222 | Palm17 _9A_T2_006 | Renal Tissue | WB |
SA015223 | Palm13 _10A_T1_009 | Renal Tissue | WB |
SA015224 | Palm31 _29_T0_017 | Renal Tissue | WB |
SA015225 | Palm18 _11A_T2_014 | Renal Tissue | WB |
SA015226 | Palm36 _11A_T1_013 | Renal Tissue | WB |
SA015227 | Palm14 _29_T6_018 | Renal 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% acetonitrile/40% water; 10mM formic acid; 10mM ammonium formate |
Solvent B: | 90% isopropanol/10% acetonitrile; 10mM formic acid; 10mM ammonium formate |
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 |