Summary of Study ST002412
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 PR001552. The data can be accessed directly via it's Project DOI: 10.21228/M8342Z 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.
Study ID | ST002412 |
Study Title | Metabolic effects of the protein kinase R |
Study Type | Biomedical research |
Study Summary | Spleen-derived macrophage from WT or Eif2ak2-/- (gene encoding PKR protein kinase) mice are treated with a synthetic RNA mimetic (polyinosinic:polycytidylic acid) to activate the kinase and metabolites were collected for analysis. The data identified 325 putative metabolites in the cell extracts, with a large number of significant differences between the Eif2ak2- /- and WT sample groups. Metabolite levels are predominantly suppressed in the WT compared to the Eif2ak2-/- cells, with depletion of specific metabolites in amino acid, carbohydrate, lipid and nucleotide pathways, while several amino acid metabolites were significantly elevated in the WT cells compared to the Eif2ak2-/-. The changes appear to delineate a pseudo-starvation response in the WT cells. Phosphate energy metabolism is altered with decreased creatine and phosphocreatine and a compensatory increase in phosphorylated guanidinoacetate in the WT compared to the Eif2ak2- /- cells. There appears to be a constraint in glycolysis in the WT cells, most clearly in the pentose phosphate pathway. |
Institute | Hudson Institute of Medical Research |
Department | CIIID |
Laboratory | Molecular Immunology |
Last Name | Sadler |
First Name | Anthony |
Address | 27-31 Wright st, Clayton, VIC 3168 |
Anthony.sadler@hudson.org.au | |
Phone | +61 4 85722722 |
Submit Date | 2022-12-15 |
Num Groups | 2 |
Total Subjects | NA |
Num Males | NA |
Num Females | NA |
Study Comments | KO vs WT |
Publications | Suppression of the nucleic acid precursor ribose 5-phosphate by RNA-mediated antiviral immunity |
Raw Data Available | Yes |
Raw Data File Type(s) | raw(Thermo) |
Analysis Type Detail | LC-MS |
Release Date | 2023-01-04 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
Analysis ID | AN003931 | AN003932 |
---|---|---|
Analysis type | MS | MS |
Chromatography type | HILIC | HILIC |
Chromatography system | Thermo Dionex Ultimate 3000 RS | Thermo Dionex Ultimate 3000 RS |
Column | Merck SeQuant ZIC-HILIC (150 x 4.6mm,5um) | Merck SeQuant ZIC-HILIC (150 x 4.6mm,5um) |
MS Type | ESI | ESI |
MS instrument type | Orbitrap | Orbitrap |
MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
Ion Mode | POSITIVE | NEGATIVE |
Units | peak height | peak height |
Chromatography:
Chromatography ID: | CH002910 |
Chromatography Summary: | pHILIC chromatography at pH9 using Orbitrap high resolution accurate mass MS detection with posneg switching |
Instrument Name: | Thermo Dionex Ultimate 3000 RS |
Column Name: | Merck SeQuant ZIC-HILIC (150 x 4.6mm,5um) |
Column Pressure: | 60 bar at starting conditions |
Column Temperature: | 25 C |
Flow Gradient: | 0 min - 80%B, 15 min - 50%B, 18 min - 5%B, 21 min - 5%B, 24 min - 80%B, 32 min - 80%B |
Flow Rate: | 0.3 ml/min |
Injection Temperature: | 4 C |
Internal Standard: | CAPS, CHAPS, PIPES |
Solvent A: | 100% water; 20 mM ammonium carbonate |
Solvent B: | 100% acetonitrile |
Analytical Time: | 32 min |
Capillary Voltage: | 3.5 kV |
Oven Temperature: | 25 C |
Washing Buffer: | syringe wash 50% IPA |
Sample Loop Size: | 25 uL |
Sample Syringe Size: | 25 uL |
Randomization Order: | yes |
Chromatography Type: | HILIC |
Chromatography ID: | CH002911 |
Chromatography Summary: | pHILIC chromatography at pH9 using Orbitrap high resolution accurate mass MS detection with posneg switching |
Instrument Name: | Thermo Dionex Ultimate 3000 RS |
Column Name: | Merck SeQuant ZIC-HILIC (150 x 4.6mm,5um) |
Column Pressure: | 60 bar at starting conditions |
Column Temperature: | 25 C |
Flow Gradient: | 0 min - 80%B, 15 min - 50%B, 18 min - 5%B, 21 min - 5%B, 24 min - 80%B, 32 min - 80%B |
Flow Rate: | 0.3 ml/min |
Injection Temperature: | 4 C |
Internal Standard: | CAPS, CHAPS, PIPES |
Solvent A: | 100% water; 20 mM ammonium carbonate |
Solvent B: | 100% acetonitrile |
Analytical Time: | 32 min |
Capillary Voltage: | 3.5 kV |
Oven Temperature: | 25 C |
Washing Buffer: | syringe wash 50% IPA |
Sample Loop Size: | 25 uL |
Sample Syringe Size: | 25 uL |
Randomization Order: | yes |
Chromatography Type: | HILIC |