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 |
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Sample Preparation:
| Sampleprep ID: | SP002507 |
| Sampleprep Summary: | Adherent macrophages were lifted with trypsin, suspended in PBS and 2x10 6 cells were collected by centrifugation. The cell pellet was rinsed in 10 mL ice cold 0.9% NaCl in water at 4 °C pelleted, then resuspended in 200 L of 4 °C extraction solvent (a 1:3:1 ratio of chloroform, methanol and water). The sample was subjected to three freeze-thaw cycles then mixed by vortex for 30 minutes at 4 °C and cell debris was removed by centrifugation at 20,000g for 10 minutes at 4 °C. The cleared supernatant was transferred (180 uL) and frozen at -80°C until LCMS analysis. |
| Extract Storage: | -80℃ |
