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 |
MS:
MS ID: | MS003669 |
Analysis ID: | AN003931 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | .raw files containing both pos and neg data (produced by using polarity switching) were converted to a readable format .mzxml, these files were combined and features aligned. Compiled data matrix was imported to IDEOM for metabolite ID and filtering. |
Ion Mode: | POSITIVE |
Capillary Voltage: | 4 kV |
Collision Gas: | NA |
Ion Source Temperature: | 120 C |
Mass Accuracy: | 1-2 ppm |
Acquisition Parameters File: | Metabolomics_pHILIC_Parkville_v1.pdf |
Analysis Protocol File: | PQMS3-MBPF-WIN-0501_analysis.pdf |
MS ID: | MS003670 |
Analysis ID: | AN003932 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | .raw files containing both pos and neg data (produced by using polarity switching) were converted to a readable format .mzxml, these files were combined and features aligned. Compiled data matrix was imported to IDEOM for metabolite ID and filtering. |
Ion Mode: | NEGATIVE |
Capillary Voltage: | 3.5 kV |
Collision Gas: | NA |
Ion Source Temperature: | 120 C |
Mass Accuracy: | 1-2 ppm |
Acquisition Parameters File: | Metabolomics_pHILIC_Parkville_v1.pdf |
Analysis Protocol File: | PQMS3-MBPF-WIN-0501_analysis.pdf |