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.

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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.

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Study IDST002412
Study TitleMetabolic effects of the protein kinase R
Study TypeBiomedical research
Study SummarySpleen-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
DepartmentCIIID
LaboratoryMolecular Immunology
Last NameSadler
First NameAnthony
Address27-31 Wright st, Clayton, VIC 3168
EmailAnthony.sadler@hudson.org.au
Phone+61 4 85722722
Submit Date2022-12-15
Num Groups2
Total SubjectsNA
Num MalesNA
Num FemalesNA
Study CommentsKO vs WT
PublicationsSuppression of the nucleic acid precursor ribose 5-phosphate by RNA-mediated antiviral immunity
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-01-04
Release Version1
Anthony Sadler Anthony Sadler
https://dx.doi.org/10.21228/M8342Z
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
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