Summary of Study ST000084
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 PR000075. The data can be accessed directly via it's Project DOI: 10.21228/M86K5H This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000084 |
| Study Title | Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation |
| Study Type | growth condition, timecourse |
| Study Summary | Macrophages are central players in immune response, manifesting divergent phenotypes to control inflammation and innate immunity through release of cytokines and other signaling factors. Recently, the focus on metabolism has been reemphasized as critical signaling and regulatory pathways of human pathophysiology, ranging from cancer to aging, often converge on metabolic responses. Here, we used genome-scale modeling and multi-omics (transcriptomics, proteomics, and metabolomics) analysis to assess metabolic features that are critical for macrophage activation. A genome-scale metabolic network for the RAW 264.7 cell line was constructed to determine metabolic modulators of activation. Metabolites well-known to be associated with immunoactivation (glucose and arginine) and immunosuppression (tryptophan and vitamin D3) were among the most critical effectors. Intracellular metabolic mechanisms were assessed, identifying a suppressive role for de-novo nucleotide synthesis. Finally, underlying metabolic mechanisms of macrophage activation were identified by analyzing multi-omic data obtained from LPS-stimulated RAW cells in the context of our flux-based predictions. This study demonstrates that the role of metabolism in regulating activation may be greater than previously anticipated and elucidates underlying connections between activation and metabolic effectors. This submission corresponds to the metabolomics data from this study. |
| Institute | Pacific Northwest National Laboratory |
| Department | Biological Separation and Mass Spectrometry |
| Last Name | Metz |
| First Name | Thomas |
| thomas.metz@pnnl.gov | |
| Submit Date | 2014-06-25 |
| Num Groups | 2 |
| Total Subjects | 12 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | cdf, d |
| Uploaded File Size | 102 M |
| Analysis Type Detail | GC-MS |
| Release Date | 2014-08-06 |
| Release Version | 1 |
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Treatment:
| Treatment ID: | TR000104 |
| Treatment Summary: | Macrophages (RAW 264.7 cells) grown for two day with suplimentation of 100ng | ml lipopolysaccharide | Macrophages (RAW 264.7 cells) grown for two days without suplimentation |
| Treatment Protocol Comments: | Macrophages (RAW 264.7 cells) were seeded at a density of 3.0E6 cells in 150 mm dishes using Dulbecco's Modified Eagle's Medium supplemented with 10% fetal calf serum, then grown for 2 days and stimulated for 24 hours with 100 ng/mL of lipopolysaccharide diluted in fresh medium. A control culture was run in parallel by incubating for the same period of time with fresh medium only. Three biological replicates were performed per condition, and two dishes were used for each replicate. / Macrophages (RAW 264.7 cells) were seeded at a density of 3.0E6 cells in 150 mm dishes using Dulbecco's Modified Eagle's Medium supplemented with 10% fetal calf serum, then grown for 2 days and stimulated for 24 hours with 100 ng/mL of lipopolysaccharide diluted in fresh medium. A control culture was run in parallel by incubating for the same period of time with fresh medium only. Three biological replicates were performed per condition, and two dishes were used for each replicate. |
| Treatment: | Abiotic |
| Treatment Compound: | lipopolysaccharide / fresh medium |
| Treatment Dose: | 100 ng/mL /-- |
| Treatment Vehicle: | fresh medium |
| Cell Growth Container: | 150 mm dishes |
| Cell Inoc Proc: | Macrophages (RAW 264.7 cells) were seeded at a density of 3.0E6 cells in 150 mm dishes |
| Cell Media: | Dulbecco's Modified Eagle's Medium supplemented with 10% fetal calf serum |
| Cell Harvesting: | After stimulation, cells were washed twice with Dulbeccos PBS, scraped out and harvested into 15-mL centrifuge tubes. |
