| Biological Samples |
| EDTA-plasma and PBMCs prepared from intravenous whole blood collection |
This paper |
N/A |
| Chemicals, Peptides, and Recombinant Proteins |
| Methanol |
Fisher Scientific |
A456-4 |
| Methyl tert-butyl ether |
Sigma-Aldrich |
650560-1L |
| Water |
Fisher Scientific |
W6-4 |
| Acetone |
Fisher Scientific |
A9291 |
| Aeconitrile |
Fisher Scientific |
A955-4 |
| Toluene |
Sigma-Aldrich |
650579-1L |
| Ammonium Acetate |
Sigma-Aldrich |
73594-25G-F |
| Acetic acid |
Sigma-Aldrich |
73594-25G-F |
| Isopropanol |
Fisher Scientific |
A461-4 |
| Dichloromethane |
Sigma-Aldrich |
34856 |
| Deposited data |
| Raw and analyzed data |
This paper |
Metabolomics Workbench: ST002112 |
| Critical Commercial Assays |
| AllPrep DNA/RNA/Protein kit |
Qiagen |
cat# 80004 |
| Clinical labs |
This paper |
N/A |
| QIAamp PowerFecal |
Qiagen |
cat# 51804 |
| Rapid DNA-seq |
Nugen |
cat# 0567-24 |
| Software and Algorithms |
| Impute |
Hastie et al., 2021 |
https://www.bioconductor.org/packages/release/bioc/html/impute.html
|
| Analyst TF |
Sciex |
https://sciex.com/products/software/analyst-tf-software
|
| Progenesis QI |
Nonlinear Dynamics |
https://www.nonlinear.com/progenesis/qi/
|
| Lipidomics Workflow Manager |
Sciex |
https://sciex.com/
|
| Mfuzz |
Bioconductor |
https://www.bioconductor.org/packages/release/bioc/html/Mfuzz.html
|
| Ingenuity pathway analysis |
Qiagen |
https://digitalinsights.qiagen.com/productsoverview/discovery-insightsportfolio/analysis-and-visualization/qiagenipa/
|
| igraph |
Bioconductor |
https://cran.rproject.org/web/packages/igraph/index.html
|
| MetaPhlAn |
Segata et al., 2012 |
https://huttenhower.sph.harvard.edu/metaphlan2/
|
