Metadata needed to run some of the scripts in this GitHub repository.
complete_metadata.corrected.csv
This is the main metadata file, which contains all sample annotations as well as personal immune profiles processed in different ways required for different types of analyses (for a clean copy of the personal immune profiles, please visit Zenodo). A brief explanation regarding the metadata column names:
- CM = circulating inflammatory markers
- CYTO = cytokines (the quality of the cytokine data is suffixed as "_good", "_ok", "_poor", "_bad" and "_excluded"; we used only variables with the "_good" quality suffix in the manuscript, but all are provided for completeness)
- PBMC_* = cell type percentages or cell counts in PBMCs
- WB_* = cell type percentages or cell counts in whole blood
- *_PERC = cell type percentages
- *_PER_ML = cell counts (million cells per ml)
- *_SYSMEX_PERC = cell type percentages measured by Sysmex hematology analyzer (XN-450)
- *_SYSMEX_PER_ML = cell counts (million cells per ml) measured by Sysmex hematology analyzer (XN-450)
- thm.* = donor scores ("thm" refers to "top half mean")
- thm.*_V3_FC1.2_responder = binarized (responder vs. non-responder) donor scores using a day-90 (V3) fold-change cut-off of 1.2
- IC_* = value at the time of inoculation (day 0, V1)
- LFC_*, LFC_V2_*, LFC_V3_* = log2 fold-changes, and log2 fold-changes at day 14 (V2) and day 90 (V3), respectively
- CORR_* = corrected (e.g. corrected for sex, age, and blood-draw time)
- V1_CORR_* = corrected only using day 0 values (e.g. corrected for blood-draw time at day 0)
gene_set_libraries
This folder contains the gene/region sets used for enrichment analyses.