Rewired type I IFN signaling is linked to age-dependent differences in COVID-19

This repository contains datasets that can be used to reproduce the analysis from Petrov. et. al. "Rewired type I IFN signaling is linked to age-dependent differences in COVID-19".Corresponding code and metadata/resources can be found in Mendeley Repository230217_recast_after_qc.rds is a pre-processed (demultiplexed, integrated and after QC) object containing all metadata needed to reproduce the analysis of PBMC scRNAseq experiment. It can be used together with RECAST_analysis.R script for primary clustering, annotation and subsetting into populations of interest.raw (filtered count tables, VDJ contigs and SNP-based donor IDs) PBMC scRNAseq data can be found on GEO under the GSE271284 accession ID. They can be used together with the 230217_Rnapipe.R script to demultiplex, integrate and clean the data, as well as for downstream analysis.20240207_RECAST_REVISION_Monos_and_DCs_FIGSHARE.rar archive contains clean, debarcoded, batch-corrected and pre-gated .fcs files of monocytes and dendritic cells from the whole blood CyTOF experiment to be used together with the respective Cytopipe script.20240207_RECAST_REVISION_CD4_T_Cells_FIGSHARE.rar archive contains clean, debarcoded, batch-corrected and pre-gated .fcs files of CD4+ T cells from the whole blood CyTOF experiment to be used together with the respective Cytopipe script.20240207_RECAST_REVISION_B_Cells_FIGSHARE.rar archive contains clean, debarcoded, batch-corrected and pre-gated .fcs files of B cells from the whole blood CyTOF experiment to be used together with the respective Cytopipe script.WB_CyTOF_DEBARCODED_RAW.rar archive contains clean, debarcoded .fcs files from the whole blood CyTOF experiment before normalization and pre-gating. Samples can be normalized using POPCORN script and pre-gated on population of interest.