Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment

When using any of this data, please cite the corresponding manuscript

Rainer Kaiser et al., Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment. Sci. Adv. 10, eadl1710 (2024). DOI:10.1126/sciadv.adl1710

Original Data

The following files contain all count data for the original data of this manuscript:

sepsis1_raw_feature_bc_matrix.h5 -> raw feature barcode matrix for sepsis1 sequencingsepsis1_velocyto.loom -> velocyto matrices for sepsis1sepsis2_raw_feature_bc_matrix.h5 -> raw feature barcode matrix for sepsis2 sequencingsepsis2_velocyto.loom -> velocyto matrices for sepsis2

sepsis_seurat.rds -> processed Seurat object containing original data cells. (Upd.: the meta.data-column "cellnames" contains the cell type annotation given in Figure 1B)

Original Data Scripts

process.R -> main analysis scriptfunctions.R -> helper functions for main analysis scriptenrichmentAnalysis.R -> script running the enrichment analysisprocess_wgcna.R -> script performing the wgcna analysisvelocities_step1.R -> script performing velocity analysis (from seurat to data matrices)velocities_step2.py -> actual velocity analysisGSE137539 Re-Analysis

gse137539_processed.Rds -> processed seurat objectgse137539_process.R -> analysis script

Bulk Analysis

MOUSE_SEPTIC_SEPTICACT.inex.DirectDESeq2.xlsx-> Raw UMI counts (intronic+exonic from zUMIs) and DE genesMOUSE_SEPTIC_SEPTICACT.inex.DirectDESeq2.tsv.GeneOntology.BP.up.gsea.tsv -> Gene Set Enrichment Analysis on up-regulated genes using Gene Ontology Biological Process