Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment
Authors/Creators
- 1. Ludwig Maximilians Universität München Lehr und Forschungseinheit Bioinformatik
- 2. Medizinische Klinik und Poliklinik I, University Hospital Ludwig-Maximilians University, Munich, Germany
- 3. DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Germany
Description
When using any of this data, please cite the corresponding manuscript
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 sequencing
sepsis1_velocyto.loom -> velocyto matrices for sepsis1
sepsis2_raw_feature_bc_matrix.h5 -> raw feature barcode matrix for sepsis2 sequencing
sepsis2_velocyto.loom -> velocyto matrices for sepsis2
sepsis_seurat.rds -> processed Seurat object containing original data cells.
Original Data Scripts
process.R -> main analysis script
functions.R -> helper functions for main analysis script
enrichmentAnalysis.R -> script running the enrichment analysis
process_wgcna.R -> script performing the wgcna analysis
velocities_step1.R -> script performing velocity analysis (from seurat to data matrices)
velocities_step2.py -> actual velocity analysis
GSE137539 Re-Analysis
gse137539_processed.Rds -> processed seurat object
gse137539_process.R -> analysis script
Bulk Analysis
MOUSE_SEPTIC_SEPTICACT.inex.DirectDESeq2.xlsx-> Raw UMI counts (intronic+exonic from zUMIs) and DE genes
MOUSE_SEPTIC_SEPTICACT.inex.DirectDESeq2.tsv.GeneOntology.BP.up.gsea.tsv -> Gene Set Enrichment Analysis on up-regulated genes using Gene Ontology Biological Process
Files
Files
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