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

<p><strong>When using any of this data, please cite the corresponding manuscript</strong></p> <div> <div> <p><a title="Rainer Kaiser&nbsp;et al.,&nbsp;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" href="https://doi.org/10.1126/sciadv.adl1710">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</a></p> </div> </div> <p><strong>Original Data</strong></p> <p>The following files contain all count data for the original data of this manuscript:</p> <p>sepsis1_raw_feature_bc_matrix.h5 -&gt; raw feature barcode matrix for sepsis1 sequencing<br>sepsis1_velocyto.loom -&gt; velocyto matrices for sepsis1<br>sepsis2_raw_feature_bc_matrix.h5 -&gt; raw feature barcode matrix for sepsis2 sequencing<br>sepsis2_velocyto.loom -&gt; velocyto matrices for sepsis2</p> <p>sepsis_seurat.rds -&gt; processed Seurat object containing original data cells. (Upd.: the meta.data-column "cellnames" contains the cell type annotation given in Figure 1B)</p> <p><strong>Original Data Scripts</strong></p> <p>process.R -&gt; main analysis script<br>functions.R -&gt; helper functions for main analysis script<br>enrichmentAnalysis.R -&gt; script running the enrichment analysis<br>process_wgcna.R -&gt; script performing the wgcna analysis<br>velocities_step1.R -&gt; script performing velocity analysis (from seurat to data matrices)<br>velocities_step2.py -&gt; actual velocity analysis<br><br><strong>GSE137539 Re-Analysis</strong></p> <p>gse137539_processed.Rds -&gt; processed seurat object<br>gse137539_process.R -&gt; analysis script</p> <p><strong>Bulk Analysis</strong></p> <p>MOUSE_SEPTIC_SEPTICACT.inex.DirectDESeq2.xlsx-&gt; Raw UMI counts (intronic+exonic from zUMIs) and DE genes<br>MOUSE_SEPTIC_SEPTICACT.inex.DirectDESeq2.tsv.GeneOntology.BP.up.gsea.tsv -&gt; Gene Set Enrichment Analysis on up-regulated genes using Gene Ontology Biological Process</p>