Immunothrombolytic monocyte-neutrophil axes dominate the single-cell landscape of human thrombosis

Original Data for the manuscript: Immunothrombolytic monocyte-neutrophil axes dominate the single-cell landscape of human thrombosis and correlate with thrombus resolution The manuscript is accessible at https://doi.org/10.1016/j.immuni.2025.03.020 . Please cite the journal publication when using any of this data. Processed scRNA-seq data seurat_humancombined_libintSubsetGroups.Rds -> fully processed Seurat objects objGroups_libint_conditions.tsv -> annotations for main Seurat object integrated_mouse_thrombus.rds -> mouse thrombus dataset arb_obj_integrated.Rds -> ARB Thrombus (Artificial thrombus, Real Thrombus, Blood) Seurat object Original Data (scRNA-seq) pat1_raw_feature_bc_matrix.h5 -> Sample 21053_0001 pat2_raw_feature_bc_matrix.h5 -> Sample 21053_0003 pat3_raw_feature_bc_matrix.h5 -> Sample sample_Thr3 pat4_5_raw_feature_bc_matrix.h5 -> Sample sample_Thr4 pat6_raw_feature_bc_matrix.h5 -> Sample sample_Thr5 pat7_raw_feature_bc_matrix.h5 -> Sample samples_ATTHR mt_raw_feature_bc_matrix.h5 -> Mouse arb_raw_feature_bc_matrix.h5 -> ARB Thrombus (Artificial thrombus, Real Thrombus, Blood) Original Data (bulk) coagulation_classical_counts.tsv coagulation_nonclassical_counts.tsv hypoxia_classical_counts.tsv hypoxia_nonclassical_counts.tsv monocytes_blood_thrombus_counts.tsv neutrophils_blood_thrombus_counts.tsv Original Data (spliced/unspliced by velocyto; matching above sample names): pat1_velocyto.loom -> Sample 21053_0001 pat2_velocyto.loom -> Sample 21053_0003 pat3_velocyto.loom -> Sample sample_Thr3 pat4_5_velocyto.loom -> Sample sample_Thr4 pat6_velocyto.loom -> Sample sample_Thr5 pat7_velocyto.loom -> Sample samples_ATTHR Scripts: functions.R -> script with helper utilities mt_process.R -> script for processing the mouse data process.R -> script for processing the main data set process_de_obj.R -> script for performing DE analysis process_label_transfer.R -> script for doing label transfer between human and mouse dataset and further analyses process_label_transfer.ipynb -> script for doing label transfer between human and mouse dataset and further analyses process_monocle.R -> script for doing monocle-based analyses process_wgcna.R -> script for doing wgcna-based analyses subset_velocities_step1.R -> Seurat to file-based data 2_velocities_monos.py-> Mono-subset velocity analysis 2_velocities_neutros.py -> Neutro-subset velocity analysis analysis_arb_process.ipynb -> Seurat processing of ARB Thrombus