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 The manuscript is accessible in bioRxiv: https://www.biorxiv.org/content/10.1101/2024.01.10.574518v1 . Please cite the preprint and any subsequent journal publications. 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 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 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 subset_velocities_step2.py -> scvelo-based script for processing each subset velocities_step1.R -> Seurat to file-based data velocities_step2.py-> scvelo-based script for processing full dataset revision_velocities_step2.py -> scvelo-based script for processing each subset (now with nice colors)本数据集对应手稿《免疫溶栓性单核细胞-中性粒细胞轴主导人类血栓形成的单细胞图谱》（Immunothrombolytic monocyte-neutrophil axes dominate the single-cell landscape of human thrombosis），该手稿可在bioRxiv平台访问：https://www.biorxiv.org/content/10.1101/2024.01.10.574518v1。请引用该预印本及后续正式期刊发表版本。 ### 已处理的单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）数据 1. `seurat_humancombined_libintSubsetGroups.Rds`：完整处理后的Seurat对象 2. `objGroups_libint_conditions.tsv`：主Seurat整合对象的注释信息 3. `integrated_mouse_thrombus.rds`：小鼠血栓数据集 ### 原始单细胞RNA测序数据 1. `pat1_raw_feature_bc_matrix.h5`：样本21053_0001 2. `pat2_raw_feature_bc_matrix.h5`：样本21053_0003 3. `pat3_raw_feature_bc_matrix.h5`：样本sample_Thr3 4. `pat4_5_raw_feature_bc_matrix.h5`：样本sample_Thr4 5. `pat6_raw_feature_bc_matrix.h5`：样本sample_Thr5 6. `pat7_raw_feature_bc_matrix.h5`：样本samples_ATTHR 7. `mt_raw_feature_bc_matrix.h5`：小鼠原始测序数据 ### 对应上述样本的velocyto剪接/未剪接计数原始数据 1. `pat1_velocyto.loom`：样本21053_0001 2. `pat2_velocyto.loom`：样本21053_0003 3. `pat3_velocyto.loom`：样本sample_Thr3 4. `pat4_5_velocyto.loom`：样本sample_Thr4 5. `pat6_velocyto.loom`：样本sample_Thr5 6. `pat7_velocyto.loom`：样本samples_ATTHR ### 分析脚本 1. `functions.R`：包含辅助工具函数的分析脚本 2. `mt_process.R`：小鼠测序数据处理脚本 3. `process.R`：主数据集处理脚本 4. `process_de_obj.R`：差异表达分析脚本 5. `process_label_transfer.R`：实现人与小鼠数据集间标签转移及后续分析的脚本 6. `process_label_transfer.ipynb`：实现人与小鼠数据集间标签转移及后续分析的交互式脚本 7. `process_monocle.R`：基于Monocle的分析脚本 8. `process_wgcna.R`：基于加权基因共表达网络分析（weighted gene co-expression network analysis, WGCNA）的分析脚本 9. `subset_velocities_step1.R`：将Seurat数据导出为文件格式的脚本 10. `velocities_step1.R`：同`subset_velocities_step1.R` 11. `subset_velocities_step2.py`：基于scvelo的子集数据处理脚本 12. `velocities_step2.py`：基于scvelo的完整数据集处理脚本 13. `revision_velocities_step2.py`：优化配色后的基于scvelo的子集数据处理脚本