DOI: 10.5281/zenodo.7529483
title: seurat objects for : "scDual-Seq of Toxoplasma gondii-infected mouse bone marrow-derived dendritic cells reveals host cell heterogeneity and differential infection dynamics"

description: <strong>Summary</strong> Here, we utilize Dual-scSeq to parse out heterogeneous transcription of bone marrow-derived dendritic cells (BMDCs) infected with T. gondii type I, RH (LDM) or type II, ME49 (PTG) parasites, over multiple time points post-infection (3 and 12h post-infection). <strong>Data</strong> This repository contains two files, one for each organism investigated (mouse and tgondii), in ".RDS" format generated using Seurat v.4.3.: <strong>1. BMDC_infected_mouse.RDS </strong>- object containing normalized read counts (SCT assay) and corresponding metadata for murine BMDCs. <strong> metadata columns </strong>describe: - orig.ident: <em>plate identity from smartSeq setup</em> - nCount_RNA: <em>UMI count before normalization</em> - nFeature_RNA: <em>Gene count before normalization</em> - nCount_RNA: <em>UMI count before normalization</em> - nUMI: <em>sum of reads per cell for both organisms (mouse + t.gondii) </em> - toxo_nUMI:<em> sum of reads per cell for t.gondii</em> - mouse_nUMI: <em>sum of reads per cell for mouse</em> - nGene: <em>sum of reads per cell for both organisms (mouse + t.gondii) </em> - toxo_nGene: <em>sum of genes per cell for t.gondii</em> - mouse_nGene: <em>sum of genes per cell for mouse</em> - cell_ID: <em>enumerated cells by well</em> - well:<em> well_ID of plate used for smartSeq2</em> - condition: <em>treatment of cell (one of 8: LDM infection for 3h, LDM infection for 12h, PTG infection for 3h, PTG infection for 12h, LDM Lysate control, PTG Lysate control, uninfected control or LPS control)</em> - percent.mt: <em>percentage of transcript mapped to the mitochondrial genome</em> - cell_ID: <em>enumerated cells by well</em> - nFeature_SCT: <em>Gene count after normalization</em> - nCount_SCT: <em>UMI count after normalization</em> - nFeature_RNA: <em>Gene count before normalization</em> - seurat_clusters: <em>Clusters identified by shared-nearest-neighbor (SNN) inspired graph-based clustering </em> - toxo_clusters: <em>Clusters of t.gondii dataset of the corresponding infected cell </em> - cell type: <em>Annotated subpopulation of infected cells</em> - condition_celltype: <em>condition (see above) combined with celltype (see above)</em> - cluster_celltype: <em>seurat_clusters (see above) combined with celltype (see above)</em> - cluster_condition: <em>seurat_clusters (see above) combined with condition (see above)</em> - UMAP_1: <em>Umap embedding coordinates x-axis</em> - UMAP_2: <em>Umap embedding coordinates y-axis</em> - cell_cycle_phase: <em>predicted cell cycle phase of murine host cells </em> - cycle_phase_t.gondii: <em>predicted cycling phase of t.gondii in the corresponding infected host cell </em> <strong>2. BMDC_infected_tgondii.RDS </strong>- object containing normalized read counts (SCT assay) and corresponding metadata for murine BMDCs. <strong> metadata columns </strong>describe: - orig.ident: <em>plate identity from smartSeq setup</em> - nCount_RNA: <em>UMI count before normalization</em> - nFeature_RNA: <em>Gene count before normalization</em> - nCount_RNA: <em>UMI count before normalization</em> - nUMI: <em>sum of reads per cell for both organisms (mouse + t.gondii) </em> - toxo_nUMI:<em> sum of reads per cell for t.gondii</em> - mouse_nUMI: <em>sum of reads per cell for mouse</em> - nGene: <em>sum of reads per cell for both organisms (mouse + t.gondii) </em> - toxo_nGene: <em>sum of genes per cell for t.gondii</em> - mouse_nGene: <em>sum of genes per cell for mouse</em> - cell_ID: <em>enumerated cells by well</em> - well:<em> well_ID of plate used for smartSeq2</em> - condition: <em>treatment of cell (one of 8: LDM infection for 3h, LDM infection for 12h, PTG infection for 3h, PTG infection for 12h, LDM Lysate control, PTG Lysate control, uninfected control or LPS control)</em> - percent.mt: <em>percentage of transcript mapped to the mitochondrial genome</em> - cell_ID: <em>enumerated cells by well</em> - nFeature_SCT: <em>Gene count after normalization</em> - nCount_SCT: <em>UMI count after normalization</em> - nFeature_RNA: <em>Gene count before normalization</em> - seurat_clusters: <em>Clusters identified by shared-nearest-neighbor (SNN) inspired graph-based clustering </em> - mouse_clusters: <em>Clusters of mouse dataset of the corresponding infected cell </em> - mouse_celltype: <em>Annotated subpopulation if infected cells</em> - condition_celltype: <em>condition (see above) combined with mouse_celltype (see above)</em> - cluster_celltype: <em>seurat_clusters (see above) combined with mouse_celltype (see above)</em> - cluster_condition: <em>seurat_clusters (see above) combined with condition (see above)</em> - UMAP_1: <em>Umap embedding coordinates x-axis</em> - UMAP_2: <em>Umap embedding coordinates y-axis</em> - cell_cycle_phase_mouse: <em>predicted cell cycle phase of murine host cells </em> - cycle_phase_t.gondii: <em>predicted cycling phase of t.gondii in the corresponding infected host cell </em>