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seurat objects for : "scDual-Seq of Toxoplasma gondii-infected mouse bone marrow-derived dendritic cells reveals host cell heterogeneity and differential infection dynamics"

Summary 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). Data This repository contains two files, one for each organism investigated (mouse and tgondii),  in ".RDS" format generated using Seurat v.4.3.:  1. BMDC_infected_mouse.RDS - object containing normalized read counts (SCT assay) and corresponding metadata for murine BMDCs.     metadata columns describe:          - orig.ident: plate identity from smartSeq setup         - nCount_RNA: UMI count before normalization         - nFeature_RNA: Gene count before normalization         - nCount_RNA: UMI count before normalization         - nUMI: sum of reads per cell for both organisms (mouse + t.gondii)          - toxo_nUMI: sum of reads per cell for t.gondii         - mouse_nUMI: sum of reads per cell for mouse         - nGene: sum of reads per cell for both organisms (mouse + t.gondii)          - toxo_nGene: sum of genes per cell for t.gondii         - mouse_nGene: sum of genes per cell for mouse         - cell_ID: enumerated cells by well         - well: well_ID of plate used for smartSeq2         - condition: 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)         - percent.mt: percentage of transcript mapped to the mitochondrial genome         - cell_ID: enumerated cells by well         - nFeature_SCT: Gene count after normalization         - nCount_SCT: UMI count after normalization         - nFeature_RNA: Gene count before normalization         - seurat_clusters:  Clusters identified by shared-nearest-neighbor (SNN) inspired graph-based clustering          - toxo_clusters:  Clusters of t.gondii dataset of the corresponding infected cell          - cell type: Annotated subpopulation of infected cells         - condition_celltype: condition (see above) combined with celltype (see above)         - cluster_celltype: seurat_clusters (see above) combined with celltype (see above)         - cluster_condition: seurat_clusters (see above) combined with condition (see above)         - UMAP_1: Umap embedding coordinates x-axis         - UMAP_2: Umap embedding coordinates y-axis         - cell_cycle_phase: predicted cell cycle phase of murine host cells          - cycle_phase_t.gondii: predicted cycling phase of t.gondii in the corresponding infected host cell  2. BMDC_infected_tgondii.RDS - object containing normalized read counts (SCT assay) and corresponding metadata for murine BMDCs.     metadata columns describe:          - orig.ident: plate identity from smartSeq setup         - nCount_RNA: UMI count before normalization         - nFeature_RNA: Gene count before normalization         - nCount_RNA: UMI count before normalization         - nUMI: sum of reads per cell for both organisms (mouse + t.gondii)          - toxo_nUMI: sum of reads per cell for t.gondii         - mouse_nUMI: sum of reads per cell for mouse         - nGene: sum of reads per cell for both organisms (mouse + t.gondii)          - toxo_nGene: sum of genes per cell for t.gondii         - mouse_nGene: sum of genes per cell for mouse         - cell_ID: enumerated cells by well         - well: well_ID of plate used for smartSeq2         - condition: 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)         - percent.mt: percentage of transcript mapped to the mitochondrial genome         - cell_ID: enumerated cells by well         - nFeature_SCT: Gene count after normalization         - nCount_SCT: UMI count after normalization         - nFeature_RNA: Gene count before normalization         - seurat_clusters:  Clusters identified by shared-nearest-neighbor (SNN) inspired graph-based clustering          - mouse_clusters:  Clusters of mouse dataset of the corresponding infected cell          - mouse_celltype: Annotated subpopulation if infected cells         - condition_celltype: condition (see above) combined with mouse_celltype (see above)         - cluster_celltype: seurat_clusters (see above) combined with mouse_celltype (see above)         - cluster_condition: seurat_clusters (see above) combined with condition (see above)         - UMAP_1: Umap embedding coordinates x-axis         - UMAP_2: Umap embedding coordinates y-axis         - cell_cycle_phase_mouse: predicted cell cycle phase of murine host cells          - cycle_phase_t.gondii: predicted cycling phase of t.gondii in the corresponding infected host cell

ShareScore

16/100

Overall dataset sharing score

Score breakdown

These five areas show where the dataset supports — or may limit — practical reuse.

Stewardship: 8
Harmonization: 4
Access: 0
Reuse readiness: 0
Engagement: 4

Topics

scDual-Seq, Toxoplasma. bone marrow-derived dendritic cells, BMDCs, heterogeneity, RH, ME49