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Dataset results
314 results for “Toxoplasma gondii”
RNA sequencing of host transcriptome of human foreskin fibroblast cells infected with Toxoplasma gondii bradyzoites, with and without myr1 (myc regulation 1)
GEO Series GSE125120. Toxoplasma gondii; Homo sapiens. 15 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide binding of the bromdomain protein TgBDP3 in the protozoan parasite Toxoplasma gondii
GEO Series GSE124251. Toxoplasma gondii. 5 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Dynamic Strain- and Stage-specific tRNA Transcription and Codon Usage in divergent Toxoplasma gondii strains
GEO Series GSE86616. Toxoplasma gondii. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
RESTRICTION checkpoint controls bradyzoite development in Toxoplasma gondii
GEO Series GSE200962. Toxoplasma gondii. 16 samples. Type: Expression profiling by high throughput sequencing.
Impaired Chromatin Remodelling at STAT1-Regulated Promoters Leads to Global Unresponsiveness of Toxoplasma gondii-Infected Macrophages to IFN-Gamma
GEO Series GSE28499. Mus musculus. 10 samples. Type: Expression profiling by array.
Alarmin S100A11 initiates a chemokine response to the human pathogen Toxoplasma gondii
GEO Series GSE119835. Homo sapiens. 15 samples. Type: Expression profiling by high throughput sequencing.
seurat objects for : "scDual-Seq of Toxoplasma gondii-infected mouse bone marrow-derived dendritic cells reveals host cell heterogeneity and differential infection dynamics"
<p><strong>Summary</strong></p> <p>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).</p> <p><strong>Data</strong></p> <p>This repository contains two files, one for each organism investigated (mouse and tgondii), in ".RDS" format generated using Seurat v.4.3.: </p> <p><strong>1. BMDC_infected_mouse.RDS </strong>- object containing normalized read counts (SCT assay) and corresponding metadata for murine BMDCs. </p> <p><strong> metadata columns </strong>describe: </p> <p> - orig.ident: <em>plate identity from smartSeq setup</em></p> <p> - nCount_RNA: <em>UMI count before normalization</em></p> <p> - nFeature_RNA: <em>Gene count before normalization</em></p> <p> - nCount_RNA: <em>UMI count before normalization</em></p> <p> - nUMI: <em>sum of reads per cell for both organisms (mouse + t.gondii) </em></p> <p> - toxo_nUMI:<em> sum of reads per cell for t.gondii</em></p> <p> - mouse_nUMI: <em>sum of reads per cell for mouse</em></p> <p> - nGene: <em>sum of reads per cell for both organisms (mouse + t.gondii) </em></p> <p> - toxo_nGene: <em>sum of genes per cell for t.gondii</em></p> <p> - mouse_nGene: <em>sum of genes per cell for mouse</em></p> <p> - cell_ID: <em>enumerated cells by well</em></p> <p> - well:<em> well_ID of plate used for smartSeq2</em></p> <p> - 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></p> <p> - percent.mt: <em>percentage of transcript mapped to the mitochondrial genome</em></p> <p> - cell_ID: <em>enumerated cells by well</em></p> <p> - nFeature_SCT: <em>Gene count after normalization</em></p> <p> - nCount_SCT: <em>UMI count after normalization</em></p> <p> - nFeature_RNA: <em>Gene count before normalization</em></p> <p> - seurat_clusters: <em>Clusters identified by shared-nearest-neighbor (SNN) inspired graph-based clustering </em></p> <p> - toxo_clusters: <em>Clusters of t.gondii dataset of the corresponding infected cell </em></p> <p> - cell type: <em>Annotated subpopulation of infected cells</em></p> <p> - condition_celltype: <em>condition (see above) combined with celltype (see above)</em></p> <p> - cluster_celltype: <em>seurat_clusters (see above) combined with celltype (see above)</em></p> <p> - cluster_condition: <em>seurat_clusters (see above) combined with condition (see above)</em></p> <p> - UMAP_1: <em>Umap embedding coordinates x-axis</em></p> <p> - UMAP_2: <em>Umap embedding coordinates y-axis</em></p> <p> - cell_cycle_phase: <em>predicted cell cycle phase of murine host cells </em></p> <p> - cycle_phase_t.gondii: <em>predicted cycling phase of t.gondii in the corresponding infected host cell </em></p> <p><strong>2. BMDC_infected_tgondii.RDS </strong>- object containing normalized read counts (SCT assay) and corresponding metadata for murine BMDCs. </p> <p><strong> metadata columns </strong>describe: </p> <p> - orig.ident: <em>plate identity from smartSeq setup</em></p> <p> - nCount_RNA: <em>UMI count before normalization</em></p> <p> - nFeature_RNA: <em>Gene count before normalization</em></p> <p> - nCount_RNA: <em>UMI count before normalization</em></p> <p> - nUMI: <em>sum of reads per cell for both organisms (mouse + t.gondii) </em></p> <p> - toxo_nUMI:<em> sum of reads per cell for t.gondii</em></p> <p> - mouse_nUMI: <em>sum of reads per cell for mouse</em></p> <p> - nGene: <em>sum of reads per cell for both organisms (mouse + t.gondii) </em></p> <p> - toxo_nGene: <em>sum of genes per cell for t.gondii</em></p> <p> - mouse_nGene: <em>sum of genes per cell for mouse</em></p> <p> - cell_ID: <em>enumerated cells by well</em></p> <p> - well:<em> well_ID of plate used for smartSeq2</em></p> <p> - 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></p> <p> - percent.mt: <em>percentage of transcript mapped to the mitochondrial genome</em></p> <p> - cell_ID: <em>enumerated cells by well</em></p> <p> - nFeature_SCT: <em>Gene count after normalization</em></p> <p> - nCount_SCT: <em>UMI count after normalization</em></p> <p> - nFeature_RNA: <em>Gene count before normalization</em></p> <p> - seurat_clusters: <em>Clusters identified by shared-nearest-neighbor (SNN) inspired graph-based clustering </em></p> <p> - mouse_clusters: <em>Clusters of mouse dataset of the corresponding infected cell </em></p> <p> - mouse_celltype: <em>Annotated subpopulation if infected cells</em></p> <p> - condition_celltype: <em>condition (see above) combined with mouse_celltype (see above)</em></p> <p> - cluster_celltype: <em>seurat_clusters (see above) combined with mouse_celltype (see above)</em></p> <p> - cluster_condition: <em>seurat_clusters (see above) combined with condition (see above)</em></p> <p> - UMAP_1: <em>Umap embedding coordinates x-axis</em></p> <p> - UMAP_2: <em>Umap embedding coordinates y-axis</em></p> <p> - cell_cycle_phase_mouse: <em>predicted cell cycle phase of murine host cells </em></p> <p> - cycle_phase_t.gondii: <em>predicted cycling phase of t.gondii in the corresponding infected host cell </em></p>
mRNA-seq of immortailized bone marrow derived macrophages (iBMDM) infected with type II Toxoplasma gondii
GEO Series GSE128752. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
AP2XI-3-dependent gene regulation in Toxoplasma gondii tachyzoites (Complementary data)
GEO Series GSE304633. Toxoplasma. 9 samples. Type: Expression profiling by high throughput sequencing.
Toxoplasma gondii RH strain tachyzoites Transcriptome or Gene expression
GEO Series GSE114386. Toxoplasma gondii RH. 2 samples. Type: Expression profiling by high throughput sequencing.
Human retinal Mueller glial cell (HMG) response to Toxoplasma gondii infection
GEO Series GSE145836. Homo sapiens. 36 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Genomic Localization of TgSMC1 in Toxoplasma gondii parasites
GEO Series GSE61806. Toxoplasma gondii; Toxoplasma gondii ME49. 6 samples. Type: Genome binding/occupancy profiling by genome tiling array.
AP2XI-3-dependent gene regulation in Toxoplasma gondii tachyzoites [RNA-seq]
GEO Series GSE285353. Toxoplasma gondii. 6 samples. Type: Expression profiling by high throughput sequencing.
GCN5a is a telomeric lysine acetyltransferase whose loss primes Toxoplasma gondii for latency (RNAseq)
GEO Series GSE286090. Toxoplasma gondii. 12 samples. Type: Expression profiling by high throughput sequencing.
Toxoplasma gondii transcription factor AP2XII-8 is a key regulator for the G1 phase progression and parasite division
GEO Series GSE275112. Toxoplasma gondii. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Profound effect of asparagine-linked glycosylation protein 11 (TgALG11) on genomic expression of Toxoplasma gondii
GEO Series GSE303275. Toxoplasma gondii. 6 samples. Type: Expression profiling by high throughput sequencing.
ATAC-seq Identification of Chromatin Accessibility in Both Human Host Cells and the Parasite Toxoplasma gondii
GEO Series GSE209866. Homo sapiens. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Expression data from cyclohexamide treated Human Foreskin Fibroblasts (HFFs) infected with type I Toxoplasma gondii and stimulated with interferon gamma.
GEO Series GSE34916. Homo sapiens. 8 samples. Type: Expression profiling by array.
Transcriptomics of Toxoplasma gondii sporulating oocysts
GEO Series GSE206344. Toxoplasma gondii. 6 samples. Type: Expression profiling by high throughput sequencing.
Expression data from cells in peritoneal cavity of CD-1 outbred mice infected with different Toxoplasma gondii strains
GEO Series GSE144854. Mus musculus; Mus musculus domesticus. 45 samples. Type: Expression profiling by array.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.