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183
datasets available to search
ShareScore release 0.9.0
Dataset results
183 results for “infection dynamics”
Dynamics of Human and Viral RNA Methylation during ZIKA Virus Infection
GEO Series GSE87516. Zika virus; Homo sapiens. 18 samples. Type: Other.
Dynamic Innate Immune Responses of Human Bronchial Epithelial Cells against SARS-CoV and DOHV infection
GEO Series GSE17400. Homo sapiens. 27 samples. Type: Expression profiling by array.
Chronic CD4+ T cell Activation & Depletion in HIV-1 Infection: Type I Interferon-Mediated Disruption of T Cell Dynamics
GEO Series GSE9927. Homo sapiens. 20 samples. Type: Expression profiling by array.
Dynamic transcriptome profiling of mouse spleen infected with extraintestinal pathogenic Escherichia coli
GEO Series GSE140637. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Multi-omics evaluation of SARS-CoV-2 infected mouse lungs reveals dynamics of host responses
GEO Series GSE196488. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
Systems biological assessment of the temporal dynamics of immunity to a viral infection in the first weeks and months of life
GEO Series GSE239787. Homo sapiens. 90 samples. Type: Expression profiling by high throughput sequencing.
Dynamic 3D Genome and Epigenetic Landscapes of Macrophage Cells Reprogramming Gene Expression during Differentiation and Infection
GEO Series GSE143984. Homo sapiens. 30 samples. Type: Other; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Transcriptome dynamics of mutualistic poxvirus infection of tropical fruit fly hosts
GEO Series GSE228918. Ceratitis capitata; Bactrocera dorsalis; Zeugodacus cucurbitae. 81 samples. Type: Expression profiling by high throughput sequencing.
Essentiality and dynamic expression of the human tRNA pool during viral infection [HCMVinfection_tRNAseq]
GEO Series GSE308475. Homo sapiens. 21 samples. Type: Other.
Essentiality and dynamic expression of the human tRNA pool during viral infection [SARSinfection_tRNAseq]
GEO Series GSE308476. Homo sapiens. 4 samples. Type: Other.
Dynamic 3D Genome and Epigenetic Landscapes of Macrophage Cells Reprogramming Gene Expression during Differentiation and Infection (RNA-Seq)
GEO Series GSE143982. Homo sapiens. 6 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>
Dynamic 3D Genome and Epigenetic Landscapes of Macrophage Cells Reprogramming Gene Expression during Differentiation and Infection (DLO Hi-C)
GEO Series GSE143980. Homo sapiens. 3 samples. Type: Other.
Essentiality and dynamic expression of the human tRNA pool during viral infection [CRISPRlib]
GEO Series GSE308477. Homo sapiens. 18 samples. Type: Other.
Essentiality and dynamic expression of the human tRNA pool during viral infection [IndividualKO_tRNAseq]
GEO Series GSE308057. Homo sapiens. 9 samples. Type: Other.
Dynamic 3D Genome and Epigenetic Landscapes of Macrophage Cells Reprogramming Gene Expression during Differentiation and Infection (ATAC-Seq)
GEO Series GSE143983. Homo sapiens. 3 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Dynamic 3D Genome and Epigenetic Landscapes of Macrophage Cells Reprogramming Gene Expression during Differentiation and Infection (ChIP-Seq)
GEO Series GSE143981. Homo sapiens. 18 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Sirtuin 1-chromatin-binding dynamics point to a common mechanism regulating microglial inflammatory targets in SIV infection and in the aging brain
GEO Series GSE95793. Macaca mulatta. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Dynamic equilibrium of lung Trm dictates waning immunity after IAV infection
GEO Series GSE86973. Mus musculus. 10 samples. Type: Expression profiling by array.
Transcriptomic Dynamics of Human Macrophage Response to Leishmania major infection
GEO Series GSE43661. Homo sapiens. 27 samples. Type: Expression profiling by array.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.