scRNA-Seq datasets from/with the Otto lab

This collection contains seven annotated single-cell RNA-seq datasets (h5ad format) spanning host-parasite interactions across multiple host and parasite species. Datasets cover Plasmodium berghei, Toxoplasma gondii, Theileria annulata, Trypanosoma brucei, and parasitic nematode infection, alongside clinical malaria PBMCs and γδ T cell biology. All datasets are compatible with the paraCell framework for host-parasite single-cell analysis and are browsable via CellxGene. Full dataset descriptions and interactive visualisations are available at https://www.bnitm.de/forschung/forschungsgruppen/data-science-center/abteilung-digitale-infektionsbiologie/datasets.

1. GD_tcell_PMC7486781.h5ad Role of β2-integrins (CD18) in γδ T cell subset thymic development and peripheral maintenance. PNAS 2020. DOI: 10.1073/pnas.1921930117

2. PBMC.Pediatric.Malaria.Ghana_PMC11738629.h5ad scRNA-seq of PBMCs from Ghanaian children with uncomplicated malaria. Reveals elevated interferon responses and TNF-α/NFκB signalling in monocytes. Experimental Biology and Medicine 2025. DOI: 10.3389/ebm.2024.10233

3. Plasmodium_berghei_Mouse_Blood_BoneMarrow_Spleen_PMC9045723.h5ad Plasmodium berghei differentiation in erythropoietic niches of the bone marrow and spleen. Host cell maturation modulates parasite invasion and sexual differentiation. PLOS Biology 2022. DOI: 10.1371/journal.pbio.3001522

4. Theileria_annulata-Bos_indicus_taurus_macrophage_PMC11840555.h5ad First dual host–parasite scRNA-seq atlas of Theileria annulata-infected bovine macrophages, comparing disease-susceptible Holstein (Bos taurus) and disease-tolerant Sahiwal (Bos indicus) breeds. Reveals an active interferon response in tolerant Sahiwal cells versus a pro-carcinogenic gene signature in susceptible Holstein cells. Nucleic Acids Research 2025. DOI: 10.1093/nar/gkaf091

5. Toxoplasma_gondii-murine.bone.marrow.derived.macrophages_PMC11840555.h5ad Dual host–parasite scRNA-seq atlas of Toxoplasma gondii-infected murine bone marrow-derived macrophages (BMDMs), with and without IFN-γ stimulation. Identifies Atp6v0d2 and Ccl8 as novel markers of infected macrophages. Nucleic Acids Research 2025. DOI: 10.1093/nar/gkaf091

6. Trypanosoma_brucei-slender2stumpy_PMC8421343.h5ad Single-cell transcriptomics of bloodstream Trypanosoma brucei reconstructing cell cycle progression and developmental quorum sensing. Nature Communications 2021. DOI: 10.1038/s41467-021-25607-2

7. TuffCells_Ovine.PMC8646091.h5ad Single-cell atlas of sheep abomasal epithelium following parasitic nematode infection. Shows tuft cell expansion and identifies evolutionarily conserved and divergent host responses. Frontiers in Immunology 2021. DOI: 10.3389/fimmu.2021.781108

Keywords: single-cell RNA-seq, host-parasite interactions, Plasmodium, Toxoplasma, Theileria, Trypanosoma, malaria, scRNA-seq, paraCell, infectious disease