Single-cell RNA-seq dataset from sorted IL-10+, TCRb+, CD4+ mouse small intestine lamina propria cells in naive or Giardia intestinalis-infected animals at 7 d.p.i. Data analyses and results are described in Sardinha-Silva et al., Nature Microbiology, 2025: "Giardia intestinalis-induced Type 2 mucosal immunity attenuates bystander intestinal inflammation". Data are Seurat objects in RDS format. Filtered-out potential doublets, low quality cells and dying cells (excluded cells with <800 genes detected, cells with >5000 genes detected and cells with mitochondrial gene expression > 10%). Data normalization, scaling and integration performed using Seurat v 4.4.0.Full filtered dataset in the "alineGiardia.combined_v4.rds" file. Related R code is found in "giardia_mouse_integration.R".T cells of interest only in the "T.seurat.rds" file. Related R code is in "TcellSubsets_sc_analysis.R".Dataset was also mapped to a reference dataset by Kiner et al., Nature Immunology, 2021. The post-mapping data is found in the "refmap_kiner.seurat.rds" file. Related R code is in "referenceMapping_Kineretal2021.R".

Single-cell RNA-seq dataset from sorted IL-10+, TCRb+, CD4+ mouse small intestine lamina propria cells in naive or Giardia intestinalis-infected animals at 7 d.p.i. Data analyses and results are described in Alves-Sardinha et al., Nature Microbiology, 2025: "Giardia intestinalis-induced Type 2 mucosal immunity attenuates bystander intestinal inflammation". Data are Seurat objects in RDS format. Filtered-out potential doublets, low quality cells and dying cells (excluded cells with <800 genes detected, cells with >5000 genes detected and cells with mitochondrial gene expression > 10%). Data normalization, scaling and integration performed using Seurat v 4.4.0.Full filtered dataset in the "alineGiardia.combined_v4.rds" file. Related R code is found in "giardia_mouse_integration.R".T cells of interest only in the "T.seurat.rds" file. Related R code is in "TcellSubsets_sc_analysis.R".Dataset was also mapped to a reference dataset by Kiner et al., Nature Immunology, 2021. The post-mapping data is found in the "refmap_kiner.seurat.rds" file. Related R code is in "referenceMapping_Kineretal2021.R".

Single-cell RNA-seq dataset from sorted IL-10+, TCRb+, CD4+ mouse small intestine lamina propria cells in naive or Giardia intestinalis-infected animals at 7 d.p.i. Data analyses and results are described in Sardinha-Silva et al., Nature Microbiology, 2025: "Giardia intestinalis-induced Type 2 mucosal immunity attenuates bystander intestinal inflammation". Data are Seurat objects in RDS format. Filtered-out potential doublets, low quality cells and dying cells (excluded cells with <800 genes detected, cells with >5000 genes detected and cells with mitochondrial gene expression > 10%). Data normalization, scaling and integration performed using Seurat v 4.4.0.Full filtered dataset in the "alineGiardia.combined_v4.rds" file. Related R code is found in "giardia_mouse_integration.R".T cells of interest only in the "T.seurat.rds" file. Related R code is in "TcellSubsets_sc_analysis.R".Dataset was also mapped to a reference dataset by Kiner et al., Nature Immunology, 2021. The post-mapping data is found in the "refmap_kiner.seurat.rds" file. Related R code is in "referenceMapping_Kineretal2021.R".

The human parasitic fluke, Schistosoma haematobium hybridizes with the livestock parasite S. bovis in the laboratory, but the frequency of hybridization in nature is unclear. Here, we analyze 34.6 million single nucleotide variants in 162 samples from 18 African countries, revealing a sharp genetic discontinuity between northern and southern S. haematobium. We find no evidence for recent hybridization. Instead the data reveal admixture events that occurred 257-879 generations ago in northern S. haematobium populations. Fifteen introgressed S. bovis genes are approaching fixation in northern S. haematobium with four genes potentially driving adaptation. Further, we identify 19 regions that are resistant to introgression; these are enriched on the sex chromosomes. These results (i) suggest strong barriers to gene flow between these species, (ii) indicate that hybridization may be less common than currently envisaged, but (iii) reveal profound genomic consequences of rare interspecific hybridization between schistosomes of medical and veterinary importance.

Single-cell RNA-seq dataset from sorted IL-10+, TCRb+, CD4+ mouse small intestine lamina propria cells in naive or Giardia intestinalis-infected animals at 7 d.p.i. Data analyses and results are described in manuscript: "Giardia intestinalis reshapes mucosal immunity toward a Type 2 response that attenuates inflammatory bowel-like diseases". Data are Seurat objects in RDS format. Filtered-out potential doublets, low quality cells and dying cells (excluded cells with <800 genes detected, cells with >5000 genes detected and cells with mitochondrial gene expression > 10%). Data normalization, scaling and integration performed using Seurat v 4.4.0.Full filtered dataset in the "alineGiardia.combined_v4.rds" file.T cells of interest only in the "T.seurat.rds" file.