Seurat objects relative to the single-cell RNA sequencing analysis of the study "4-1BB immunotherapy reveals the Eomes dependency of exhausted CD4+ T cell lineage maintenance and function in anti-tumor immunity" by Arantxa Agesta and co-authors."

merged_clusterd_seurat_without_Tregs_with_TcR_info.rds: this seurat v5 object contains mouse CD4 CD44hi T cells sorted from the spleen of mice harbouring myeloma-like tumors (Vk*myc) and treated with an agonistic anti-41bb antibody, or isotype control. Mice are wild-type C57BL/6 or genetically engineered to lack the expression of Eomes either constitutively or upon induction with tamoxifen. Further experimental details are described in the associated manuscript, as well as in the associated github code. This object is the starting point of the script 41bb_Eomes_CD4_analysis_mouse_public.Rmd. The object merged_clusterd_seurat_without_Tregs_Tex_only_TcR_info.rds is a subset of the previous object and also needs to be imported to perform the analysis carried out in the github script 41bb_Eomes_CD4_analysis_mouse_public.Rmd. The objects melanoma_patients_Blood_CD4_seurat_object.rds and melanoma_patients_TIL_CD4_seurat_object.rds contain human CD4 T cells from blood and tumor of patients with advanced melanoma. These data have already been published in the papers "Circulating clonally expanded T cells reflect functions of tumor-infiltrating T cells" by Lucca et al, 2021 (DOI: 10.1084/jem.20200921) and "Circulating tumor-reactive KIR+CD8+ T cells suppress anti-tumor immunity in patients with melanoma" by Lu et al., 2025 (DOI: 10.1038/s41590-024-02023-4). The raw data has already been deposited in dbGaP, under the accession numbers phs002289 and phs002289.v2.p1