Cytokine responses in the mouse Immune Dictionary and the human Cytokine Dictionary: counts, pseudobulks and edgeR results

Reprocessed data and differential expression (DE) results for two cytokine atlases. The mouse Immune Dictionary (Cui et al., Nature 2024, https://doi.org/10.1038/s41586-023-06816-9; GEO GSE202186) profiles lymph-node cells after in vivo injection of 86 cytokines or PBS. The human Cytokine Dictionary is the Parse Biosciences 10 Million Human PBMCs dataset (Oesinghaus et al., bioRxiv 2025, https://doi.org/10.64898/2025.12.12.693897), with 12 donors, 90 cytokines and PBS. The data accompany a manuscript in preparation. Mouse files: immdict_mouse_cellbender_counts.h5ad: 309,036 cells x 78,348 genes, CellBender-corrected UMI counts. Reads were aligned with STARsolo (STAR 2.7.11b) to GRCm39 with GENCODE vM39; hashtags were demultiplexed with hashsolo; ambient RNA was removed with CellBender 0.3.2; doublets were removed with scDblFinder. Cells carry the authors' 25 cell-type labels (SCP2554). mouse_pseudobulk.tar: the pseudobulks. mouse_edgeR.tar: edgeR quasi-likelihood results (~ batch + cytokine, PBS reference) for every tested gene x cytokine in 12 cell types. Human files: human_pseudobulk_all.h5: (donor x cytokine x cell type) pseudobulks for all 40,352 genes, with expressing-cell counts. human_pseudobulk.tar: the per-cell-type edgeR inputs. human_edgeR.tar: edgeR results (~ donor + cytokine) for every tested gene x cytokine in 18 cell types, ERV panel results and ERVH48-1 repeat fits. Shared files: figure_source_tables.tar: percent-expressing and detection tables. ligand_name_map.tsv and celltype_lineage_map.tsv: maps for joining the two species. README.md describes every file, the cell selection, the DE models, multiple testing and numeric precision. MD5SUMS.txt lists checksums. Licence of the human files: they are derived from the Parse Biosciences dataset, which is distributed under CC BY-NC 4.0. Reuse of human_pseudobulk_all.h5, human_pseudobulk.tar, human_edgeR.tar and human_pct_cells.tsv (in figure_source_tables.tar) is subject to that licence's non-commercial term. These results can be browsed gene by gene in the single-cell gene browser (https://github.com/ericmalekos/single-cell-gene-browser).