Reanalysis of Tabula Muris, Tabula Senis scRNA-seq: immune-cell subset

The immune-cell subset of the Tabula Muris and Tabula Senis reanalysis (FACS-sorted SmartSeq2 scRNA-seq; mice aged 3, 18 and 24 months), as a SingleCellExperiment R object. It complements the global objects in Zenodo record 18765151 (https://zenodo.org/records/18765151). Files: sce_subset_all_ages_pca_umap.rds: 30,411 cells of all ages from 11 cell ontology classes: B cell, CD4+ and CD8+ alpha-beta T cell, granulocyte, hematopoietic stem cell, macrophage, microglial cell, monocyte, myeloid dendritic cell, neutrophil and NK cell. The object carries the consortium's annotations. MD5SUMS.txt: checksums. Methods: Quantification is as in the global objects: Salmon against GENCODE vM38 transcripts, summed per gene name with tximport. Cells with at least 500 detected genes and 50,000 counts were kept. Expression is log(1 + CPM), natural log; the values equal those of the same cells in the global object. On the subset, highly variable genes were those with a biological variance component above 0.5 (the top 3,000 if fewer than 1,000 pass). These were followed by 50 principal components, a UMAP (10 neighbours, min_dist 0.5; reduced dimension UMAP) and Louvain clustering (k = 20), giving 12 clusters. The random seed was 42. Pipeline code: https://github.com/ericmalekos/scRNAseq. Gene-by-gene browser: https://github.com/ericmalekos/single-cell-gene-browser.