Extended Data Fig. 2: Absence of major batch effects in hippocampal snRNA-seq data from 250-day old mice. | Nature Aging

Extended Data Fig. 2: Absence of major batch effects in hippocampal snRNA-seq data from 250-day old mice.

From: Interleukin-12 signaling drives Alzheimer’s disease pathology through disrupting neuronal and oligodendrocyte homeostasis

Extended Data Fig. 2

a. UMAP visualization of three individual biological replicates per genotype, showing mostly equal representations in each cluster. b-d. Entropy-based quantification of batch effects. The distribution of relative entropy values for cells of three individual biological replicates per genotype grouped by sample (original identity) or genotype was greater than randomizing these labels across cells (b). c-d. Different cell types grouped by genotype (c) and sample (d) (original identity); boxplots show: middle, median; lower hinge, 25% quantile; upper hinge, 75% quantile; upper/lower whisker, largest/smallest observation less/greater than or equal to upper/lower hinge ± 1.5 x IQR. Relative entropy per cell type was highest for cell types that differed biologically between genotypes, for example microglia and oligodendrocytes which react most strongly to amyloid and inflammatory conditions. Thus, differences were driven by biological meaningful distinctions rather than technical errors.

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