Extended Data Fig. 9: White matter-associated astrocytes are not well-defined in integrated datasets.

Integration of current study with published astrocyte datasets to visualize white matter-associated astrocytes a, t-SNE projection of 89,420 astrocytes identified by unique astrocyte clusters (top) and original dataset (bottom). b, Dotplot showing genes enriched in white matter-associated astrocytes, split by dataset and cluster. Data: 5xFAD³⁴ (purple), Trem2^-/-/5xFAD³⁵ 7-month (red) and 15-month (yellow), and current study (blue). c, Violin plots of white matter-associated astrocyte transcripts split by dataset and disease. Only data from integrated cluster 7 (that is, integrated white matter-associated astrocyte subpopulation) are visualized. d, t-SNE projection of 100,471 astrocytes identified by unique astrocyte clusters (top) and original dataset (bottom). e, Dotplot showing genes enriched in white matter-associated astrocytes, split by dataset and cluster. Data: EAE from two isolated populations³⁶ - one un-sorted (green) and the other Gfap^TdT-sorted (orange), and current study (blue). f, Violin plots of white matter-associated astrocyte transcripts split by dataset and disease. Only data from integrated cluster 8 (that is, integrated white matter-associated astrocyte subpopulation) are visualized. g, t-SNE projection of 83,684 astrocytes identified by unique astrocyte clusters (top) and original dataset (bottom). h, Dotplot showing genes enriched in white matter-associated astrocytes, split by dataset and cluster. Data: stab wound³⁷ (pink) and current study (blue). i, Violin plots of white matter-associated astrocyte transcripts split by dataset and model. Only data from integrated cluster 5 (that is, integrated white matter-associated astrocyte subpopulation) are visualized. Abbreviations: 5X, 5xFAD; AD, Alzheimer’s disease; B6, C57BL/6 J mice; CNT, control; EAE, experimental autoimmune encephalomyelitis; LPS, lipopolysaccharide; CFA, complete Freund’s adjuvant.