Extended Data Fig. 7: Extended lipidomics analysis of reactive human iAstrocytes.

a) Volcano plots of lipid species changed in reactive vs control iAstrocytes in independent replicate experiments in Kolf2.1J set #1 ApoE3/3 and BIONi037 ApoE3/3. b) Bar graphs of lipid class levels in reactive and control iAstrocytes from all datasets presented in Fig. 5c. N=6, three independent experiments from two ApoE3 lines, Mean + sd. c) Relative levels of cholesterol in the medium in control vs reactive iAstrocytes (ApoE3). N=4, two independent experiments from two ApoE3 lines, Mean *P<0.05 one sample t-test. (Kolf2.1J set #1). d) Fold change of cholesterol ester (left panel) or triacylglyceride (right panel) species with indicated number of double bonds in reactive vs control iAstrocytes (ApoE3). All experiments presented in Fig. 5c are included here. Mean. e) Summary data of changes in all detected lipid classes in reactive vs control iAstrocytes from the Kampmann lab (WTC11 iPSC line, ApoE3/3 cultured in 2% FBS). n=3 wells per condition. f-g) Fold change of phospholipid (f) or triacylglyceride (g) species with indicated number of double bonds in reactive vs control iAstrocytes (WTC11, ApoE3). n=3 wells per condition. h) Summary data of changes in all detected lipid classes in reactive vs control iAstrocytes (ApoE4). N=4, two independent experiments from two ApoE4 lines. (Kolf2.1J set #1). i) Fold change of phospholipid, triacylglyceride or cholesterol ester species with indicated number of double bonds in reactive vs control iAstrocytes (ApoE4). All experiments presented in H are included here. Mean. j) Relative membrane MHC I levels (stained for anti-HLA-A,B,C) by flow cytometry in reactive vs control iAstrocytes (ApoE4). N=7, three or four independent experiments from two ApoE4 lines, Mean ****p<0.0001 one sample t-test. (Kolf2.1J set #1). In all panels open triangles or circles indicate mean per experiment, while solid dots represent all independent wells.