Extended Data Fig. 10. Differential regulation of ER membrane shaping proteins upon loss of ER-phagy receptors.

a, ER lumenal proteins that accumulate with additional ER-phagy receptor knockout. Top panels are β coefficient values and lower panels are Log₂FC; green asterisks in β coefficient for single protein heatmaps indicate significant change (adjusted p-value < 0.05) in β coefficient. b, ER lumenal protein heatmaps reflecting the change in abundance (Log₂FC) for deletion of ATG12 or PKO, reflecting β coefficient values for QKO to PKO, (left panel) or reflecting the change in abundance (Log₂FC) for single deletion of CCPG1 (right panel). c, Experimental scheme for multiplexed total proteome analysis of WT, ATG12^−/− or TEX264^−/−/CCPG1^−/− iNeurons (n = 3) and violin plots for total ER, ER-lumen, and ER-membrane proteins derived from this analysis. Violin plots from a TMT 18-plex experiment comparing WT, ATG12^−/−, and another ER-phagy receptor allelic combination (TEX264^−/− +CCPG1^−/−) with complementary comparisons of Log₂FC (mutant/WT) distributions of ER proteins (top), ER lumenal proteins (middle), or ER membrane proteins (bottom) to distributions of randomized selections of the same number of proteins (100 iterations). p-values for each comparison are calculated with a Kolmogorov–Smirnov Test (two-sided) test. Together these reflect accumulation of the ER, ER lumen and ER membrane for Log2FC (ATG12^−/−/WT) but only the ER lumenal proteome accumulates for Log₂FC (TEX264^−/− +CCPG1^−/− /WT). d, ER contact site protein VAPB accumulates with additional ER-phagy receptor knockout. Plot is annotated as in panel a.