Extended Data Fig. 8: Proteomic profiling of postnuclear supernatant (PNS) and Endo-IP from TMEM9^-/- and TMEM9/9B^DKO iNeurons.

a, Volcano plots for PNS (post-nuclear supernatants) proteomic analysis from TMEM9^-/- and two clones of TMEM9/9B^DKO iNeurons (day 21) compared to WT (n = 3 biologically independent replicates). b, Volcano plots for Endo-IP proteomic analysis from TMEM9^-/- and one clone of TMEM9/9B^DKO iNeurons compared to WT (n = 3 biologically independent replicates). c, Immunoblots of input and Endo-IP samples from the experiment outlined in Fig. 4i. Blots were probed with the indicated antibodies. d, Heatmap showing the abundance fold-changes (log₂) for all significantly regulated proteins in Endo-IPs from TMEM9^-/- and TMEM9/9B^DKO iNeurons (day 21) compared to WT. Asterisks indicate significantly regulated proteins (q-value < 0.05 and fold-change > 1.5). Abundance fold-changes in PNS are also indicated, except for proteins not detected (nd).