Extended Data Fig. 1: Landscape of ER remodelling via autophagy during hESC differentiation to iNeurons in vitro.
From: Combinatorial selective ER-phagy remodels the ER during neurogenesis
a, Landscape of the ER proteome and the effect of autophagy on accumulation of individual proteins. The ER proteome (359 proteins, Supplementary Data Table 1) is organized into functional modules and protein attributes (involved in ER membrane curvature, ER-associated, ER-membrane, ER-Lumen or ER-phagy receptor) are indicated by the respective outline box colour (see inset legend). For proteins with transmembrane segments, the number of segments are indicated after the protein name (_1, _2, etc) based on data in Uniprot. The text of each protein name is coloured based on day12 ATG12−/− vs WT Log2FC (see inset legend). (Supplementary Data Table 3). b, Changes in the abundance of the ER proteome (267 detected proteins) during conversion of WT hESCs to iNeurons are shown in as heatmaps (Log2FC) at the indicated day of differentiation relative to hESCs. Data are from our previous analysis of iNeuron differentiation. Annotations of the type of ER protein are indicated by the relevant colours. c, hESCs were differentiated to iNeurons and stained with antibodies against CKAP4 enriched in ER sheets (magenta) and RTN4 enriched in ER-tubules (green) at day 0, 4 and 12 of one differentiation. RTN4 staining is evident throughout neuronal projections. Scale bar, 100 microns in full images, 25 microns in all zooms. d, Violin plots for relative abundance of proteins located in the indicated organelles in ATG12−/− versus WT day 12 iNeurons. e, Immunoblots of cell extracts from WT or ATG12 −/− hESCs for the indicated day of differentiation for one differentiation. Blots were probed with the indicated antibodies, with α-HSP90 employed as a loading control. f, For the immunoblots in e, relative levels of each protein to HSP90 were quantified. Source numerical data and unprocessed blots are available in source data.
