Fig. 2: Culture batch and inter-individual variation contribute to the total variance.

A Schematic overview of the study, indicating sources of variation: inter-individual variation (i.e., variation introduced by including different individuals; orange box) and culture batch variation (i.e., variation introduced by acquiring data from different culture batches; purple box). Note that for this study, five iPSC-derived lines were used for morphological characterization, four lines for electrophysiology, and three lines for proteomic analyses. For the proteomics analysis, neurons were either cultured on a glia feeder layer (‘co-culture’) or on coating without glia (‘neuron-only’). B The contribution of different sources of variance is assessed by plotting the proportion of variance explained by culture batch (purple) and line (orange) for each parameter, as calculated following Nakagawa 2017 [17] for details, see Supplementary Methods). Values per parameter are included in Supplementary Table 2. Together, the variance contributed by line and culture batch accounted for a median of 10% (IQR: 6.0–21%) of total variance. C The explained variance calculated for all proteins in the proteomics dataset from neuron-glia co-cultures (top violin plot) and neuron-only cultures (bottom violin plot). For co-cultures, median variance explained by culture batch is 14.8% and for line 9.4%. For neuron-only cultures, the median variance explained by culture batch is 5.5% and 34.3% for line.