Extended Data Fig. 3. TDP-43 does not interact with stress granule proteins in transdifferentiated neurons.

a–c, Confocal fluorescence images of the splicing proteins in the indicated cell types. Scale bar = 10 μm. d, Left, confocal fluorescence images of the indicated splicing proteins in the Tdiff.Y1 neuron line; Scale bar = 10 μm. Right, quantification of the nuclear fraction (n = 3 replicates) of TdiffY.1 versus Tdiff.1 (reproduced from Fig. 2a) for the indicated spliceosome protein. The box plot represents the 25th to 75th percentile of all values, the centerline denotes the median and the error bars represent the range of all values. Statistics were calculated using a two-tailed Welch’s t test. e, Airyscan fluorescence images of TDP-43 in transdifferentiated neurons. White scale bar = 10 μm; yellow scale bar = 2 μm. f, Airyscan fluorescence images of TDP-43 and G3BP1 in iPSC-derived neurons treated with arsenite for 1 h. White scale bar = 10 μm; yellow scale bar = 2 μm. g, Scatter plot of TDP-43 pulldown fold change plotted with the proteomic fold change for each detected protein (n = 2 replicates). P values were detected using a two-tailed Welch’s t test. h, Volcano plot of all detected proteins identified by TDP-43 pulldown and mass spectroscopy for Tdiff.1 neurons versus iPSC-diff.1 neurons (n = 2 replicates) treated with sodium arsenite for 1 h. P values were calculated using a two-tailed Welch’s t test. Detected proteins were highlighted as in g. i, Same as h, but for unstressed and stressed iPSC-diff.1 neurons. j, Scatter plot of the TDP-43 pulldown fold change for spliceosome (dark blue) and stress granule (orange) proteins in Tdiff.1 neurons compared to unstressed and stressed iPSC-diff.1 neurons (n = 2 replicates). k, Venn diagram of which stress granule proteins were detected in any replicate of the indicated neuron TDP-43 pulldown (n = 2 replicates). l, Raw mass spectrometry values of two core stress granules (G3BP2 and CAPRIN1) detected by TDP-43 pulldown.