Fig. 3

RNA-seq analysis of compartmentalized Tdp-43 knockdown motoneurons. a Bar graphs showing Tdp-43 levels in Tdp-43 knockdown (shTdp-43) and control motoneurons transduced with empty lentiviral expression vector. Transcript levels were measured as FPKM values by RNA-seq analysis and by qPCR. Data represent mean ± SD. ****p ≤ 0.0001; unpaired t-test. b Scatter plots of somatodendritic and axonal transcript FPKM values following differential expression analysis of Tdp-43 knockdown motoneurons compared to controls. Transcripts significantly (p < 0.05) dysregulated in Tdp-43 knockdown motoneurons are colour-coded as red for upregulated and as blue for downregulated transcripts. c Venn diagram presenting the overlap of transcripts dysregulated in the somatodendritic and axonal compartment of Tdp-43 knockdown motoneurons. d Scatter plot depicting the logarithmized fold changes of the 96 transcripts altered in both the somatodendritic and axonal compartment of Tdp-43 knockdown motoneurons relative to controls. eNefl, Tubb2a and Tuba1b transcript levels in axons of Tdp-43 knockdown and control motoneurons measured by RNA-seq (as FPKM values) and qPCR. Data represent mean ± SD