RNA - seq analysis of compartmentalized Smn-deficient motoneurons. (A) Values of fragments per kilobase of transcript per million mapped reads (FPKM) measured by RNA-seq of the somatodendritic compartment of GFP controls and Smn knockdown motoneurons (n = 4/6, Two-tailed unpaired t test, ***P ≤ 0.001). Data are presented as mean ± SD. (B) Scatter plots of logarithmized FPKM values derived from cuffdiff analysis of Smn knockdown versus GFP-expressing control motoneurons within the somatodendritic and axonal compartment. Red dots represent significantly (P ≤ 0.05) upregulated transcripts while blue marked genes are significantly (P ≤ 0.05) downregulated. (C) Venn diagram of genes down- and upregulated in the somatodendritic and the axonal compartment with an intersection of 132 transcripts from both compartments. (D) Log2 fold changes of the 132 transcripts. (E) GO term analysis of transcripts up- or downregulated in the somatodendritic and axonal compartment of Smn knockdown motoneurons. (F) Scatter plots of logarithmized FPKMs of actin-related proteins revealed by GO term analysis downregulated in the axonal compartment of Smn knockdown motoneurons. (G) FPKM expression values and log2 fold changes of the actin-related genes which are downregulated in the axonal compartment. Top 10 downregulated transcripts are marked in yellow. (H) FPKM values of Pls3 measured by RNA-seq of the axonal compartment of GFP controls and Smn knockdown motoneurons (n = 4/6; Two-tailed unpaired t test, ***P ≤ 0.001). Data are presented as mean ± SD.
