Supplementary Figure 3: Laser capture and RNA sequencing analysis of lumbar spinal motor neurons.

(a) Nissl staining of lumbar spinal cord showing anterior horn motor neurons before and after laser capture (n = 4 wild-type, 4 TDP−43^Q331K/+, 4 TDP−43^Q331K/Q331K mice). Scale bar, 300 μm. (b) Quality control measures of laser−capture RNA sequencing data. A mean of 49.9 million reads−per−mouse (range 43.7−57.3million) were obtained. Displayed is the percentage of reads that are mapped within genes and exons; reads from ribosomal or mitochondrial RNA; percentage of annotated genes measured and the percentage of reads that are mapped to the sense strand. Colored dots represent individual libraries prepared from each mouse sequenced.(c) Filtering of lumbar spinal cord DESeq2 alternative splice events that are significantly different between wild−type and TDP−43^Q331K/Q331K mice. Non−expression hits reflect changes in splice junction usage that exceed a 1.5−fold change relative to expression of the gene from which they are derived. Log Reg hits include splice junctions whose usage changes relative to another junction with the same start or end position. (d) MA plot and (e) hierarchical clustering of alternative splice events in the lumbar spinal cord of wild−type and TDP−43^Q331K/Q331K mice (n = 4 wild-type, 4 TDP−43^Q331K/+, 4 TDP−43^Q331K/Q331K mice). Comparison: DESeq2 wild−type v TDP−43^Q331K/Q331K. (f) Immunohistochemistry for AOX1 in lumbar motor neurons of 5−month−old mice (n = 4 wild-type, 4 TDP−43^Q331K/Q331K mice). Representative images shown. Scale bar, 100μm.