Table 2. RNA-seq read statistics. All RNA samples used to perform RNA-Seq analaysis had RIN > = 8 and 260/280 ratio > 1.5, as recommended in manufacturer’s protocol.

Sample	Number of input reads	Average input read length	Uniquely mapped reads %	Number of reads mapped to multiple loci	% of reads mapped to multiple loci	Seq. batch
CTRL1	9.85E + 07	2 × 75	22.68%	5.55E + 07	56.38%	1
CTRL2	8.51E + 07	2 × 75	25.65%	5.49E + 07	64.53%	1
CTRL3	9.00E + 07	2 × 75	26.99%	5.53E + 07	61.47%	2
CTRL4	2.00E + 07	2 × 75	6.50%	1.23E + 07	61.53%	2
CTRL5	2.28E + 08	2 × 75	11.02%	1.71E + 08	74.93%	3
CTRL6	1.05E + 08	2 × 150	4.17%	2.88E + 07	27.54%	4
CTRL7	5.53E + 07	2 × 150	2.96%	1.77E + 07	31.95%	4
ALS-s1	8.30E + 07	2 × 75	26.69%	3.96E + 07	47.72%	1
ALS-s2	9.25E + 07	2 × 75	27.52%	5.73E + 07	61.92%	1
ALS-s3	9.39E + 07	2 × 75	33.88%	5.23E + 07	55.73%	1
ALS-s4	9.10E + 07	2 × 75	37.71%	2.56E + 07	28.17%	1
ALS-s5	9.18E + 07	2 × 75	31.32%	5.51E + 07	60.00%	2
ALS-s6	8.74E + 07	2 × 75	32.43%	5.29E + 07	60.55%	2
ALS-s7	1.03E + 08	2 × 75	17.58%	7.60E + 07	73.79%	2
ALS-s8	7.73E + 07	2 × 75	28.06%	4.71E + 07	60.97%	2
ALS-s9	7.32E + 07	2 × 75	24.14%	3.69E + 07	50.35%	3
ALS-s10	9.12E + 07	2 × 75	14.76%	5.79E + 07	63.49%	3
ALS-s11	7.83E + 07	2 × 75	34.72%	4.48E + 07	57.26%	3
ALS-s12	4.11E + 07	2 × 150	7.12%	2.12E + 07	51.64%	4
ALS-s13	7.17E + 07	2 × 150	17.87%	3.76E + 07	52.36%	4
ALS-s15	5.36E + 07	2 × 150	10.09%	3.52E + 07	65.63%	4
ALS-s16	8.36E + 07	2 × 150	7.68%	5.53E + 07	66.15%	4
FUS-m1	9.63E + 07	2 × 150	22.49%	6.84E + 07	71.03%	4
FUS-m2	9.82E + 07	2 × 75	13.62%	7.33E + 07	74.65%	2
FUS-m3	1.65E + 06	2 × 150	10.43%	1.28E + 07	81.24%	4
SOD1-m1	1.14E + 08	2 × 75	28.38%	6.86E + 07	60.15%	3
SOD1-m2	8.50E + 07	2 × 75	31.92%	4.88E + 07	57.46%	1
SOD1-m3	3.51E + 07	2 × 75	22.36%	2.33E + 07	66.42%	3
TARDBP-m1	1.16E + 08	2 × 75	31.21%	6.21E + 07	53.46%	3
TARDBP-m2	7.94E + 07	2 × 75	29.40%	3.50E + 07	44.14%	3
VCP-m1	2.98E + 07	2 × 75	13.46%	2.07E + 07	69.66%	1