Table 2.

Comparison of transcript quantification between real-time PCR (qPCR) and RNA-seq

		2-day ST/control		5-day ST/control
Gene Name	Pathway	RNA-seq	qPCR	RNA-seq	qPCR
fbxo32 (atrogin-1)	proteasome-associated	4.948#	5.184 ± 0.923*	2.354#	1.742 ± 1.058
foxo3b	proteasome-associated	3.453#	2.576 ± 0.635+	1.260	0.756 ± 0.138
trim63 (MuRF1)	proteasome-associated	3.412#	4.869 ± 0.857*	1.535	0.628 ± 0.231*
ube2a	proteasome-associated	2.814	5.106 ± 0.771*	1.483	1.427 ± 0.343
ncl	proteasome	0.963	1.267 ± 0.090	0.881	0.756 ± 0.284
psmb1	proteasome	1.908	1.888 ± 0.216	1.555	1.627 ± 0.375
psmc2	proteasome	2.472	3.316 ± 0.311*	1.543	2.146 ± 0.649
psmc5	proteasome	2.134	2.314 ± 0.215*	1.597	1.507 ± 0.452
psmc6	proteasome	2.375	3.032 ± 0.404	1.228	2.473 ± 1.111
psmd12	proteasome	3.145	2.316 ± 0.205*	2.064	1.664 ± 0.407
psmd3	proteasome	3.959#	7.985 ± 0.572*	1.825	2.876 ± 1.389
psmd4b	proteasome	2.872	1.326 ± 0.262	2.170	1.105 ± 0.343
psmd7	proteasome	2.666	2.455 ± 0.271+	1.567	1.687 ± 0.550
zfand5	proteasome	7.271#	17.064 ± 3.010*	1.186	1.780 ± 1.199*
atg12	autophagy-related	2.064	1.288 ± 0.144	2.197	1.102 ± 0.199
becn1	autophagy-related	1.697	2.690 ± 0.051*	1.212	1.413 ± 0.177
bnip3	autophagy-related	6.441#	11.195 ± 1.770*	2.118	1.630 ± 0.777*
gabarapa	autophagy-related	2.245	2.014 ± 0.152*	1.531	1.065 ± 0.138
ctsll	autophagy	6.761#	4.298 ± 0.561*	3.540#	1.972 ± 0.753

Data for qPCR are the same as shown in Fig. 6. Corresponding RNA-seq ratios based on sample size of n = 1 for control, 2-day spinally transected, and 5-day spinally transected ventral muscle were selected based on the transcript sequence amplified by qPCR primers. Results for qPCR are shown as means ± SE with statistically significant results indicated (

^*, +) as in Fig. 6. Results for RNA-seq data are shown and those genes flagged as differentially expressed by DESeq2 are indicated (#).