Table 1. List of analyzed genes, RPKM value, fold difference and brief summary of function.

Gene name	Control RPKM	Smo tKO RPKM	Fold Change(Smo tKO/Control)	p-value	Function
Asporin	16.19	6.63	−3.91	<0.001	leucine-rich repeat (LRR)
Biglycan	1147.60	1371.00	1.20	<0.001	Small leucine-rich repeat proteoglycan (SLRP)
Collagen, type II, alpha 1	1494.34	862.30	−1.70	<0.001	Collagen II protein
Gli1	14.50	1.25	−12.46		Hedgehog downstream target
Glypican 3	9.66	3.90	−2.46	<0.001	Glypican-related integral membrane proteoglycan family (GRIPS)
Lumican	28.20	17.48	−1.75	<0.001	SLRP
Runx2	22.60	12.79	−1.70	<0.001	Transcription factor
Smoothened	36.49	0.73	−99.31	<0.001	Hedgehog signaling receptor
Tenasin-C	9.77	8.53	−1.3	<0.001	Extracellular matrix (ECM) protein

RPKM, reads per kilobase exon per million mapped sequences