Table 3. BestKeeper rankings.

	All data	All healthy	All DMD	All 6wk	All 10wk	All 24wk	All skeletal muscle	All DIA	All Hearts	All TA	6wk healthy	6wk DMD	10wk healthy	10wk DMD	24wk healthy	24wk DMD
Most	FBXW2	CSNK2A2	FBXW2	HPRT1	FBXW2	HTATSF1	FBXW2	RPL13A	HTATSF1	FBXW2	ACTB	CSNK2A2	CSNK2A2	AP3D1	HTATSF1	ACTB
stable	AP3D1	FBXW2	AP3D1	CSNK2A2	HPRT1	FBXW2	CSNK2A2	AP3D1	CSNK2A2	18S	HPRT1	AP3D1	ACTB	RPL13A	FBXW2	HTATSF1
	CSNK2A2	ACTB	RPL13A	RPL13A	HTATSF1	ACTB	AP3D1	HTATSF1	AP3D1	HPRT1	CDC40	HPRT1	SDHA	FBXW2	ACTB	FBXW2
	ACTB	HTATSF1	ACTB	ACTB	RPL13A	AP3D1	CDC40	FBXW2	CDC40	AP3D1	CSNK2A2	FBXW2	RPL13A	ACTB	AP3D1	RPL13A
	RPL13A	RPL13A	HTATSF1	FBXW2	CSNK2A2	CSNK2A2	ACTB	ACTB	FBXW2	RPL13A	HTATSF1	HTATSF1	FBXW2	GAPDH	CSNK2A2	AP3D1
	HTATSF1	AP3D1	CSNK2A2	CDC40	AP3D1	RPL13A	RPL13A	GAPDH	RPL13A	CDC40	RPL13A	CDC40	HPRT1	HPRT1	18S	HPRT1
	HPRT1	SDHA	HPRT1	AP3D1	GAPDH	18S	HPRT1	B2M	HPRT1	GAPDH	FBXW2	RPL13A	B2M	CSNK2A2	GAPDH	CSNK2A2
	18S	GAPDH	18S	HTATSF1	SDHA	SDHA	18S	CSNK2A2	SDHA	ACTB	AP3D1	SDHA	AP3D1	HTATSF1	RPL13A	PAK1IP1
	CDC40	B2M	PAK1IP1	18S	PAK1IP1	B2M	HTATSF1	PAK1IP1	GAPDH	CSNK2A2	SDHA	18S	HTATSF1	B2M	SDHA	B2M
	B2M	HPRT1	CDC40	B2M	B2M	PAK1IP1	PAK1IP1	18S	ACTB	SDHA	B2M	GAPDH	GAPDH	18S	B2M	SDHA
	PAK1IP1	18S	B2M	PAK1IP1	ACTB	GAPDH	B2M	SDHA	18S	HTATSF1	18S	B2M	CDC40	PAK1IP1	PAK1IP1	18S
Least	SDHA	CDC40	SDHA	SDHA	CDC40	HPRT1	GAPDH	HPRT1	PAK1IP1	B2M	PAK1IP1	ACTB	PAK1IP1	CDC40	HPRT1	CDC40
stable	GAPDH	PAK1IP1	GAPDH	GAPDH	18S	CDC40	SDHA	CDC40	B2M	PAK1IP1	GAPDH	PAK1IP1	18S	SDHA	CDC40	GAPDH

Bestkeeper results for the entire dataset or subsets (as indicated), ranked from top to bottom by Pearson correlation (r) with the BestKeeper. Bold: r > = 0.85; italics: r < 0.6