Table 3.

Comparison on the performance of the TaKaRa kit and the KAPA kit with different quality total RNA from FFPE samples

Samples	Sample13		Sample14		Sample15		Sample16		Sample17		Sample18		Sample19		Sample20		Sample21		Sample22	Sample23	Sample24	Sample25	Sample26	Sample27	R-Sample22	R-Sample23	R-Sample24	R-Sample25	R-Sample27
DV200(%)	75		77		76		61		51		52		52		46		42		2	1	11	17	26	27	2	1	11	17	27
Kits	T	K	T	K	T	K	T	K	T	K	T	K	T	K	T	K	T	K	T	T	T	T	T	T	T	T	T	T	T
PCR cycles	13	15	13	15	13	15	13	15	13	15	13	15	13	15	13	15	13	15	13	13	13	13	13	13	13	13	13	13	13
Library (ng)	115.6	48.8	448.0	31.2	242.0	17.2	91.2	9.3	472.0	24.4	280.0	38.6	62.4	5.6	200.0	13.9	155.2	4.4	48.8	83.2	216.0	98.0	161.2	344.0	8.3	14.1	58.4	20.0	123.2
Total raw data (G)	18.1	43.7	19.2	37.3	21.8	28.3	11.6	5.0	13.6	16.8	13.8	28.6	12.2	–	12.1	8.3	12.0	–	12.5	10.6	10.7	10.9	10.3	11.2	8.6	11.2	11.0	8.9	12.0
Downsampled data (G)	18.0	18.0	18.0	18.0	18.0	18.0	10.0	5.0	10.0	10.0	10.0	10.0	10.0	–	10.0	8.3	10.0	–	10.0	10.0	10.0	10.0	10.0	10.0	8.6	11.2	11.0	8.9	12.0
Clean bases (G)	15.4	15.9	15.2	16.3	14.7	16.1	6.7	4.6	7.1	9.4	7.2	9.3	7.1	–	6.0	6.6	5.0	–	3.6	5.2	7.0	6.1	6.6	6.1	2.3	5.2	8.0	4.8	6.2
rRNA (%)	5.24	5.27	4.78	2.07	10.08	5.31	20.29	1.62	14.32	0.84	14.92	1.33	12.01	–	28.24	14.96	39.42	–	47.13	35.78	15.00	38.30	24.70	41.03	47.59	34.50	11.37	31.46	39.02
Q30 (%)	94.13	91.86	94.58	92.11	93.98	92.19	91.53	92.62	92.28	93.40	92.36	93.42	89.81	–	92.12	93.00	91.51	–	77.57	83.75	90.66	87.62	91.66	92.74	73.78	82.37	89.04	84.89	90.43
GC (%)	45.27	49.86	47.05	49.16	48.40	49.70	50.79	46.64	51.58	46.71	51.02	45.99	48.20	–	48.91	46.07	52.38	–	51.23	56.66	48.76	54.56	52.66	55.30	49.17	58.32	46.99	51.75	55.23
Total mapping rate (%)	83.47	93.94	89.11	94.09	82.30	95.16	82.13	97.65	92.06	98.34	90.81	97.86	83.77	–	85.57	97.66	74.45	–	64.92	78.71	90.58	75.13	78.59	79.15	58.24	78.68	90.65	75.04	82.26
Uniquely mapping rate (%)	71.29	84.63	78.79	84.82	67.87	84.20	69.59	90.75	81.53	90.98	80.20	91.10	74.44	–	76.58	91.60	63.62	–	48.73	60.68	77.32	58.19	65.33	62.98	43.58	60.25	82.44	61.53	69.46
Multiple mapping rate (%)	12.18	9.31	10.32	9.27	14.43	10.96	12.54	6.90	10.53	7.36	10.61	6.76	9.33	–	8.99	6.06	10.83	–	16.19	18.03	13.26	16.94	13.26	16.17	14.66	18.43	8.21	13.51	12.80
Exon (%)	59.52	66.59	60.61	57.39	67.71	71.48	57.56	49.35	58.56	47.48	55.42	46.88	38.56	–	41.19	33.20	42.10	–	32.98	43.84	31.52	47.36	36.54	57.09	25.40	44.02	29.46	43.89	56.80
Intron (%)	38.31	31.86	37.68	40.92	30.50	27.40	40.80	48.93	39.86	50.68	43.08	51.40	58.92	–	57.05	64.95	55.48	–	59.33	51.77	64.92	48.06	60.59	40.88	61.77	51.68	67.10	51.15	41.47
Intergenic (%)	2.17	1.55	1.71	1.68	1.79	1.12	1.63	1.72	1.58	1.85	1.50	1.72	2.53	–	1.76	1.85	2.43	–	7.69	4.39	3.56	4.59	2.88	2.03	12.83	4.30	3.43	4.96	1.74
Transcript (FPKM 0.3~1)	5662	4724	6142	3729	5844	3118	5689	3003	6545	4496	6394	5441	5447	–	5212	2426	4885	–	2858	4560	5389	4819	5135	5755	2134	3840	4407	3636	4956
Transcript (FPKM 1~5)	9132	8294	10,045	8337	8398	6828	10,700	8659	11,841	10,819	11,566	10,839	10,888	–	10,865	8175	11,333	–	9972	10,364	11,455	10,959	11,847	9961	7588	8939	10,665	9193	9535
Transcript (FPKM 5~10)	3444	3644	3882	4359	3156	3437	3446	3627	4277	4991	3934	4192	4849	–	5003	4838	5554	–	4687	4814	5797	4918	5690	4198	4316	4544	5926	4806	4335
Transcript (FPKM10~50)	3938	4311	4146	5053	3568	4052	2539	3226	3735	4300	3132	3375	5195	–	4762	5441	4723	–	3796	4759	5538	3849	4562	4359	4175	4982	5886	4446	4572
Transcript (FPKM> = 50)	747	741	712	662	763	706	570	433	566	467	595	481	633	–	601	516	555	–	474	525	586	593	585	658	620	599	603	597	640