CAGE-TSSchip: promoter-based expression profiling using the 5'-leading label of capped transcripts

Table 1 Cross-validation by qRT-PCR and CAGE in mouse liver versus E17.5

Target gene	CAGE-TSSchip		qRT-PCR	CAGE
	Probe ID	Ratio^a	Ratio^a	Ratio^a
Scp2	pT04R06588376_1_55	1.54	2.22	2.25
Phyh	pT02F004A4350_1_56	1.47	1.48	2.09
H2-Q7	pT17F02067AF1_1_1	1.33	1.44	2.52
Gcgr	pT11F072A22AF_1_56	1.10	1.32	1.58
1500017E21Rik	pT19R022303AA_2_11	1.08	1.09	0.39^b
H2-K1	pT17R01EFDD1A_2_55	1.08	1.36	3.04
Ttr	pT18F01417BA8_1_61	1.03	1.27	0.47^b
Creb3l3	pT10R04D401D2_1_59	0.99	1.18	1.76
Aldh7a1	pT18R0366ABBD_1_60	0.95	0.39^b	2.17
Apoa1	A_65_P16973as	0.93	1.14	0.76
Ttr	pT18F014197F5_1_51	0.93	1.14	0.56
Ppara	pT15F0521ABCF_1_61	0.92	0.92	1.77
Bdh	pT16F01DD69D0_1_61	0.83	0.91	0.93
Hhex	pT19F022F5EF6_1_61	0.75	0.88	1.63
H2-K1	pT17R01EF8909_1_61	0.67	-0.35^b,c	2.89
Trf	A_65_P04625as	0.65	0.59	0.94
Mdh1	A_51_P218179as	0.57	0.19^b	0.03^b
Mcm7	pT05R08145E66_1_60	-0.52	-0.87	-0.33^b
Nisch	pT14R019FAD28_1_56	-0.54	-0.27^b	0.67^c
D0H4S114	pT18R02055333_1_60	-0.67	-1.04	-0.95

Primer sequences are available in Additional data file 9. We assume that the absolute calue of the log ratio >0.5 is significantly different expression between liver and E17.5. ^aRatio = log₁₀(liver/E17.5). ^bNon-significance. ^cTendency for the sample to be highly different from the CAGE-TSSchip result. CAGE, cap analysis gene expression; qRT-PCR, quantitative reverse transcription polymerase chain reaction.

ISSN: 1474-760X