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Table 2
Genes differentially expressed in LongSAGE data and validated by QPCR
Gene	Method*	Fold changes of gene expression in different skeletal muscle samples

		T33	T65	T90	L33	L65	L90

MYLPF	QPCR	1.00^a	8.00^b	16.00^c	0.71^a	10.56^b	39.40^d
	SAGE	1.00	4.10	4.63	0.67	2.31	2.34
MYL2	QPCR	1.00^a	4.92^b	2.46^ab	0.31^c	4.59^b	2.64^b
	SAGE	1.00	1.41	2.56	0.23	2.70	2.23
MYL1	QPCR	1.00^a	9.85^b	13.00^c	0.41^a	12.13^bc	34.30^d
	SAGE	1.00	6.62	11.85	0.38	6.31	5.77
SLN	QPCR	1.00^a	40.50^b	78.79^c	0.71^a	64.00^b	207.94^d
	SAGE	1.00	16.70	29.30	0.20	14.70	24.00
TNNC2	QPCR	1.00^a	22.63^b	6.50^c	0.27^d	6.96^c	8.57^c
	SAGE	1.00	6.74	5.52	0.26	4.03	3.58
TOB1	QPCR	1.00^a	2.30^a	7.46^b	1.53^a	3.73^c	1.87^a
	SAGE	1.00	3.00	11.00	1.00	3.00	2.00
CRABP1	QPCR	1.00^a	0.07^b	0.04^b	2.64^c	0.05^b	0.05^b
	SAGE	1.00	0.00	0.00	3.36	0.00	0.00
LGALS1	QPCR	1.00^a	0.57^b	0.62^bc	0.41^b	0.74^b	0.38^b
	SAGE	1.00	0.86	0.86	0.88	1.26	0.80
GNB2L1	QPCR	1.00^a	0.01^b	0.76^a	0.76^a	1.00^a	0.54^a
	SAGE	1.00	0.30	1.02	0.93	1.02	0.80
TPT1	QPCR	1.00^a	0.00^b	2.00^c	1.07^a	2.83^c	1.74^ac
	SAGE	1.00	0.74	2.69	0.93	1.61	1.41
RPS28	QPCR	1.00^a	0.81^ab	1.00^a	0.62^b	0.81^ab	0.81^ab
	SAGE	1.00	0.39	1.02	0.81	1.06	1.06
TncRNA	QPCR	1.00^a	0.81^a	5.66^b	0.27^c	1.00^a	1.62^d
	SAGE	1.00	1.50	29.50	0.50	1.00	5.00

The QPCR row provides the ratio of the 2^-ΔΔCtvalue for each breed/stage sample to the 2^-ΔΔCtof T33. For the T33 sample, the fold change in gene expression relative to the T33 equals one, by definition. For each row, different superscript letters (a, b or c) indicate a statistically significant difference in gene expression between skeletal muscles at p < 0.05 in the QPCR experiment; the same superscript letters indicate no statistically significant difference (p > 0.05). For values with two superscript letters, gene expression in that sample was not significantly different from the expression in the other two samples compared, but the other two samples were significantly different in gene expression; for example, for the MYL2* gene, the value 2.46^abindicates that the expression in T90 was not statistically significantly different from that of both T33 and T65, but there was a significant difference between the expression of T33 (1.00^a) and T65 (4.92^b). The SAGE row provides the frequency of each breeds/stage sample relative to T33 frequency in the LongSAGE data. T, Tongcheng; L, Landrace; 33, 65 and 90 refer to days post coitus.
Tang et al. Genome Biology 2007 8:R115 doi:10.1186/gb-2007-8-6-r115

Table 2