Table 4.

Comparison of differentially expressed microRNAs (TCDD vs. DMSO, 60 hpf) identified by three SOLiD sequencing analyses. The highlighted values are statistically significant. For comparison, results from both microarray platforms were included for all microRNAs identified as significant in the SOLiD sequencing data.

	CLC Workbench		Genome Mapping1		DNASTAR QSeq		Exiqon Arrays		Agilent Arrays
miRNA	Fold Diff.	p-value	Fold Diff.	p-value	Fold Diff.	p-value	Fold Diff.	p-value	Fold Diff.	pvalue
mir- 216b-2	−66.0	3.84E- 15	NA	NA	NA	NA	NA	NA	NA	NA
mir- 216b-1	−60.8	6.12E- 15	−29.67	1.28E- 20	NA	NA	NA	NA	NA	NA
mir-216b	NA	NA	NA	NA	−5.2	0.289	ND	ND	1.109	0.03
mir-454b	20.4	2.00E- 12	8.27	1.81E- 09	6.2	0.32	ND	ND	1.07	0.88
mir-454a	6.2	5.05E- 07	2.57	0.049	1.3	0.857	ND	ND	1.022	0.93
mir-27e	5.2	3.05E- 05	4.87	2.5E-05	6.0	0.00467	1.3	0.00555	1.08	0.03
mir-24- 2*	5.7	9.36E- 05	NA	NA	NA	NA	NA	NA	NA	NA
mir- 216b-2*	25.7	0.0228	NA	NA	NA	NA	NA	NA	NA	NA
mir-489	4.1	0.0254	3.98	0.001	3.0	0.138	ND	ND	−1.038	0.88
mir-19c	−3.6	0.0471	−2.36	0.095	−1.4	0.791	−1.07	0.0805	1.018	0.92
mir-19d	−3.6	0.0471	−3.13	0.006	−1.8	0.152	−1.04	0.144	−1.016	0.93
mir-23a	−0.63	1.00	−0.63	0.877	1.5	0.00467	1.25	8.17E-04	1.288	1.0E-5
mir-738	NA	NA	NA	NA	−3.2	0.017	ND	ND	1.024	0.92
mir-1388	3.2	0.157	2.93	0.032	3.1	0.0419	NA	NA	NA	NA
mir-153b	−2.4	0.369	−1.97	0.406	−2.3	0.0458	1.03	0.577	1.064	0.88
mir-93	−2.08	0.601	−3.28	0.004	−12.8	0.434	ND	ND	1.024	0.92
mir-19b	−2.77	0.216	−2.67	0.032	−2.1	0.184	−1.07	0.048	1.002	0.97

NA = Not applicable due to inability of method to detect that specific miRNA isomer

ND = Not detected, probe was present on the array but hybridization intensity was not sufficient for accurate quantification

¹precursor miRNA reads