Table 3.

Results obtained with designed probes for a mixture of phenanthrene and fluoranthene.

Gene name	phnA1a		phnA2a		ahdA1c		ahdA2c		bphB		bphC		bphA3		ahdA4
Targeted region	A	B	A	B	A	B	A	B	A	B	A	B	A	B	A	B
Total number of specific probes	256	384	48	128	128	1024	1024	768	768	384	128	128	576	768	1024	512
Number of specific probes giving a positive signal (SNR' > 3)	1	2	0	1	3	1	2	1	4	1	1	1	3	1	0	0
Highest median SNR' obtained for each targeted region	18.32 ± 3.64	6.62 ± 0.31	X	22.64 ± 3.21	8.61 ± 1.59	9.93 ± 1.32	8.92 ± 1.52	16.26 ± 2.45	5.79 ± 1.73	4.09 ± 0.66	4.47 ± 0.30	4.54 ± 0.81	36.87 ± 7.83	9.79 ± 1.39	X	X
Specific probe for EPA505 gene giving highest median SNR'	Yes	No	No	Yes	No	Yes	Yes	Yes	Yes	No	Yes	No	Yes	Yes	No	No
For comparison, total number of specific probes giving a positive signal with glucose	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0

For each degenerate probe defined targeting two different regions (A and B) of genes (phnA1a, phnA2a, ahdA1c, ahdA2c, bphB, bphC, bphA3 and ahdA4), total number of specific probes stemming from the degenerate sequence, total number of specific probes giving a 'positive' signal (with a SNR' > 3), highest median SNR' visualized for each targeted region of each gene and whether the probe specific to the strain EPA505 gene gives this highest signal median SNR'.