Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces

Table 1 Sequencing statistics for the eleven conditions ¹

Condition	Mappable reads			rRNA	RPKM background transcription	Significant active genes (p ≤ 0.05)	% hypotheticals in active genes	Significant active hypotheticals (p ≤ 0.05)
	Genome	Plasmid	Total
LB (SOLiD)	1,990,326	46,497	2,036,823	13.0%	0.2	4,557	29.7%	1355
LB (Illumina)	3,301,130	5,215	3,306,345	25.2%	0.5	4,463	29.4%	1313
LB-pH9	2,953,471	40,607	2,994,078	22.3%	0.1	4,445	29.4%	1308
LB-pH4	1,315,629	5,353	1,320,982	7.3%	0.03	3,441	27.0%	930
LB-15°C	2,251,249	42,964	2,294,213	11.3%	0.1	4,360	29.7%	1292
LB-nitrite	2,143,433	48,449	2,191,882	29.7%	0.2	4,377	29.2%	1277
LB-antibiotics	718,712	3,615	722,327	14.0%	0.03	2,892	27.1%	785
LB-solid	1,679,329	18,652	1,697,981	20.0%	0.02	4,006	28.7%	1150
minimal medium	1,496,231	34,135	1,530,366	25.4%	0.1	4,017	28.7%	1151
spinach juice	1,638,842	71,874	1,710,716	8.8%	0.08	4,131	29.4%	1215
radish sprouts (SOLiD)	1,355,143	9,876	1,365,019	38.1%	0.09	4,079	28.9%	1180
radish sprouts (Illumina)	3,724,713	31,160	3,755,873	60.3%	0.29	3,852	26.8%	1035
feces	1,184,557	4,457	1,189,014	30.5%	0.05	2,979	28.9%	861
total	25,752,765	362,854	26,115,619	26.4%	Ø 0.14	5,142	26.5%	1621

¹The number of mappable reads within each condition is listed for the genome and plasmid. The percentage of remaining rRNA is shown below.

ISSN: 1471-2164