Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli

BMC Genomics

Table 1 The 16 most abundant intergenic candidate sRNAs with predicted sigma 70 promoters

sRNA name	Size (nt)	Mean no. of Reads*^a	Northern blot band size*^b(nt)		Ref.*^c
			Total	LM
ECS001	89	872.9	~1130	-	-
ECS002	51	360.4	~300	-	[16]
ECS004	78	306.0	-	-	[11]
ECS005	62	197.9	~190	-	-
ECS006	89	83.3	-	-	-
ECS007	50	79.5	~90	~90	-
ECS009	186	52.0	~190, ~155	~155	[9, 13, 17]
ECS0010	74	47.5	~75	~75	[9]
ECS0014	107	31.0	-	-	-
ECS0016	73	24.8	-	-	-
ECS0019	66	19.6	-	-	-
ECS0020	179	18.8	smear	~115	-
ECS0022	79	17.1	~80	~80	[16]
ECS0023	87	16.7	~840	-	-
ECS0024	74	14.9	-	-	-
ECS0025	60	14.5	~65	~65	-

Sixteen intergenic candidate sRNAs were extracted from classes A and B (Figure 1B) for northern blot analysis. *^a The average number of deep sequencing reads mapped to each candidate sRNA: total number of reads divided by the length of the candidate sRNA, to compare the relative expression levels. *^b Major signal sizes detected by northern blotting (Figure 2). Total, total RNA; LM, low-molecular-weight RNA. Bold letters indicate that each signal size was approximately the same as the predicted length of the sRNA based on the deep sequencing analysis. Hyphens indicate that no signal was detected in the northern blot analysis. *^c References to predicted sRNAs in previous studies located around each candidate sRNA. The details of the candidate sRNAs are given in Additional File 4.

ISSN: 1471-2164