Table 1.

Summary of RNA-Seq sequencing and data analysis results

Samples from R1	R11	R12	R13	R14	R15	R16	R17	R18	---	Total
Time collected (h)	3	5	7	10	13	16	20	28	---
Total number of reads	32934519	29367899	15075431	30451579	37230096	26184184	36117022	32444284	---	241287505
No. of reads mapped	31098649	27046332	14016757	29094448	34907591	24836210	34255629	30754172	---	227240126
No. of reads unambiguously mapped	29844200	26282300	13592284	28326600	34233900	24012800	33747700	30065800	---	221417584
No. of genes with detectable expression1	5070	5056	5032	5075	5084	5062	5087	5085	---	5088
Range in expression levels (RPKM)	7.4 × 10-3	1.1 × 10-2	5.7 × 10-3	2.3 × 10-2	1.6 × 10-3	1.5 × 10-3	2.3 × 10-2	2.3 × 10-2	---	1.5 × 10-3
	~ 2.0 × 104	~ 1.8 × 105	~ 8.6 × 104	~ 5.0 × 104	~ 9.2 × 104	~ 1.1 × 105	~ 2.2 × 105	~ 8.8 × 104		~ 2.2 × 105
Samples from R2	R21	R22	R23	R24	R25	R26	R27	R28	R23-22	Total3
Time collected (h)	10	12	14	17	20	23	28	36	14
Total number of reads	25350444	38025575	31352222	33877714	26099516	42485421	38176862	33624379	33916811	268992133
No. of reads mapped	23995017	35773620	29542453	32664767	24890605	40877908	36397654	31652246	32399849	255794270
No. of reads unambiguously mapped	22098900	31363000	27534800	31668100	24198000	39820500	35617800	30760200	31451300	243061300
No. of genes with detectable expression1	5059	5063	5058	5077	5084	5088	5088	5084	5081	5088
Range in expression levels (RPKM)	2.3 × 10-2	6.2 × 10-3	2.4 × 10-2	1.6 × 10-3	2.8 × 10-2	4.7 × 10-2	2.6 × 10-2	3.6 × 10-2	2.9 × 10-2	1.6 × 10-3
	~ 1.1 × 105	~ 1.0 × 105	~ 1.3 × 105	~ 1.5 × 105	~ 4.6 × 104	~ 6.7 × 104	~ 1.3 × 105	~ 1.2 × 105	~ 1.1 × 105	~ 1.5 × 105

¹Pseudogenes included.

²R23-2 is a biological replicate for sample R23; it was taken at the same fermentation time as for R23, but from a replicate reactor operated under the identical conditions.

³R23-2 is excluded.