Table 2. Number of chlamydial genes expressed at 1 and 24 hpi, by cutoff and by replicate (R).

	Standard gene expression cutoff				“Highly expressed” gene cutoff
	>0.1 RPKM (10 reads minimum)				>1 RPKM (50 reads minimum)
	R1	R2	R3	Avg (std dev)	R1	R2	R3	Avg (std dev)
1 hpi	205*	365	432	399 (34)	37*	141	165	153 (12)
24 hpi	815	802	811	809 (5)	219	221	219	220 (1)

^*Excluded (insufficient reads).