TABLE 5.

Levels of very-low-abundance mRNAs in B. subtilis spores prepared and purified differently^a

Gene	RPKM value with spore prepn
	Plates, 7 days, HPb	Plates, 7 days, HP, DCc	Plates, 1 day, DCc	Liquid, 7 days, HPd	Liquid, 7 days, LPd	Liquid, 7 days, HP, DCe
Genes under the control of σF/G
ygzC	229	212	416	172	194	195
yjzC	329	616	2,098	440	469	742
ykuS	130	225	612	470	383	193
sspL	441	976	1,693	349	391	976
yphA	83	122	206	13	10	147
spoIVB	82	138	211	93	95	146
yraF	167	258	818	37	49	341
yraG	414	581	1,767	60	68	811
adhB	179	417	934	29	26	408
spoIIQ	37	89	128	62	62	72
Genes under the control of σE/K
cotD	161	83	71	74	62	65
cotV	174	39	27	4	20	26
spoVID	99	67	38	1	1	41
gerE	10	175	7	3	28	89
lytH	41	198	71	92	93	70
cotG	74	66	1,059	12	106	56
Genes under the control of σΑ
ansA	37	86	151	3	5	69
ansB	40	105	174	6	7	78
ansR	183	253	177	174	171	111
ptsG	25	62	19	7	6	33
speD	292	251	274	135	102	123
tcyL	99	77	41	2	32	91
sufB	36	52	76	51	62	54
serS	41	86	39	13	17	53
Genes under the control of an unknown σ factor
yqxK	151	199	85	154	162	106
ytjP	16	66	13	3	3	38

^aValues shown are from RNA-seq, as described in Materials and Methods, on RNA from (i) three spore preparations harvested after 2 days that were highly purified over ∼7 days to give three RNA preparations, after which RNA-seq data for all three were averaged; (ii) one spore preparation prepared on plates and harvested after 1 day and then either highly purified (HP) over 7 days and then chemically decoated (DC) or purified for only ∼4 h and then chemically decoated; (iii) one spore preparation that was made in liquid, harvested after 2 days, and divided into three equal aliquots, one of which was highly purified over 7 days and two of which were less well purified (LP) over 7 days, after which RNA-seq data with the RNA from the two less-well-purified spore preparations were averaged; and (iv) one spore preparation prepared in liquid, highly purified over 7 days, and then chemically decoated, all as described in Materials and Methods.

^bSpores were from one preparation that was divided into three equal samples that were purified separately to give three RNA samples.

^cSpores were prepared on the same batch of sporulation plates and harvested at the same time but purified for only 1 day or 7 days prior to decoating and RNA isolation.

^dSpores were from one batch of liquid medium and harvested at the same time but purified differently.

^eSpores were prepared separately from those described in footnote d.