TABLE 4.

Levels of the most abundant mRNAs in B. subtilis spores prepared and purified in different ways^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
Most abundant
sspA	10,848	7,101	2,558	82,252	74,270	7,964
sspE	577,971	195,633	307,920	1,680,099	1,682,101	207,023
sspF	131,260	256,602	141,093	73,546	76,555	128,480
sspJ	133,439	68,934	125,571	162,439	146,117	102,419
sspK	23,696	28,553	45,106	9,312	10,937	35,108
sspM	25,626	58,428	42,904	6,428	6,833	55,389
sspN	201,551	101,257	231,754	70,065	69,888	227,852
sspO	102,766	94,637	113,429	19,089	18,530	90,525
sspP	86,361	63,492	74,849	13,805	13,860	52,905
tlp	202,343	176,853	186,473	67,845	56,567	204,990
yfhD	177,547	176,800	272,126	124,322	119,052	216,922
yhcN	7,464	7,715	13,405	3,651	3,007	6,249
yhcQ	13,540	9,189	20,905	11,083	1,130	9,728
yhcV	161,470	102,408	111,900	325,933	347,985	79,119
yhdB	82,876	111,283	141,329	32,185	42,392	108,510
yizC	75,142	31,984	55,033	64,672	68,169	43,288
ykzE	271,743	232,006	241,481	83,154	82,219	230,510
ykzP	480,746	460,080	436,876	169,218	168,247	534,888
ymfJ	85,309	74,482	136,945	56,091	60,290	95,673
yozQ	9,528	11,683	18,217	1,622	1,480	9,246
ypzF	827,125	847,377	95,592	360,382	370,698	1,071,770
ypzG	465,198	577,580	593,031	412,715	412,193	717,523
yqfX	39,843	67,657	78,389	59,215	57,190	44,988
yrzQ	81,387	129,290	95,592	41,102	42,065	101,654
yrzR	17,332	17,844	23,238	8,397	8,505	20,738
ytzC	269,462	199,868	182,090	137,144	132,765	218,097
ytzL	157,337	216,142	187,257	48,820	49,262	174,765
yuzA	9,616	8,584	7,101	6,148	5,671	6,864
yxeD	7,175	5,323	10,280	4,581	4,867	6,115
Less abundant
sspB	2,972	4,257	2,201	38,450	35,951	3,706
sspH	2,415	4,473	8,782	1,608	1,443	6,035
yhcM	4,044	4,010	9,478	2,982	2,850	4,903
yraE	3,249	6,239	12,225	553	368	7,292
yrrD	2,674	2,254	2,218	4,748	4,193	2,074
yusG	2,087	2,098	1,919	1,366	1,320	1,513
yusN	2,082	2,095	4,330	859	820	2,336
Much less abundant
pdhA	683	811	881	55	52	807
sscA	1,767	117	139	127	148	40
sspI	843	2,187	2,462	341	297	2,117
yhcO	1,429	1,578	2,475	1,269	1,429	1,179
ykzD	714	1,889	2,251	416	395	2,341
yoyE	1,462	4,147	6,214	1,371	1,442	5,416
ypzI	850	1,264	3,695	596	498	1,372
yraD	843	1,391	3,446	150	139	1,342
yrzB	567	521	1,662	291	234	667
yutC	636	671	955	698	681	553

^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 (HP) 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 over 7 days and then chemically decoated (DC) or purified for only ∼4 h and then chemically decoated; (iii) one spore preparation 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 for 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. The order of mRNAs is alphabetical within each group.

^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.