TABLE 8.

Abundance of HSV-1 transcripts at various times following infection of HeLa cells with RP3 or RP4 virus^a

Transcript set	Kinetic class and IDb	Abundance																		% RP3 vs % RP4c
		Infection by RP3									Infection by RP4
		2 hpi			4 hpi			8 hpi			2 hpi			4 hpi			8 hpi
		Median	SD	%	Median	SD	%	Median	SD	%	Median	SD	%	Median	SD	%	Median	SD	%	2 hpi	4 hpi	8 hpi
RICP0	IE-1	34,380	27,220	13.4	21,780	12,930	2.2	15,560	4,720	1.4	320	540	1.0	1,010	480	0.7	4,970	1,140	1.1	0.00	0.00	0.32
U54	IE-2	14,610	29,530	5.7	91,290	65,700	9.1	19,290	3,070	1.7	220	90	0.7	7,110	3,800	4.7	8,310	2,120	1.8	0.04	0.10	0.50
RICP4	IE-3	58,490	30,190	22.8	44,550	25,330	4.4	11,730	6,170	1.0	7,070	3,080	21.1	6,580	2,480	4.4	5,370	1,730	1.2	0.36	0.73	0.96
R/S22	IE-4	14,420	31,680	5.6	66,120	37,570	6.6	32,250	5,070	2.8	510	280	1.5	5,520	1,160	3.7	11,920	2,740	2.6	0.03	0.00	0.20
U4-5′	E-1	450	190	0.2	5,470	2,360	0.5	7,180	3,000	0.6	210	620	0.6	1,110	180	0.7	1,990	1,100	0.4	0.20	0.11	0.68
U4/5	E-2	8,290	4,340	3.2	14,180	7,170	1.4	19,850	6,180	1.7	890	450	2.7	3,350	1,110	2.2	7,800	3,260	1.7	0.69	0.14	0.89
U8/9	E-3	840	370	0.3	6,060	2,470	0.6	9,440	5,480	0.8	370	390	1.1	1,100	220	0.7	3,000	1,440	0.6	0.08	0.25	0.57
U8-5′	E-4	2,380	970	0.9	4,510	2,160	0.4	5,590	1,840	0.5	1,300	650	3.9	980	280	0.6	1,690	930	0.4	0.02	0.39	0.86
U21	E-5	330	160	0.1	2,890	1,790	0.3	13,080	2,820	1.1	30	70	0.1	510	210	0.3	4,850	1,180	1.0	0.67	0.46	0.96
U23	E-6	2,770	1,820	1.1	37,180	25,550	3.7	14,610	5,940	1.3	340	180	1.0	5,550	1,200	3.7	5,900	4,590	1.3	0.13	0.22	0.37
U29	E-7	660	300	0.3	21,030	11,940	2.1	15,840	5,590	1.4	0	70	0.0	3,760	1,570	2.5	8,050	3,160	1.7	0.11	0.83	0.74
U30	E-8	1,760	840	0.7	16,980	4,830	1.7	11,650	4,590	1.0	220	330	0.7	3,820	860	2.5	4,160	1,440	0.9	0.34	0.00	0.53
U37	E-9	280	140	0.1	4,200	2,230	0.4	11,360	6,180	1.0	140	230	0.4	530	180	0.4	4,460	1,360	1.0	0.14	0.69	0.47
U39-5′	E-10	1,370	630	0.5	26,410	9,300	2.6	21,850	1,830	1.9	160	90	0.5	5,850	1,800	3.9	10,580	3,550	2.3	0.66	0.06	0.41
U39/40	E-11	1,360	750	0.5	41,560	9,980	4.1	26,890	4,010	2.3	260	150	0.8	6,630	2,440	4.4	12,780	3,310	2.7	0.13	0.17	0.43
U42	E-12	1,280	220	0.5	25,500	3,190	2.5	35,930	3,550	3.1	250	210	0.7	3,940	660	2.6	12,470	2,350	2.7	0.63	0.77	0.12
U43	E-13	3,090	740	1.2	3,900	1,570	0.4	4,550	6,050	0.4	1,070	570	3.2	780	270	0.5	1,120	980	0.2	0.03	0.16	0.41
U50	E-14	1,480	450	0.6	28,180	8,820	2.8	25,800	6,390	2.2	280	610	0.8	4,340	1,120	2.9	11,160	2,990	2.4	0.29	0.50	0.74
U52-5′	E-15	870	1,800	0.3	3,420	2,710	0.3	560	660	0.0	200	150	0.6	220	310	0.1	230	170	0.0	0.75	0.13	0.98
U55	E-16	290	160	0.1	5,550	3,890	0.6	8,300	5,170	0.7	0	20	0.0	1,180	500	0.8	3,460	2,180	0.7	0.04	0.90	0.98
U56	E-17	1,530	1,130	0.6	8,370	6,810	0.8	12,680	5,690	1.1	250	130	0.7	1,550	490	1.0	5,440	3,330	1.2	0.74	0.65	0.46
US2	E-18	1,410	450	0.6	3,750	2,970	0.4	32,200	7,130	2.8	220	240	0.7	1,210	380	0.8	9,410	1,960	2.0	0.44	0.03	0.04
U1	L-1	940	1,060	0.4	22,140	12,220	2.2	19,910	5,200	1.7	170	100	0.5	2,640	1,230	1.7	9,820	5,050	2.1	0.68	0.63	0.32
U3	L-2	280	150	0.1	2,680	1,920	0.3	14,400	6,020	1.3	110	350	0.3	360	200	0.2	5,880	3,110	1.3	0.18	0.64	0.70
U10	L-3	1,670	670	0.7	5,830	3,910	0.6	24,100	4,960	2.1	370	230	1.1	1,000	720	0.7	9,830	3,410	2.1	0.13	0.46	0.99
U16/17	L-4	1,480	500	0.6	5,810	3,130	0.6	16,670	2,800	1.5	400	230	1.2	1,070	310	0.7	6,250	1,480	1.3	0.08	0.76	0.36
U15	L-5	780	280	0.3	1,440	1,870	0.1	6,690	2,760	0.6	360	300	1.1	250	210	0.2	2,240	1,820	0.5	0.08	0.90	0.89
U18/20	L-6	270	130	0.1	15,410	6,920	1.5	31,520	23,200	2.7	0	70	0.0	2,850	980	1.9	13,560	4,150	2.9	0.85	0.59	0.65
U19/20	L-7	930	210	0.4	10,690	6,970	1.1	33,360	22,220	2.9	140	370	0.4	3,970	1,100	2.6	12,820	4,220	2.8	0.32	0.04	0.46
U19-5′	L-8	2,040	690	0.8	5,410	4,600	0.5	14,100	4,090	1.2	350	480	1.0	1,060	580	0.7	3,650	1,250	0.8	0.36	0.58	0.48
U22	L-9	210	140	0.1	4,320	3,090	0.4	22,670	3,470	2.0	60	40	0.2	610	240	0.4	5,460	2,020	1.2	0.12	0.92	0.04
U24	L-10	720	320	0.3	6,190	2,890	0.6	20,710	3,770	1.8	20	100	0.1	1,690	600	1.1	7,760	1,220	1.7	0.27	0.01	0.96
U25	L-11	740	190	0.3	18,180	6,010	1.8	32,310	20,880	2.8	80	200	0.2	3,100	890	2.0	12,770	3,500	2.7	0.56	0.74	0.55
U27/28	L-12	2,500	570	1.0	32,810	10,760	3.3	28,170	2,280	2.5	530	370	1.6	5,380	700	3.6	11,490	860	2.5	0.14	0.91	0.60
U27-5′	L-13	1,280	490	0.5	28,950	14,040	2.9	28,330	2,950	2.5	190	90	0.6	3,960	1,070	2.6	12,200	1,510	2.6	0.63	0.17	0.27
U31/34	L-14	980	780	0.4	5,620	1,930	0.6	19,620	6,520	1.7	340	220	1.0	540	390	0.4	4,950	1,880	1.1	0.06	0.81	0.26
U35	L-15	1,130	190	0.4	12,270	3,280	1.2	28,660	3,810	2.5	290	290	0.9	1,260	340	0.8	8,780	2,980	1.9	0.24	0.13	0.61
U38	L-16	1,720	710	0.7	4,460	2,690	0.4	21,530	6,230	1.9	480	410	1.4	840	470	0.6	7,620	2,680	1.6	0.11	0.45	0.37
U41	L-17	90	90	0.0	1,710	1,600	0.2	13,950	6,080	1.2	50	70	0.1	200	90	0.1	3,270	2,770	0.7	0.10	0.27	0.54
U44-5′	L-18	1,330	650	0.5	4,670	2,970	0.5	29,200	26,940	2.5	260	120	0.8	1,460	440	1.0	12,610	4,420	2.7	0.76	0.03	0.86
U44/45	L-19	2,350	480	0.9	17,420	4,000	1.7	32,830	10,510	2.9	930	430	2.8	2,810	290	1.9	13,620	2,920	2.9	0.02	0.39	0.56
U46/47	L-20	10,500	2,700	4.1	26,870	15,430	2.7	37,800	17,800	3.3	1,970	1,350	5.9	5,480	980	3.6	15,340	3,790	3.3	0.39	0.13	0.87
U48	L-21	300	140	0.1	4,330	1,740	0.4	10,550	4,940	0.9	100	140	0.3	2,400	1,070	1.6	18,340	8,100	3.9	0.26	0.00	0.01
U51	L-22	4,510	1,520	1.8	8,280	3,040	0.8	21,320	3,110	1.9	1,080	1,130	3.2	1,410	530	0.9	7,180	2,940	1.5	0.12	0.19	0.64
RLXY	L-23	140	100	0.1	1,600	1,470	0.2	9,540	2,630	0.8	120	210	0.4	80	100	0.1	4,730	1,990	1.0	0.18	0.01	0.90
RLX	L-24	7,670	1,650	3.0	7,560	5,410	0.8	11,410	5,970	1.0	1,620	1,500	4.8	1,620	700	1.1	4,360	1,790	0.9	0.09	0.33	0.90
RICP34.5	L-25	2,460	610	1.0	5,310	3,300	0.5	3,630	1,200	0.3	350	290	1.0	560	190	0.4	940	710	0.2	0.91	0.22	0.99
US5-5′	L-26	3,610	970	1.4	3,130	1,700	0.3	980	530	0.1	1,260	460	3.7	1,010	380	0.7	580	320	0.1	0.01	0.03	0.16
US8-5′	L-27	2,870	620	1.1	7,370	4,510	0.7	10,860	4,030	0.9	1,330	1,090	4.0	1,480	430	1.0	3,780	1,810	0.8	0.07	0.76	0.78
US8/9	L-28	2,300	1,640	0.9	65,390	59,470	6.5	27,980	13,230	2.4	230	300	0.7	6,060	5,120	4.0	14,540	3,990	3.1	0.48	0.58	0.35
RLAT-5′	LT-1	1,320	280	0.5	650	800	0.1	2,080	650	0.2	200	100	0.6	270	180	0.2	800	430	0.2	0.38	0.04	0.63
RHA6	LT-2	970	630	0.4	260	720	0.0	3,320	2,380	0.3	520	520	1.6	160	140	0.1	1,240	640	0.3	0.10	0.09	0.90
RLATX	LT-3	1,130	380	0.4	1,060	730	0.1	14,620	3,580	1.3	450	290	1.3	360	150	0.2	6,310	3,120	1.4	0.16	0.00	0.15
RLAT-3′	LT-4	2,510	1,000	1.0	3,150	1,590	0.3	16,010	5,720	1.4	630	330	1.9	870	600	0.6	8,020	1,170	1.7	0.04	0.02	0.29
U1X	?	360	250	0.1	170	250	0.0	350	260	0.0	50	290	0.1	30	120	0.0	140	340	0.0	0.37	0.34	0.38
U6/7	L/?	4,000	1,170	1.6	7,620	3,010	0.8	16,880	7,430	1.5	890	230	2.7	1,950	450	1.3	6,370	2,680	1.4	0.15	0.10	0.89
U11/13	L/E/L	310	290	0.1	22,000	9,380	2.2	24,870	7,260	2.2	180	140	0.5	3,500	720	2.3	9,310	1,600	2.0	0.05	0.80	0.91
U36	E/L	170	40	0.1	2,010	1,260	0.2	14,810	1,820	1.3	80	220	0.2	210	110	0.1	5,070	1,710	1.1	0.20	0.41	0.21
U43.5-5′	?	440	190	0.2	300	480	0.0	830	800	0.1	30	70	0.1	70	80	0.0	400	160	0.1	0.95	0.46	0.77
U49	E/L	1,870	900	0.7	34,250	9,110	3.4	29,940	25,440	2.6	370	200	1.1	5,140	630	3.4	14,270	4,350	3.1	0.22	0.61	0.79
U52/53	E/L	1,070	220	0.4	12,790	6,410	1.3	19,520	3,890	1.7	180	170	0.5	1,820	670	1.2	6,780	1,680	1.5	0.77	0.98	0.90
RLAT-1	LAT	910	130	0.4	770	660	0.1	3,440	1,040	0.3	200	120	0.6	220	130	0.1	1,470	390	0.3	0.54	0.09	0.63
ROP	?	2,190	870	0.9	1,350	1,870	0.1	1,460	870	0.1	800	420	2.4	250	170	0.2	820	200	0.2	0.02	0.50	0.48
US3-5′	L?	5,910	1,870	2.3	11,220	5,490	1.1	1,500	1,030	0.1	700	300	2.1	2,420	940	1.6	790	490	0.2	0.81	0.07	0.46
US3/4	E/L?	1,080	200	0.4	13,900	6,660	1.4	6,810	4,890	0.6	280	210	0.8	2,140	1,360	1.4	2,770	1,480	0.6	0.05	0.58	0.92
US5/6/7	EL/E/E	1,340	800	0.5	36,670	16,300	3.6	27,750	4,410	2.4	170	260	0.5	4,470	3,520	3.0	10,520	2,810	2.3	0.79	0.93	0.60
US10/11/12	E/E/IE	22,870	15,800	8.9	38,180	16,250	3.8	34,200	23,200	3.0	340	230	1.0	5,550	870	3.7	16,760	4,060	3.6	0.00	0.16	0.83
Total		256,590			1,005,080			1,147,380			33,570			151,210			465,330

^aHeLa cells were infected with equivalent virion numbers of RP3 or RP4, corresponding to 5 or 0.5 PFU per cell. Median values are based on six, ten, or five experiments for RP3 (at 2, 4, and 8 hpi, respectively) and on six, nine, or five experiments for RP4 (at 2, 4, and 8 hpi, respectively). Bold entries represent either single transcripts or multiple transcripts of the same kinetic class.

^bSee Table 1, footnote b.

^cRelative abundance values of each transcript at each time point in infections by RP3 and RP4 were compared by using Student's t test with two-tail distribution and assuming unequal variance. The null hypothesis is that the values for the RP3 and RP4 infections will be identical. The value 0.00 is used to indicate P values of <0.01.