TABLE 2.

64 pairwise analyses^a

Study	Pairwise comparison	Expt no.	Details	No. of sRNAs alteredb
001	1	001.1	UAMS-1 anaerobic 0 min vs nor KO 0 min	5
	2	001.2	UAMS-1 anaerobic 120 min vs nor KO 120 min	9
	3	001.3	UAMS-1 anaerobic 240 min vs nor KO 240 min	14
	4	001.4	UAMS-1 anaerobic 0 min vs nos KO 0 min	68
	5	001.5	UAMS-1 anaerobic 120 min vs nos KO 120 min	102
	6	001.6	UAMS-1 anaerobic 240 min vs nos KO 240 min	3
	7	001.7	UAMS-1 0 mM DEA NONOate vs WT 2mM DEA NONOate	11
	8	001.8	UAMS-1 0 mM DEA NONOate vs nor KO 0 mM	9
	9	001.9	UAMS-1 0 mM DEA NONOate vs nos KO 0 mM	4
	10	001.10	UAMS-1 2 mM DEA NONOate vs nor KO 2 mM DEA NONOate	12
	11	001.11	UAMS-1 2 mM DEA NONOate vs nos KO 2 mM DEA NONOate	26
	12	001.12	UAMS-1 anaerobic 0 min vs UAMS-1 anaerobic 120 min	8
	13	001.13	UAMS-1 anaerobic 0 min vs UAMS-1 anaerobic 240 min	18
002	14	002.1	UAMS-1 ES vs delta fad	3
	15	002.2	UAMS-1 ES vs delta mocR	12
	16	002.3	UAMS-1 ES vs UAMS-1 LE	26
	17	002.4	UAMS-1 ES vs UAMS-1 EE	34
	18	002.5	UAMS-1 LE vs WT EE	15
	19	002.6	UAMS-1 LE vs delta mocR	7
	20	002.7	UAMS-1 EE vs delta mocR	3
003	21	003.1	Newman vs sulfide treated	15
	22	003.2	Newman vs delta cstR	44
	23	003.3	Newman vs nitroxyl treated	66
	24	003.4	Newman vs calprotectin treated	77
004	25	004.1	USA300 vs PBT2 and Zinc treated	15
005	26	005.1	JE2 vs NE13041	12
	27	005.2	JE2 vs patient P nasal	64
	28	005.3	JE2 vs patient P blood	69
	29	005.4	JE2 vs patient S nasal	73
	30	005.5	JE2 vs patient S blood	73
	31	005.6	Patient P nasal vs patient P blood	17
	32	005.7	Patient S nasal vs patient S blood	7
006	33	006.1	Newman vs walK D119A mutant	50
	34	006.2	Newman vs walK V149A mutant	51
	35	006.3	Newman vs DHBP treated	15
007	36	007.1	HG003 vs rsaE mutant	6
	37	007.2	HG003 vs rsaE plasmid complementation uninduced	57
	38	007.3	HG003 vs rsaE plasmid complementation induced with aTc	52
	39	007.4	rsaE mutant vs rsaE plasmid complementation uninduced	70
	40	007.5	rsaE mutant vs rsaE plasmid complementation induced with aTc	55
	41	007.6	rsaE plasmid complementation uninduced vs induced with aTc	6
008	42	008.1	USA300 vs floxuridine treated	85
	43	008.2	USA300 vs streptozotocin treated	37
009	44	009.1	LYO-S2 4-h biofilm no treatment vs 4-h biofilm fosfomycin treatment	52
	45	009.2	LYO-S2 24-h biofilm no treatment vs 24-h biofilm fosfomycin treatment	127
	46	009.3	LYO-S2 4-h biofilm no treatment vs 24-h biofilm no treatment	53
	47	009.4	4-h biofilm fosfomycin treated vs 24-h biofilm fosfomycin treated	103
010	48	010.1	USA300 untreated vs 10 μM linoleic acid treated	19
011	49	011.1	USA300 30°C vs 37°C	13
012	50	012.1	JE2 MT02-sensitive treated with MT02 vs JE2 MT02-resistant treated with MT02	17
013	51	013.1	USA300 untreated vs treated with spermine NONOate	58
014	52	014.1	IPLA 1 biofilm vs treated with phage phiIPLA-RODI	78
015	53	015.1	ATCC 29213 biofilm untreated vs biofilm treated with TTO	16
016	54	016.1	MRSA1679a vs ATCC 29213	57
017	55	017.1	PR01 vs RNase Y deletion	52
018	56	018.1	MRSA BD02-25 vs delta rsp	42
019	57	019.1	BUSA2288 blue light treatment vs no light treatment	29
020	58	020.1	PR01 0-s decay vs C-terminal deletion of cshA 0-s decay	27
020	59	020.2	PR01 0-s decay vs delta cshA 0-s decay	18
	60	020.3	C-terminal deletion of cshA 0-s decay vs delta cshA 0-s decay	32
021	61	021.1	Newman vs delta saePQRS	23
	62	021.2	Newman vs saeS repaired	18
	63	021.3	Delta saePQRS deletion vs saeS repaired	31
022	64	022.1	Newman untreated vs 10 mM hydrogen peroxide treated	18

^aKO, knockout; nor, nitric oxide reductase gene; nos, nitric oxide synthase gene; DEA NONOate, nitric oxide donor diethylamine NONOate; ES, early stationary; LE, late exponential; EE, early exponential; fad, fatty acid desaturase gene; mocR, mocR regulator gene; cstR, CsoR-like sulfurtransferase repressor gene; PBT2, zinc ionophore; walK, sensor kinase of WalKR two-component system gene; DHBP, 2,4-dihydroxybenzophenone; aTc, anhydrotetracycline; floxuridine, chemotherapy drug (liver cancer); streptozotocin, chemotherapy drug (pancreatic cancer); fosfomycin, cell wall synthesis inhibiting antibiotic; linoleic acid, polyunsaturated omega-6 fatty acid; MT02, DNA replication inhibiting antibiotic; spermine NONOate, nitric oxide donor; TTO, tea tree oil; MRSA16791, methicillin-resistant chicken isolate; ATCC 29213, methicillin-sensitive strain; rsp, transcriptional regulator gene; BUSA2288, human nasal isolate; saeS, histidine kinase sensor of SaePQRS system gene.

^bValues represent numbers of sRNAs with expression increased or decreased >3-fold (total = 303).