Compatible solutes from hyperthermophiles improve the quality of DNA microarrays

BMC Biotechnology

Table 1 Hypersolutes improve DNA microarray quality parameters

Compatible solute	HECT				DGP				MG
*Concentration (mM)*	10	25	50	*150*	10	25	50	*150*	10	25	50	*150*
Mean raw Q ± SD	2.1 ± 0.05	1.8 ± 0.1	2.6 ± 0.2	2.6 ± 0.2	2.0 ± 0.1	2.0 ± 0.1	2.6 ± 0.4	3.2 ± 0.4	1.9 ± 0.1	2.0 ± 0.1	2.4 ± 0.1	2.5 ± 0.2
% raw Q s vs control	+3.1	-8.3	+0.8	+4.6	-0.5	+1.0	+4.2	+26.5	-5.7	-0.4	-4.0	-0.8
p (t-Test s vs controls)	0.15	0.04*	0.45	0.19	0.43	0.38	0.31	0.01*	0.06	0.45	0.22	0.44
Mean bkg ± SD	69.9 ± 0.9	61.0 ± 3.4	84.5 ± 9.2	89.2 ± 8.4	67.2 ± 1.9	68.9 ± 3.8	91.0± 14.1	117. ± 18.7	62.2 ± 4.4	67.6 ± 1.2	81.3 ± 8.1	86.8 ± 6.0
% bkg s vs control	+3.0	-10.2	-4.1	+1.3	-1.0	+1.4	+3.3	+32.8	-8.4	-0.4	-7.7	-1.4
p (t-Test s vs controls)	0.12	0.01*	0.30	0.43	0.35	0.35	0.37	0.02*	0.04*	0.43	0.16	0.42
Mean SF ± SD	3.9 ± 0.3	4.2 ± 0.3	2.9 ± 0.3	3.2 ± 0.2	4.1 ± 0.1	4.2 ± 0.1	3.4 ± 0.6	2.8 ± 0.4	4.1 ± 0.2	4.0 ± 0.2	2.8 ± 0.1	3.2 ± 0.4
% SF s vs control	-8.0	-0.1	-9.6	-0.4	-1.7	-0.7	+7.9	-11.0	-1.5	-4.0	-11.4	-1.0
p (t-Test s vs controls)	0.04*	0.49	0.17	0.48	0.25	0.40	0.26	0.14	0.33	0.10	0.09	0.46
Mean %P ± SD	29.8 ± 0.4	30.5 ± 1.1	30.4 ± 0.8	29.6 ± 0.7	30.0 ± 0.8	30.1 ± 1.0	30.5 ± 1.6	30.4 ± 1.1	29.7 ± 1.1	29.7 ± 0.9	31.0 ± 1.0	30.8 ± 0.5
%P s vs control	+3.0	+5.3	+1.3	-1.1	+3.6	+3.9	+1.9	+1.3	+2.7	+2.5	+3.6	+2.9
p (t-Test s vs controls)	0.08	0.04*	0.30	0.33	0.08	0.08	0.29	0.32	0.16	0.17	0.11	0.12

Affymetrix quality control parameters; raw Q, background (bkg), scaling factor (SF) and percent present calls (%P): mean and standard deviation (SD) among replicates; % gain of solute(s) respect to the controls, with relative p values. HECT: hydroxyectoine; DGP: potassium diglycerol-phosphate; MG: potassium mannosylglycerate. * p-value < 0.05

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