Performance of the Human TReg Chip. (a) Comparability to Affymetrix. Splitted samples (FOXP3 or GFP transfected T cells) were hybridized to Affymetrix HG_U133A microarrays and Human TReg Chips, respectively. Differentially expressed genes on the Affymetrix platform (regulation of at least 1.5-fold based on significant signal) were compared with those significant fold changes arising from the Human TReg Chip platform. As demonstrated, 29 out of 36 genes exhibited similar regulation on the Human TReg Chip compared with Affymetrix, resulting in a correlation of 81%. (b) Hybridization controls. Normalized signal intensities versus concentration of used hybridization controls are plotted as means of 5 (1.5 pmol/l, 25 pmol/l and 100 pmol/l) and 59 experiments applying the Human TReg Chip. Standard deviations are indicated by error bars. Linear regression yields a correlation coefficient of >0.96 demonstrating a linear hybridization process covering more than three orders of magnitude of concentrations. (c) Reproducibility of the Human TReg Chip. The same sample was hybridized to several Human TReg Chips. A log-log plot of normalized signal intensities of two example selected slides is illustrated, showing that 99.7% of all signals are located along the bisecting line within the twofold range, reflecting low measurement noise in the data, even for low signal intensities. (d) Coefficients of variation (CV). The ratios of standard deviation and mean were calculated for each gene probed in eight replicates per microarray. CVs of all 59 experiments applying the Human TReg Chip contributing to the expression profile of human TReg cells are presented as means. As demonstrated, 73% of all signals have a CV below 0.3.
Pfoertner et al. Genome Biology 2006 7:R54 doi:10.1186/gb-2006-7-7-r54