Scatter-plot of differential hybridization of fluorescently labeled cDNA from a 3-hour salt shock treated cell culture versus an untreated sample. Log phase cultures were subjected to an upshift in NaCl concentration from ~25 mM to 650 mM. Synechocystis is halotolerant and grows at concentrations up to approximately 1.2 M NaCl. Fluorescently labeled (Cy-3) cDNA derived from total RNA extracted from cells exposed 3 hours to the higher salt concentration was co-hybridized with Cy-5-labelled cDNA derived from the culture immediately prior to the upshift (control cells). The full genome Synechocystis sp. PCC 6803 high-density microarrays contain DNA features printed in triplicate on glass slides. The gene names according to original annotation are behind the arrows. As indicated with arrows, signals from the replicated elements exhibited similarity in the estimated expression ratio. Each data point corresponds to a different gene address on the microarray and each gene is replicated at three separate and spatially distant addresses. The X and Y axes correspond to the normalized fluorescence intensity of fluorescence-labeled cDNA of the control sample (Y-axis, Cy-5, 532 nm fluorescence) and the 650 mM NaCl three hour time point (X-axis, Cy-3, 635 nm fluorescence).