Figure 1.

Cross-validity of Tat samples and RNA isolation. (A) Cross-validity of the duplicate Tat samples analyzed. With a total of 32 gene chips, we analyzed the reliability of the gene chip samples relative to their respective replicate. The scatter graph logarithmically plots the signal intensity values of probe sets for one sample against those for a sample replicate. Each graph point indicates a common probe set between the two data sets and the value is determined by the intersection of the x and y values for that probe set. 2-fold, 3-fold, and 10-fold change lines are defined by the following equations: y = 2x and y = 1/2x, y = 3x and y = 1/3x, y = 10x and y = 1/10x, y = 30x and y = 1/30x. Yellow spots represent probes with absent-absent, absent-marginal, marginal-absent, and marginal-marginal detection calls on sample replicates. Blue spots represent those with absent-present, present-absent, marginal-present, and present-marginal calls, while red spots represent probe sets with present-present detection calls. (B) Cytoplasmic RNA was isolated from all experimental and corresponding control samples, and quantitated by UV spectrophotometric analysis; 3 μg was run on a 1% agarose gel for visual inspection. (C) IP/Westerns for Tat protein. Lanes 1–3 are from eTat extracts and Lanes 4–6 are from control pCep4 cells; unsynchronized cells are shown in Lanes 1 and 4.