Figure 2

A) Median intensity for all barcodes, including downtags, uptags and unassigned barcodes (used to measure background). Median is used due to non-normal intensity distributions (see B). Tiling intensities are consistently higher than TAG4, which are higher than TAG3. This trend is intensified by the addition of antibody staining. Downtags are consistently higher than uptags, as previously described [14]. Background intensity on all three generations is similar. B) Distributions of downtag intensity. Downtag intensity axis is shown on a logarithmic scale. Magnified view of high intensity values in inset. TAG3 and TAG4 arrays have more downtags at a lower intensity than the tiling array. As expected, after antibody staining, intensities were amplified, and the distributions have longer tails.