Trevigen’s 96-Well CometChip® System (Figure 1) is a high through-put 96 well platform to treat, electrophorese and measure DNA damage, in one or more cell types, on a single slide using the comet assay. The CometChip® is an array of spatially encoded micropores patterned on agarose. 96 separate macrowells, each containing ~400 micropores, are created by inserting the CometChip® into a magnetically sealable cassette. Cells added to each macrowell are deposited by gravity into the micropores - creating a pattern of non-overlapping cells (Figure 3A, Section IX Data Interpretation). Multiple experimental conditions are performed and evaluated in parallel by the addition of different chemicals to respective wells. Once treatment is complete and the CometChip® removed from the magnetic cassette, an LMAgarose overlay is added to immobilize the cells within the micropores. When performing the Alkaline CometAssay®, the CometChip® is immersed in Lysis Buffer for gentle cellular lysis, followed by Alkaline Solution to unwind and denature the DNA and hydrolyze sites of damage. Comets are developed by alkaline electrophoresis using Trevigen’s CometAssay® Electrophoresis System. Subsequent staining with SYBR® Gold, a fluorescent DNA intercalating dye, allows visualization of the comet tail shape for assessment of DNA damage by fluorescence microscopy.