Assuming that the cells of interest are healthy and intact prior to beginning the procedure, the biggest source of failure comes from variations in cell number. In general, the addition of too many cells leads to “under transposition” (with a majority of large fragments), while the addition to too few cells leads to “over transposition” and a preponderance of short fragments on the gel, and the possible elimination of any banding pattern. When applying this protocol to non-human cells, we see large differences in the number of required cells depending on the species; however, variation in outcome can also come from different cell types as well. If results using the standard protocol are not ideal, an efficient method for optimization is to scale the reaction down 10x and to optimize the lysis methods as well as the cell number, starting from 5,000 cells per reaction. The nucleosomal banding pattern shown in Figure 2 is correlated with high quality libraries.
