Factors that influence HSC clonal counts at different stages of analysis. Methodologic steps of planning, implementation of experiments, and barcode data analysis are shown. For each step, we indicate how experimental setup and approach may influence conclusions of analysis. The diagram aims to point out the factors that we found critical in the currently described experiments, but it is not exhaustive. For instance, the setup of transplantation experiments, number of transplanted cells, and irradiation regimens can also influence clonal counts.