What is the difference between negative control and baseline for flow cytometry calcium assays?

A negative control refers to when a sample is designed to have little to no response in terms of the measured factor (in this case calcium signaling). The negative control in a flow cytometry experiment should consist of cells which do not have the specific target protein or antigen. Ideally, these cells would be from a knockout cell line. The negative control cells are treated in the same way as the cells in the main study and subjected to the same experimental conditions. The negative control is used to define specific regions in the data (known as gating regions) and to distinguish between cells that show a positive response and those that don't. 

On the other hand, the baseline is the initial measurement taken before any experimental alterations, serving as a marker for analyzing changes in the measured parameter over time or in response to stimuli. Setting a baseline allows researchers to see how calcium levels change over time or in response to certain treatments. It serves as a starting point for comparison, helping to understand the impact of experimental manipulations on the measured parameter.