CyTOF Immune Cell Profiling Panels

For CyTOF, two panels were used (Supplementary Table S1). The panel design tool provided by Fluidigm (now Standard BioTools Inc.) was used. Noisy channels (e.g., 157 Gd) were unused to minimize signal spill over. Antibodies against bright/widely expressed antigens were in “dimmer” channels and antibodies against rare or low expressing proteins were used in channels with high sensitivity/less prone to spill over. The first panel with 42 markers was used on live/nonfixed samples and consisted of antibodies targeting proteins on the cell surface of immune cells. This panel was used on BM cells and included marker used to identify progenitor cells in this tissue. The second panel contained lineage antibodies and antibodies targeting intracellular proteins. In this case, samples were fixed. Markers that were not required for delineating major cell populations (CD150, CD24) or targets that did not withstand fixation (e.g., CD103) were removed to reduce background. Flow cytometry antibodies are listed in Supplementary Table S2.