For downstream analyses, technical replicates on each plate were aggregated using average values. Analogously to the processing steps for gene expression arrays, we regressed out batch (derived from the date of staining), media type, gender, passage number, plating technician, fixation technician, and the technician in charge of the staining. Analyses of proportions of responding cells are based on estimates of the proportion of responding cells (Fig. 1c,d). Analyses that consider intensities were based on quantitative expression estimates, averaged across individual markers for a given layer (Extended Data Fig. 1c).
