Fig. 3

Cell Hashing enables efficient experimental optimization and identification of low-quality cells. a–c We performed a titration series to assess optimal staining concentrations for a panel of CITE-seq immunophenotyping antibodies. Normalized ADT counts for CD8 (a), CD45RA (b), and CD4 (c) are depicted for the different concentrations used per test. d Titration curve depicting the staining index (SI; “Methods” section) for these three antibodies across the titration series. The signal/noise ratio for these antibodies begins to saturate at levels similar to manufacturer recommended staining concentrations typical for flow cytometry antibodies. e Cells with low UMI counts can be distinguished from ambient RNA using HTO classifications. Classified singlets group into canonical hematopoietic populations. f Barcodes classified as “negative” do not group into clusters and likely represent “empty” droplets containing only ambient RNA