strategy that allows two transcripts to be identified by a single bead color (STAR Methods and Figure 1B). 955 shRNAs targeting landmark transcripts were used to empirically validate L1000 probes (Figure 1C). The final assay, which we call L1000, contains 1,058 probes for 978 landmark transcripts and 80 control transcripts (Table S2) chosen for their invariant expression across cell states (see STAR Methods). The reagent cost of the L1000 assay is approximately $2.
