Data quality of expression measurements of FACS-sorted cells. a Enrichment of genes in two replicates of sorting by a pha-4 reporter. Known pharyngeal genes defined as early or late embryonic in Gaudet et al.  are shown in red and blue, respectively. b Enrichment of mRNAs corresponding to markers used for sorting. Promoter fusions are shown in red, while protein fusions are shown in green. c Comparison of number of sorted cell identities (out of 1341 embryonic cell identities) in a sorted fraction with the number of genes enriched (red) or depleted (blue). d Number of genes enriched or depleted in different numbers of sorted fractions. e Enrichment of time-specific genes in cells sorted by cnd-1. The proportion of the total cells expressing the cnd-1 reporter is shown in blue. (The lineage data ends at 400 min. The dotted line indicates that by eye, expression appears to continue through hatch in a similar number of cells.) f Same as (e), except for cells sorted using a pros-1 reporter. g Comparison of tissues present in sorted fractions, with enrichment of known tissue-specific genes found by Spencer et al. . There is one point for each pairing of a tissue t with a sort fraction s. The x-axis shows the enrichment of cells with known tissue t in sort fraction s. The y-axis shows the average enrichment in sort fraction s of genes annotated as expressed in tissue t by Spencer et al.