Fig. 1. Use of homeotic mutants to deconvolve lineage-specific expression from transcript profiles. Wild-type and mutant embryos were staged in small cohorts by morphology at the four-cell stage and collected in replicate at the ten time points indicated by black dots in A. The complete lineage through the 190-cell stage is depicted for wild type in A, and hypothetical lineages are depicted for pie-1(zu154) in B and mex-3(zu155); skn-1(RNAi) in C. Lineages specified by SKN-1 and PAL-1 are blue and red, respectively, and the pattern of cell fates produced is indicated below the wild-type lineage in A. (D) Approximate fraction of the embryo with different lineage identities for each genotype, with expected changes in transcript abundance for lineage-specific genes in parentheses.