Figure 3. Differential transcript enrichment of notch target genes in cells that could not be distinguished by global transcript signatures.

(A) AB descendants from five replicates of the 8-cell stage embryo.

(B) Genome browser tracks of ABxx transcriptomes, sorted into groups based on expression of notch target genes hlh-27, ref-1 and tbx-38 (Extended Methods). Last exons only are shown.

(C) Example of smFISH targeting hlh-27 (C´, yellow arrows) and ref-1 (C′, purple arrows) transcripts in intact 6- or 8-cell stage embryos (hlh-27 pattern seen in 100% of embryos, n=4. ref-1 pattern seen in 75% of embryos, n=4. Remaining embryo showed ubiquitous ref-1 staining).

(D) Example of smFISH targeting tbx-38 (D´, yellow arrows) in intact 8-cell stage embryos (pattern seen in 33% of embryos, n=3. 67% of embryos showed equal tbx-38 expression in ABal and ABar). (D′) nos-2 (P₃-specific) marks the posterior of the embryo.

(E) AB descendants from six replicates of the 16-cell stage embryo.

(F) Genome browser tracks of ABxxx transcriptomes, sorted into four groups based on a PCA using only notch target gene expression (shown in Figure S2D). Last exons only are shown.

(G) Example of smFISH targeting hlh-27 (G´, yellow arrows) and ref-1 (G′, purple arrows) transcripts in intact 15-cell stage embryos (both patterns seen in 100% of embryos, hlh-27 n=5, ref-1 n=2).

(H) Example of smFISH targeting tbx-38 (H´, yellow arrows) in intact 15-cell stage embryos (pattern seen in 100% of embryos, n=14). nos-2 (P₄-specific) marks the posterior of the embryo. See Figures S1 and S2 for further identification of ABx, ABxx, and ABxxx transcriptomes.

See also Figure S1, S2