Figure 2

Expression variation among the samples. (A) and (B) show scatter plot comparisons of the mean Nog+Dkk or Dor stg. 10 log₂ expression values vs the mean stg. 10 Ven log₂expression values. Probe sets measuring two known organizer genes, otx2 (green) and gsc (red), are labeled within the plots (otx2 probe sets: Xl.1268.1.S1_at, Xl.3004.1.A1_at, Xl.11672.1.A1_at, and XlAffx.1.11.S1_at; gsc probe sets: Xl.801.1.A1_at, Xl.801.1.S1_at, and Xl.801.1.S1_s_at). (C) R-square regression value summaries for each experimental condition compared to the stage-matched ventral condition. (D) Scatter plot comparison of the mean Nog and Ven clutch-1 log₂ expression values vs. the mean Nog and Ven clutch-2 log₂ expression values. Note that the clutch variation clearly exceeds differences between the experimental conditions (A-C). Contributing to this variation, many genes show a shift in the average expression between the two clutches, but retain a similar pattern in response to the experimental conditions. As an example, log₂ expression values for otx5-A (Xl.3452.1.A1_at) are shown in (E). After standardizing the average log₂ expression of both clutches, on a gene-by-gene basis, the comparison from (D) was repeated in (F), eliminating most clutch variation.