Fig 1

Fig 1

(A) Images of 2-cell and 8-cell amphioxus embryos, with an illustration of the strategy for RNA-seq. Dashed lines indicate the planes separating blastomeres of each paired sample. The presumptive germ granule-positive (p) and germ granule-negative (n), and animal-tier (a) vs. vegetal-tier (v) blastomeres are indicated. (B) A schematic representation of the experiment using single blastomeres from 2-cell stage embryos (six biological replicates). Blue dot denotes the germ granule in the presumptive germ granule-positive blastomere in each embryo (from 1p to 6p) based on qPCR analysis (S1 Fig); the other cell from the same embryo is designated as the germ granule-negative cell (from 1n to 6n). (C) Hierarchically clustered heatmap based on the Euclidean distances between 2-cell stage samples. Identification of the samples and their batch of origin are shown at the bottom of the heatmap. (D) PCA of the twelve 2-cell stage samples shows strong embryo and batch effects. (E) PCA of the twelve 2-cell stage samples after data normalization to account for individual embryo differences. (F) A schematic representation of the experiment on animal (1a-6a) and vegetal tiers (1v-6v) from 8-cell stage embryos (six biological replicates). Blue dots denote the germ granule that is present in one of the blastomeres of the vegetal tier. (G) Hierarchically clustered heatmap based on the Euclidean distances between 8-cell stage samples. Identification of the samples and batch of origin are shown at the bottom of the heatmap. Batch identities of 5a/v and 6a/v were not recorded. (H) PCA of the twelve 8-cell stage samples shows strong embryo and batch effects. (I) PCA of the twelve 8-cell stage samples after data normalization to account for individual embryo differences.