Figure 1

Transcript isoform analysis pipeline. Mapped reads from the egg and three pre-MBT samples (1-cell, 16-cell and 256-cell) were merged to represent the maternal transcriptome. This period is characterized by absence of transcription and pluripotent blastomeres. Two samples were merged to represent the first zygotic transcriptome, representing the embryo when cells start to differentiate and transcription has begun. The RNA-seq reads were mapped using two different aligners (Tophat and Bioscope) and Cufflinks was used to construct transcriptomes guided by Ensembl annotation. This resulted in a complete gene annotation set (‘all’) comprising both expressed and non-expressed genes and one dataset with robust >3 FPKM level of expression (FPKM > 3). Embryo illustrations are from Kimmel et al. (1995).