• Co-profiling of translatome and transcriptome reveals dynamic gene expression regulation during Drosophila embryogenesis.
• Identification of 2,267 differentially expressed genes between early embryos and S2R+ cells, with 2,147 upregulated in embryos.
• Transcript isoform usage is widespread in both transcription and translation, with an average of 1.9 transcribed and 1.8 translated transcripts per gene.
• High-quality RNA-seq libraries with >85% unique mapping and <6% rRNA contamination enable reliable analysis of translational regulation.