CRISPR-Cas9-based platform to assess the effect of transcription factor knockout on diapause and development gene expression programs in injected (F0) embryos in the African turquoise killifish (upper). Scheme of the stages for RNA-seq analysis (lower). Six transcription factors (TFs) were selected: REST, FOXO3a, FOXO3b, PPARAa, PPARAb, and PPARG. CRISPR-Cas9-mediated knockouts were conducted by injecting 3 single guide (sgRNAs) per gene in single-cell embryos. Non-injected embryos (wild type) and embryos injected with scrambled sgRNAs (scramble) were used as controls. Genotyping and RNA-seq on individual embryos were performed at two stages: diapause (Dia, blue, 6 days) or development (Dev, orange). A total of 130 single-embryo RNA-seq libraries were generated and analyzed.
