TALE- and NF-Y-dependent Genes in 12 hpf Zebrafish Embryos

In this RNA-seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE (PBCAB) or NF-Y (NF-YA DN). We normalized each dominant negative condition to GFP. For PBCAB, we find 646 downregulated and 854 upregulated genes. For NF-YA DN, we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription, development, and homeodomain ontologies, while genes downregulated by NF-YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF-YA DN; these genes are enriched for transcription, development, and homeodomain ontologies. Zebrafish embryos were injected at the 1-cell stage with either a dominant negative Pbx (PBCAB), dominant negative NF-YA (NF-YA DN), or GFP (control). Three replicates of 50-100 embryos per condition were collected at 12 hpf and total RNA was extracted. Libraries of polyadenylated RNAs were prepared and sequenced using the BGISEQ-500 platform.