Gene regulatory network (GRN) construction pipeline flowchart. Avisualization of how an embryonic transcriptome fits into the workflow forconstructing a validated GRN. The transcriptome forms the foundation of theGRN because it represents all the transcripts present in the scope of thenetwork. The next immediate datasets to produce are represented at thesecond level: a high-density, quantitative RNA-seq timecourse which will bemapped to the full transcriptome, for the purpose of high resolutioncovariance analysis, a ‘Perturbation-seq’ where RNA-seq is usedon embryos treated with drugs to major signaling pathways, and a globalsequencing effort for cis- regulatory elements using eitherFAIRE-seq or DNase hypersensitivity. Computational analysis of thesedatasets will produce an interactome with important nodes highlighted. Moresensitive investigation of spatial expression, coexpression and perturbationexpression (after morpholino treatment) will take the interactome to thelevel of a preliminary GRN. Finally, cis- regulatory analysis ofsubcircuit function will produce a verified GRN.