The system-level identification and analysis of molecular and cellular networks in mammals can be accelerated by 'next-generation' genetics, defined as genetics that does not require crossing of multiple generations of animals to achieve the desired genetic makeup. We recently established a highly efficient procedure for producing knock-out (KO) mice by ‘Triple-CRISPR’ method that targets a single gene by triple gRNAs in the CRISPR/Cas9 system achieves almost perfect KO efficiency (96%-100%). We also established a highly efficient procedure for producing knock-in (KI) mice within a single generation, by ‘ES-mouse’ method, where we treat ES cells using three inhibitors to keep their potency and then inject such ES cells into 8-cell-stage embryos. These procedures dramatically shorten the time required to produce KO or KI mice from about a couple of year down to ∼3 months. The produced KO and KI mice can be also systematically profiled at a single-cell resolution by whole-organ cell profiling realized by a tissue-clearing method ‘CUBIC’ and the advanced light-sheet microscopy. In this talk, I will describe the establishment and application of these technologies to analyze three states (NREM Sleep, REM sleep and awake) of mammalian brains and discuss the current challenges and future opportunities in next-generation mammalian genetics and whole-organ cell profiling for organism-level systems biology.