Merav Cohen, Amir Giladi, Oren Barboy, Pauline Hamon, Baoguo Li, Mor Zada, Anna Gurevich-Shapiro, Cristian Gabriel Beccaria, Eyal David, Barbara B. Maier, Mark Buckup, Iris Kamer, Aleksandra Deczkowska, Jessica Le Berichel, Jair Bar, Matteo Iannacone, Amos Tanay, Miriam Merad, Ido Amit, Weizmann Institute of Science [Rehovot, Israël], Sackler School of Medicine, Tel Aviv University (TAU), Icahn School of Medicine at Mount Sinai [New York] (MSSM), Hubrecht Institute [Utrecht, Netherlands], University Medical Center [Utrecht]-Royal Netherlands Academy of Arts and Sciences (KNAW), IRCCS San Raffaele Scientific Institute [Milan, Italie], Universita Vita Salute San Raffaele = Vita-Salute San Raffaele University [Milan, Italie] (UniSR), Chaim Sheba Medical Center, Interactions cerveau-immunité - Brain-immune communication, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), We thank T. Wiesel for artwork and the Dean’s Flow Cytometry CORE and Biorepository and Pathology CoRE Laboratory of the Icahn School of Medicine at Mount Sinai. The research of I.A. and A.T. is supported by the Seed Networks for the Human Cell Atlas of the Chan Zuckerberg Initiative and by Merck KGaA, Darmstadt. I.A. is an Eden and Steven Romick Professorial Chair, supported by the HHMI International Scholar Award, the European Research Council Consolidator grant (no. 724471-HemTree2.0), an MRA Established Investigator award (no. 509044), DFG (no. SFB/TRR167), the Ernest and Bonnie Beutler Research Program for Excellence in Genomic Medicine, the Helen and Martin Kimmel awards for innovative investigation and the SCA award of the Wolfson Foundation and Family Charitable Trust. The Thompson Family Foundation Alzheimer’s Research Fund and the Adelis Foundation also provided support. The laboratory of A.T. is supported by the European Research Council (no. 724824), the I-CORE for chromatin and RNA regulation, a grant from the Israel Science Foundation and a grant from the Kahn Foundation. A.T. is a Kimmel investigator. The laboratory of M.M. is supported by R01 CA257195, R01 CA254104 and Samuel Waxman Cancer Research Foundation. A.G. is funded by the Rothschild Postdoctoral Fellowship of the Yad Hanadiv Foundation., European Project: 724471,ERC-2016-COG,HemTree2.0(2017), and European Project: 724824,scAssembly