Sankaran, V. G. et al. Human fetal hemoglobin expression is regulated by the developmental stage-specific repressor BCL11A. Science 322, 1839–1842 (2008).
Google Scholar
Sawai, C. M. et al. Hematopoietic stem cells are the major source of multilineage hematopoiesis in adult animals. Immunity 45, 597–609 (2016).
Google Scholar
Eaves, C. J. Hematopoietic stem cells: concepts, definitions, and the new reality. Blood 125, 2605–2613 (2015).
Google Scholar
Ikuta, K. & Weissman, I. L. Evidence that hematopoietic stem cells express mouse c-kit but do not depend on steel factor for their generation. Proc. Natl Acad. Sci. USA 89, 1502–1506 (1992).
Google Scholar
Morrison, S. J. & Weissman, I. L. The long-term repopulating subset of hematopoietic stem cells is deterministic and isolatable by phenotype. Immunity 1, 661–673 (1994).
Google Scholar
Ogawa, M. et al. B cell ontogeny in murine embryo studied by a culture system with the monolayer of a stromal cell clone, ST2: B cell progenitor develops first in the embryonal body rather than in the yolk sac. EMBO J. 7, 1337–1343 (1988).
Google Scholar
Adolfsson, J. et al. Upregulation of Flt3 expression within the bone marrow Lin–Sca1+c-kit+ stem cell compartment is accompanied by loss of self-renewal capacity. Immunity 15, 659–669 (2001).
Google Scholar
Christensen, J. L. & Weissman, I. L. Flk-2 is a marker in hematopoietic stem cell differentiation: a simple method to isolate long-term stem cells. Proc. Natl Acad. Sci. USA 98, 14541–14546 (2001).
Google Scholar
Kiel, M. J. et al. SLAM family receptors distinguish hematopoietic stem and progenitor cells and reveal endothelial niches for stem cells. Cell 121, 1109–1121 (2005).
Google Scholar
Yang, L. et al. Identification of Lin–Sca1+kit+CD34+Flt3– short-term hematopoietic stem cells capable of rapidly reconstituting and rescuing myeloablated transplant recipients. Blood 105, 2717–2723 (2005).
Google Scholar
Arinobu, Y. et al. Reciprocal activation of GATA-1 and PU.1 marks initial specification of hematopoietic stem cells into myeloerythroid and myelolymphoid lineages. Cell Stem Cell 1, 416–427 (2007).
Google Scholar
Cabezas-Wallscheid, N. et al. Identification of regulatory networks in HSCs and their immediate progeny via integrated proteome, transcriptome, and DNA methylome analysis. Cell Stem Cell 15, 507–522 (2014).
Google Scholar
Oguro, H., Ding, L. & Morrison, S. J. SLAM family markers resolve functionally distinct subpopulations of hematopoietic stem cells and multipotent progenitors. Cell Stem Cell 13, 102–116 (2013).
Google Scholar
Ooi, A. G. et al. The adhesion molecule esam1 is a novel hematopoietic stem cell marker. Stem Cells 27, 653–661 (2009).
Google Scholar
Pietras, E. M. et al. Functionally distinct subsets of lineage-biased multipotent progenitors control blood production in normal and regenerative conditions. Cell Stem Cell 17, 35–46 (2015).
Google Scholar
Rodriguez-Fraticelli, A. E. et al. Clonal analysis of lineage fate in native haematopoiesis. Nature 553, 212–216 (2018).
Google Scholar
Wilson, A. et al. Hematopoietic stem cells reversibly switch from dormancy to self-renewal during homeostasis and repair. Cell 135, 1118–1129 (2008).
Google Scholar
Wilson, N. K. et al. Combined single-cell functional and gene expression analysis resolves heterogeneity within stem cell populations. Cell Stem Cell 16, 712–724 (2015).
Google Scholar
Yamamoto, R. et al. Clonal analysis unveils self-renewing lineage-restricted progenitors generated directly from hematopoietic stem cells. Cell 154, 1112–1126 (2013).
Google Scholar
Yokota, T. et al. The endothelial antigen ESAM marks primitive hematopoietic progenitors throughout life in mice. Blood 113, 2914–2923 (2009).
Google Scholar
Ng, S. Y., Yoshida, T., Zhang, J. & Georgopoulos, K. Genome-wide lineage-specific transcriptional networks underscore Ikaros-dependent lymphoid priming in hematopoietic stem cells. Immunity 30, 493–507 (2009).
Google Scholar
Mansson, R. et al. Molecular evidence for hierarchical transcriptional lineage priming in fetal and adult stem cells and multipotent progenitors. Immunity 26, 407–419 (2007).
Google Scholar
Herman, J. S., Sagar & Grun, D. FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data. Nat. Methods 15, 379–386 (2018).
Google Scholar
Gilfillan, S., Dierich, A., Lemeur, M., Benoist, C. & Mathis, D. Mice lacking TdT: mature animals with an immature lymphocyte repertoire. Science 261, 1175–1178 (1993).
Google Scholar
Alberti-Servera, L. et al. Single-cell RNA sequencing reveals developmental heterogeneity among early lymphoid progenitors. EMBO J. 36, 3619–3633 (2017).
Google Scholar
Balciunaite, G., Ceredig, R., Massa, S. & Rolink, A. G. A B220+CD117+CD19− hematopoietic progenitor with potent lymphoid and myeloid developmental potential. Eur. J. Immunol. 35, 2019–2030 (2005).
Google Scholar
Klein, F. et al. Accumulation of multipotent hematopoietic progenitors in peripheral lymphoid organs of mice over-expressing interleukin-7 and Flt3-ligand. Front Immunol. 9, 2258 (2018).
Google Scholar
Dress, R. J. et al. Plasmacytoid dendritic cells develop from Ly6D+ lymphoid progenitors distinct from the myeloid lineage. Nat. Immunol. 20, 852–864 (2019).
Google Scholar
Rodrigues, P. F. et al. Distinct progenitor lineages contribute to the heterogeneity of plasmacytoid dendritic cells. Nat. Immunol. 19, 711–722 (2018).
Google Scholar
Stoeckius, M. et al. Simultaneous epitope and transcriptome measurement in single cells. Nat. Methods 14, 865–868 (2017).
Google Scholar
Melania Barile, K. B. et al. Hematopoietic stem cells self-renew symmetrically or gradually proceed to differentiation. Preprint at CellPress https://doi.org/10.2139/ssrn.3787896 (2021).
Gazit, R. et al. Transcriptome analysis identifies regulators of hematopoietic stem and progenitor cells. Stem Cell Rep. 1, 266–280 (2013).
Google Scholar
Heng, T. S. et al. The Immunological Genome Project: networks of gene expression in immune cells. Nat. Immunol. 9, 1091–1094 (2008).
Google Scholar
Carrelha, J. et al. Hierarchically related lineage-restricted fates of multipotent haematopoietic stem cells. Nature 554, 106–111 (2018).
Google Scholar
Mitjavila-Garcia, M. T. et al. Expression of CD41 on hematopoietic progenitors derived from embryonic hematopoietic cells. Development 129, 2003–2013 (2002).
Google Scholar
Street, K. et al. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 19, 477 (2018).
Google Scholar
Ishibashi, T. et al. ESAM is a novel human hematopoietic stem cell marker associated with a subset of human leukemias. Exp. Hematol. 44, 269–281 e261 (2016).
Google Scholar
Sudo, T. et al. The endothelial antigen ESAM monitors hematopoietic stem cell status between quiescence and self-renewal. J. Immunol. 189, 200–210 (2012).
Google Scholar
Sun, J. et al. Clonal dynamics of native haematopoiesis. Nature 514, 322–327 (2014).
Google Scholar
Busch, K. et al. Fundamental properties of unperturbed haematopoiesis from stem cells in vivo. Nature 518, 542–546 (2015).
Google Scholar
Sommerkamp, P. et al. Mouse multipotent progenitor 5 cells are located at the interphase between hematopoietic stem and progenitor cells. Blood 137, 3218–3224 (2021).
Google Scholar
Pei, W. et al. Polylox barcoding reveals haematopoietic stem cell fates realized in vivo. Nature 548, 456–460 (2017).
Google Scholar
Boyer, S. W., Schroeder, A. V., Smith-Berdan, S. & Forsberg, E. C. All hematopoietic cells develop from hematopoietic stem cells through Flk2/Flt3-positive progenitor cells. Cell Stem Cell 9, 64–73 (2011).
Google Scholar
Buza-Vidas, N. et al. FLT3 expression initiates in fully multipotent mouse hematopoietic progenitor cells. Blood 118, 1544–1548 (2011).
Google Scholar
Drexler, H. G., Sperling, C. & Ludwig, W. D. Terminal deoxynucleotidyl transferase (TdT) expression in acute myeloid leukemia. Leukemia 7, 1142–1150 (1993).
Google Scholar
Cuneo, A. et al. Clinical review on features and cytogenetic patterns in adult acute myeloid leukemia with lymphoid markers. Leuk. Lymphoma 9, 285–291 (1993).
Google Scholar
Campagnari, F., Bombardieri, E., de Braud, F., Baldini, L. & Maiolo, A. T. Terminal deoxynucleotidyl transferase, TdT, as a marker for leukemia and lymphoma cells. Int. J. Biol. Markers 2, 31–42 (1987).
Google Scholar
Srinivas, S. et al. Cre reporter strains produced by targeted insertion of EYFP and ECFP into the ROSA26 locus. BMC Dev. Biol. 1, 4 (2001).
Google Scholar
Muzumdar, M. D., Tasic, B., Miyamichi, K., Li, L. & Luo, L. A global double-fluorescent Cre reporter mouse. Genesis 45, 593–605 (2007).
Google Scholar
Trichas, G., Begbie, J. & Srinivas, S. Use of the viral 2A peptide for bicistronic expression in transgenic mice. BMC Biol. 6, 40 (2008).
Google Scholar
Jacobi, A. M. et al. Simplified CRISPR tools for efficient genome editing and streamlined protocols for their delivery into mammalian cells and mouse zygotes. Methods 121–122, 16–28 (2017).
Google Scholar
Haueter, S. et al. Genetic vasectomy-overexpression of Prm1-EGFP fusion protein in elongating spermatids causes dominant male sterility in mice. Genesis 48, 151–160 (2010).
Google Scholar
Klein, F. et al. The transcription factor Duxbl mediates elimination of pre-T cells that fail beta-selection. J. Exp. Med. 216, 638–655 (2019).
Google Scholar
Pronk, C. J. et al. Elucidation of the phenotypic, functional, and molecular topography of a myeloerythroid progenitor cell hierarchy. Cell Stem Cell 1, 428–442 (2007).
Google Scholar
von Muenchow, L. et al. Permissive roles of cytokines interleukin-7 and Flt3 ligand in mouse B-cell lineage commitment. Proc. Natl Acad. Sci. USA 113, E8122–E8130 (2016).
Nakano, T., Kodama, H. & Honjo, T. Generation of lymphohematopoietic cells from embryonic stem cells in culture. Science 265, 1098–1101 (1994).
Google Scholar
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Google Scholar
Griffiths, J. A., Richard, A. C., Bach, K., Lun, A. T. L. & Marioni, J. C. Detection and removal of barcode swapping in single-cell RNA-seq data. Nat. Commun. 9, 2667 (2018).
Google Scholar
Lun, A. T., Bach, K. & Marioni, J. C. Pooling across cells to normalize single-cell RNA sequencing data with many zero counts. Genome Biol. 17, 75 (2016).
Google Scholar
McCarthy, D. J., Campbell, K. R., Lun, A. T. & Wills, Q. F. Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. Bioinformatics 33, 1179–1186 (2017).
Google Scholar
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e29 (2021).
Google Scholar
Amezquita, R. A. et al. Orchestrating single-cell analysis with Bioconductor. Nat. Methods 17, 137–145 (2020).
Google Scholar
Murtagh, F. L. P. Ward’s hierarchical agglomerative clustering method: which algorithms implement Ward’s criterion? J. Classification 31, 274–295 (2014).
Langfelder, P., Zhang, B. & Horvath, S. Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics 24, 719–720 (2008).
Google Scholar
Scialdone, A. et al. Computational assignment of cell-cycle stage from single-cell transcriptome data. Methods 85, 54–61 (2015).
Google Scholar
Aran, D. et al. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat. Immunol. 20, 163–172 (2019).
Google Scholar
Yoshida, H. et al. The cis-regulatory atlas of the mouse immune system. Cell 176, 897–912.e20 (2019).
Google Scholar
Biddy, B. A. et al. Single-cell mapping of lineage and identity in direct reprogramming. Nature 564, 219–224 (2018).
Google Scholar
Dong, F. et al. Differentiation of transplanted haematopoietic stem cells tracked by single-cell transcriptomic analysis. Nat. Cell Biol. 22, 630–639 (2020).
Google Scholar
Rodriguez-Fraticelli, A. E. et al. Single-cell lineage tracing unveils a role for TCF15 in haematopoiesis. Nature 583, 585–589 (2020).
Google Scholar
Becht, E. et al. Dimensionality reduction for visualizing single-cell data using UMAP. Nat. Biotechnol. 37, 38–44 (2018).
Saelens, W., Cannoodt, R., Todorov, H. & Saeys, Y. A comparison of single-cell trajectory inference methods. Nat. Biotechnol. 37, 547–554 (2019).
Google Scholar
Cao, J. et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature 566, 496–502 (2019).
Google Scholar
Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902 (2019).
Google Scholar
