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Given that ESCs and NSCs are selected as cells engaged in the cell cycle, whereas HSCs are thought to be predominantly quiescent (37, 38), one would expect the ESC/NSC overlap (relative to the ESC/HSC overlap) to be enriched for genes with cell cycle functions. However, this is not the case: 11.7% of genes overlapping between ESCs and NSCs contain the annotation "cell cycle," whereas that number is 13.1% in the ESC/HSC overlap (12). In fact, this high ESC/NSC overlap is not biased for genes containing other Gene Ontology annotations such as "growth," "nucleus/nucleic," "cell communication," "metabolism," or "stress/response," and only minor biases can be detected in the categories "cytoplasm" and "chaperone" (12). It is unlikely that the preferential overlap between ESCs and NSCs has to do with the fact that both are cultured in vitro, because ESCs and NSCs are grown in very different conditions: ESCs attached to fibroblast feeders in serum and NSCs in floating clusters without serum (12). Moreover, the ESC/NSC overlap is very extensive, including more than 60% of ESC-enriched genes.
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We thank M. C. Kao and W. Wong for calculating the P value for the enrichment of chromosome 17 for SC-enriched genes. We thank C. Stewart for C57BI/6 ESC, and the following people for advice: S. Kume (ESC culture), F. Doetsch (NSC culture), R. Baugh (mRNA amplification), J. Couget (array hybridization), and C. Li and W. Wong (dChip software). We thank W. Wong, N. Benvenisty, F. Doetsch, R. Baugh, S. Haggarty, E. Lammert, D. Cavalieri, and C. Annerén for critical reading of the manuscript. M.R.-S. was supported in part by a predoctoral fellowship from the Foundation for Science and Technology, Portugal, and dedicates this article to the memory of Francisco Varela (1946-2001), neuroscientist, theoretical biologist, and co-author of the concept of "autopoiesis," an inspiration for this world Research was supported by NIH grants R24 DK56947 (D.A.M.) and P60 HL54785 (R.C.M.) and in part by a grant from Amgen (R.C.M.); R.C.M. is an equity-holding consultant for Amgen; D.A.M. is an investigator of the HHMI. Inquiries regarding HSC purification should be addressed to R.C.M. (mulligan@rascal.med.harvard.edu).
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