Extended Data Fig. 9. Quantification and validation of clonal structure alteration in aging hematopoiesis.

a, Identification of “expanded clades” in young and aged donors, which are defined as the clades with more than 0.5% of total cell numbers and with expansion significance lower than 0.01. b, The percentage of cells that are contributed from expanded clades are summarised for each donor. c, Related to Fig. 5d, Measuring the clonal contribution by changing the parameters that affect the definition of “clones”. The parameters involved are m (minimum number of cells as a clone, default is 50), n(minimum number of cumulative variants on the branch to cut, default is 1), p (The probability of the variant to be assigned, default is 0.6), and D (Dump small clones with less than D cells). d, Related to Fig. 5f. Single-cell fitness analysis in donor aged-2. e, Related to Fig. 5g. Cell type contributions for each expanded clade for donor aged-2. f-h, Cell-cycle gene expression analysis for expanded versus non-expanded cells. n = 9,519 and 14,715 cells for Aged-1 and Aged-2. Boxplot displays data from the 25th to 75th percentile, and whiskers extending to the minimum and maximum within 1.5 IQR. i-j, Identification of cells with loss of chromosome Y. i, The normalized number of reads on chromosome Y per cell across different donors. j, Binomial test to identify cells that significantly lose chromosome Y with fold-change <0.1 and q-value < 0.001.