Quantification of early intrathymic niches using multicongenic fate mapping. Up to 12-code library of congenic/fluorescent tagged BM progenitors (multicongenic library) was generated by intercrossing of several mouse strains (Table S1). A mixture (4.8 × 10⁴ to 15 × 10⁴ cells/recipient mouse) consisting of defined ratios of such progenitors (Table S1, input [I], [II[, and [III]) was injected into nonmanipulated WT and DKO recipient mice (three independent experiments). Thymi of recipient mice were analyzed 21 d after progenitor injection. (A) Quantification of TSPNs was performed using an algorithm based on Monte Carlo simulation. Bold numbers above each boxplot represent the median number of TSPNs for each genotype. Numbers in brackets indicate 95% confidence intervals. Data from two experiments are depicted, n = 10 (WT), n = 4 (IL-7Rα^−/−), n = 18 (DKO). (B) Distribution of individual tags (each color represents one tag) within donor cells (100%) in different recipient mice 21 d after transfer. Input bar represents distribution of 12 tags within the progenitor mixture, which was injected into individual recipients at day 0. Numbers above each column indicate missing tags in each representative recipient; n = 6 (WT), n = 4 (IL-7Rα^−/−), n = 6 (DKO). Recipient mice were 4 to 7 wk old. Donor mice were 7 to 10 wk old.