Extended Data Fig. 4. IM niche refilling is independent of Nr4a1 and repopulated IMs are largely similar to native IMs 14 days post-DT in IM^DTR mice.

a, Bar graphs showing % of Nr4a1^+/+ donor, Nr4a1^−/− donor and host chimerism in the indicated cell populations from lethally-irradiated, thorax-protected CD45.1/CD45.2 IM^DTR mice transplanted with a 1:1 mix of CD45.2 Nr4a1^−/− and CD45.1 Nr4a1^+/+ BM cells, injected with 50 ng DT i.p. 4 weeks later and evaluated at day 7 post-DT. b, Principal Component (PC) analysis plot with % indicating the variability explained by each PC component, obtained by bulk RNA-seq analysis of lung cMo, AMs, CD206⁻ IMs and CD206⁺ IMs from untreated IM^DTR mice, and of lung CD206⁻ IMs and CD206⁺ IMs from DT-treated IM^DTR mice at day 14 post-DT (n = 3 pooled mice per replicate, 3 replicates per condition). c, Volcano plots depicting the DEG between native and repopulated CD206⁻ IMs (left) and native and repopulated CD206⁺ IMs (right). Transcripts significantly upregulated in native and repopulated IM subsets are colored in blue and red, respectively (log₂ fold-change ± 1 and adjusted P value < 10⁻²). d, Bar graph showing lung IM numbers assessed by flow cytometry in IM^DTR mice treated or not with DT i.p. at day 0 and 14, and analyzed 24 h after the last DT treatment (day 15). Data show mean ± SEM and are pooled from 2 independent experiments (a,d) (a,d: n = 4,7-8 mice per group, respectively). P values were calculated using a one-way ANOVA with Tukey’s post-hoc tests, and compare donor CD45.1 Nr4a1^+/+ chimerism between cell populations in a. Raw data and P values are provided as a source data file. ^**, P < 0.01; ^****, P < 0.0001. ns, not significant.

Source data