Figure 6: Clonal dynamics of adult hematopoiesis following perturbation.

A. 8-week old CARLIN mice were labelled with doxycycline and injected with 5-FU after 10 days. After another 10 days, bone marrow cells were sorted and encapsulated for single-cell RNA sequencing. Schematic created with BioRender.

B. UMAP representation of pooled transcriptome data from control and 5-FU treated mice. See Supplementary Figure 6C,D for the breakdown of clusters and markers used for annotation. Cluster labels as in Figure 5B.

C. Number of statistically significant clones in the first control and 5-FU treated mouse (FDR=0.05; Methods) after downsampling the 5-FU treated mouse to have the same number of cells marked by statistically significant alleles as the control mouse. The control mouse has many small clones. The colors correspond to the legend for (D) below with blue clones containing only HSCs, yellow clones containing only non-HSCs, and green clones containing both.

D. Statistically significant CARLIN alleles (as defined in C) overlaid onto the transcriptome indicating childless HSCs (blue), parent HSCs (green circles), non-HSC cells in an HSC-rooted clone (green diamonds) and non-HSC cells not in an HSC-rooted clone (yellow). The green shaded area corresponds to the HSC cluster in the transcriptome shown in (B).

E. Violin plot showing the distribution of the number of cells in statistically significant HSC-rooted clones (as defined in C) in the first control and 5-FU treated mouse (the green and blue markers in D). The total number of cells in statistically significant HSC-rooted clones is shown in brackets under the sample label.

F. Heatmap indicating occurrence frequency of statistically significant alleles (as defined in C) across different cell types in the first control and 5-FU animals. The clone labels are colored according to the scheme in (D). The number of clones has been downsampled for both animals.

G. Violin plots of log-normalized expression levels of selected genes differentially expressed between the parent and childless HSC cluster group (as defined in Supplementary Figure 6C).

H. Heatmap of the z-score of log-normalized expression levels of genes most differentially expressed between the parent and childless HSC cluster group (as defined in Supplementary Figure 6C).