Fig. 3

Clonal tracking in blood and bone marrow cells exerts high overlap between detected clones. A UMAP plot showing single-cell transcriptomes of sorted BM populations in which barcodes (BC) were detected (all cells which had over 50,000 reads, mitochondrial gene count < 10%, and barcode read count > 3 were included), analyzed cell numbers and cell QC (Additional file 5: Table S3, Additional file 8: Fig. S4B-E. B UMAP plot showing cell clusters based on single-cell transcriptomes of BM populations in mouse 2 (28 weeks post-transplantation). C UMAP plot representing clone A cells carrying barcode rank 9 in mouse 2 in the BM, bar plot representing PB lineage output (multilineage—PEMB, contribution to all 4 lineages > 0.089% at 2 consecutive time points) and the distribution of this barcode within the BM cell types profiled—depicted as a bar plot scaled from 0 to 100%, with labels at 25, 50, 75, and 100%. The adjacent bar shows the contribution of this clone to blood lineages, where total blood output is expressed as 100% and major ticks are 25, 50, and 75%. D As for C, but clone B is shown. This clone was classified as having platelet-erythroid-myeloid-restricted output (PEM, contribution to P, E, M > 0.089% and B lineages < 0.089% at 2 time points) and the distribution of this barcode within the BM cell types profiled—depicted as a bar scaled from 0 to 100%, with labels at 25, 50, and 75%. The adjacent bar shows the contribution of this clone to blood lineages, where total blood output is expressed as 100%, and major ticks are 25, 50, and 75%. E–H Clonal contribution of LT-HSC at 12 and 28 weeks post-transplantation in control animals injected with PBS. Heat maps representing the log fractional contributions of the top 90% most abundant contributing clones retrieved from each different bone marrow (BM) and peripheral blood (PB) cell lineage population, which were normalized per 1000. Each individual row represents the fractional contributions from an individual barcode (clone), and each individual column represents a sample. The rows are ordered by unsupervised hierarchical clustering using Euclidean distances to group barcoded clones together that manifest similar patterns of clonal contributions. The color scale on the right depicts the log10 fractional contribution size. Samples include Lin-Sca1 + cKit + CD150 + 48 − hematopoietic stem cells (LT-HSC), megakaryocytic progenitors (MkP), erythroid progenitors (CFU-E), platelets, erythroid cells (E), B cells (B), and CD11b + monocytes (Mac). I Bubble plot depicting the cumulative PB contribution of different types of clones in 4 control, vehicle-treated animals (mice 1–4). For the analysis, only dominant barcodes were included. To consider the clone as contributing to the lineage, it had to contribute > 0.089% at 2 time points. Abbreviations: PEMB, platelet-erythroid-myeloid-B cell; PEM, platelet-erythroid-myeloid; PE, platelet-erythroid; PB, platelet-B cell; EB, erythroid-B cell; PEB, platelet-erythroid-B cell; ME, myeloid-erythroid; MB, myeloid-B cell; PM, platelet-myeloid; B, B cell; MEB, myeloid-erythroid-B cell; M, myeloid; E, erythroid. J Volcano plot representing differentially expressed genes in LT-HSC clones producing only progenitors compared to LT-HSCs contributing to platelet and erythroid cells in PB, full list of differentially expressed genes Additional file 11: Table S6