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Fig. 1 | Simultaneous single-cell lineage and transcriptome sequencing maps functional HSC heterogeneity. a, Experimental design for studying HSC heterogeneity with the <t>LARRY</t> lentiviral <t>barcoding</t> library. All panels are representative from n = 3 independent labelling experiments (five mice). LTR, long terminal repeat; bc, barcode. b, Schemes of low-output (top) and high-output (bottom) HSC clones. Prog, progenitors. c, Single-cell map that shows clonal HSC output activity values. LARRY barcodes are used to assign each cell to an HSC clone, and then all cells from each clone are coloured based on its calculated output activity. Major progenitor cell populations are labelled. Ba, basophil; Ery, erythroid; GM, granulocyte–monocyte; MPP, multipotent progenitor; preB, pre-B cell; preDC, pre-dendritic cell. d, The distribution of high-output (output activity of >1) and low-output (output activity of <1) HSC cells and clones (shown as % of total HSCs). Mean ± s.d. is shown. e, Schemes of lineage-balanced (top) and lineage-biased (bottom) HSC clones. f, Single-cell map showing clonal Mk-bias values. g, Distribution of Mk-biased and multilineage HSCs (cells and clones), Mk cells and non-Mk cells (shown as % of total). Mean ± s.d. is shown. h, Genes differentially expressed in low-output (right, n = 7,254 cells) versus high-output (left, n = 3,512 cells) HSCs. Genes with an adjusted P < 0.01 (Benjamini–Hochberg-corrected t-test) and fold change of >2 are coloured. Selected genes are labelled. i, Genes differentially expressed in Mk-biased (right, n = 3,399 cells) versus multilineage (left, n = 3,771 cells) HSCs. Genes with an adjusted P < 0.01 (Benjamini– Hochberg-corrected t-test) and fold change of >2 are coloured. j, Single-cell map of HSCs, coloured by the signature score values. k, Heatmap that shows the Pearson correlation between different signature scores across all HSCs (n = 10,837). l, Scatter plot of Mk bias and output activity (log-transformed) for each HSC clone, coloured by clone HSC frequency (freq). The dashed lines are the output activity threshold (Ai = 1) and the Mk-bias threshold (Bi = 4). Only clones with a HSC frequency of >0.005 are depicted (n = 62).
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Fig. 1 | Simultaneous single-cell lineage and transcriptome sequencing maps functional HSC heterogeneity. a, Experimental design for studying HSC heterogeneity with the LARRY lentiviral barcoding library. All panels are representative from n = 3 independent labelling experiments (five mice). LTR, long terminal repeat; bc, barcode. b, Schemes of low-output (top) and high-output (bottom) HSC clones. Prog, progenitors. c, Single-cell map that shows clonal HSC output activity values. LARRY barcodes are used to assign each cell to an HSC clone, and then all cells from each clone are coloured based on its calculated output activity. Major progenitor cell populations are labelled. Ba, basophil; Ery, erythroid; GM, granulocyte–monocyte; MPP, multipotent progenitor; preB, pre-B cell; preDC, pre-dendritic cell. d, The distribution of high-output (output activity of >1) and low-output (output activity of <1) HSC cells and clones (shown as % of total HSCs). Mean ± s.d. is shown. e, Schemes of lineage-balanced (top) and lineage-biased (bottom) HSC clones. f, Single-cell map showing clonal Mk-bias values. g, Distribution of Mk-biased and multilineage HSCs (cells and clones), Mk cells and non-Mk cells (shown as % of total). Mean ± s.d. is shown. h, Genes differentially expressed in low-output (right, n = 7,254 cells) versus high-output (left, n = 3,512 cells) HSCs. Genes with an adjusted P < 0.01 (Benjamini–Hochberg-corrected t-test) and fold change of >2 are coloured. Selected genes are labelled. i, Genes differentially expressed in Mk-biased (right, n = 3,399 cells) versus multilineage (left, n = 3,771 cells) HSCs. Genes with an adjusted P < 0.01 (Benjamini– Hochberg-corrected t-test) and fold change of >2 are coloured. j, Single-cell map of HSCs, coloured by the signature score values. k, Heatmap that shows the Pearson correlation between different signature scores across all HSCs (n = 10,837). l, Scatter plot of Mk bias and output activity (log-transformed) for each HSC clone, coloured by clone HSC frequency (freq). The dashed lines are the output activity threshold (Ai = 1) and the Mk-bias threshold (Bi = 4). Only clones with a HSC frequency of >0.005 are depicted (n = 62).

Journal: Nature

Article Title: Single-cell lineage tracing unveils a role for TCF15 in haematopoiesis.

doi: 10.1038/s41586-020-2503-6

Figure Lengend Snippet: Fig. 1 | Simultaneous single-cell lineage and transcriptome sequencing maps functional HSC heterogeneity. a, Experimental design for studying HSC heterogeneity with the LARRY lentiviral barcoding library. All panels are representative from n = 3 independent labelling experiments (five mice). LTR, long terminal repeat; bc, barcode. b, Schemes of low-output (top) and high-output (bottom) HSC clones. Prog, progenitors. c, Single-cell map that shows clonal HSC output activity values. LARRY barcodes are used to assign each cell to an HSC clone, and then all cells from each clone are coloured based on its calculated output activity. Major progenitor cell populations are labelled. Ba, basophil; Ery, erythroid; GM, granulocyte–monocyte; MPP, multipotent progenitor; preB, pre-B cell; preDC, pre-dendritic cell. d, The distribution of high-output (output activity of >1) and low-output (output activity of <1) HSC cells and clones (shown as % of total HSCs). Mean ± s.d. is shown. e, Schemes of lineage-balanced (top) and lineage-biased (bottom) HSC clones. f, Single-cell map showing clonal Mk-bias values. g, Distribution of Mk-biased and multilineage HSCs (cells and clones), Mk cells and non-Mk cells (shown as % of total). Mean ± s.d. is shown. h, Genes differentially expressed in low-output (right, n = 7,254 cells) versus high-output (left, n = 3,512 cells) HSCs. Genes with an adjusted P < 0.01 (Benjamini–Hochberg-corrected t-test) and fold change of >2 are coloured. Selected genes are labelled. i, Genes differentially expressed in Mk-biased (right, n = 3,399 cells) versus multilineage (left, n = 3,771 cells) HSCs. Genes with an adjusted P < 0.01 (Benjamini– Hochberg-corrected t-test) and fold change of >2 are coloured. j, Single-cell map of HSCs, coloured by the signature score values. k, Heatmap that shows the Pearson correlation between different signature scores across all HSCs (n = 10,837). l, Scatter plot of Mk bias and output activity (log-transformed) for each HSC clone, coloured by clone HSC frequency (freq). The dashed lines are the output activity threshold (Ai = 1) and the Mk-bias threshold (Bi = 4). Only clones with a HSC frequency of >0.005 are depicted (n = 62).

Article Snippet: The LARRY barcoding tool is available at Addgene (no. 140024).

Techniques: Sequencing, Functional Assay, Clone Assay, Activity Assay, Transformation Assay