Supplementary Figure 9: FateID reveals fate bias in myeloid progenitors. | Nature Methods

Supplementary Figure 9: FateID reveals fate bias in myeloid progenitors.

From: FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data

Supplementary Figure 9

(a) A t-SNE map based on transcriptome similarity highlighting the origin of each cell is shown. The published dataset1 comprises common myeloid progenitors (CMP), Irf8-GFP+MHC-II+ dendritic cell progenitors, Flt3+Csf1r+ monocyte progenitors, and Cd41+ megakaryocyte progenitors sorted from the CMP gate. (b) Shown is a t-SNE map highlighting clusters of cells with similar transcriptomes derived by RaceID3. Clusters 17, 1, 11, 5, and 8 were used as FateID target clusters for the erythrocyte, megakaryocyte, dendritic, monocyte, and granulocyte lineage. (c-g) The fate bias, corresponding to the probability of a cell to be assigned to a given lineage, is color-coded in the t-SNE map. The fate bias predicted by FateID (left) and STEMNET2 (middle) is shown along with log2-transformed normalized expression of a lineage marker. Fate bias and marker gene expression is shown for (c) the megakaryocyte, (d) the dendritic, (e) the granulocyte, (f) the monocyte, and (g) the erythrocyte lineage. (h) Barplot comparing Spearman’s correlation coefficient between the expression levels of early lineage markers and fate bias computed by FateID and STEMNET. Error bars correspond to standard errors of Fisher’s z-transformed correlation values calculated across all cells after removal of target clusters (1,927 cells from n=4 animals). P-values were derived from the difference of z-scores divided by the standard error assuming a standard normal distribution using William’s test (*P < 0.05, **P < 0.001). (i) Depicted is a t-SNE map highlighting expression of Flt3, showing that Flt3 does not discriminate between the monocyte and the dendritic cell lineage. (j-n) Shown are scatterplots comparing fate bias predicted by FateID and STEMNET for (j) the megakaryocyte, (k) the monocyte, (l) the granulocyte, (m) the dendritic cell, and (n) the erythrocyte lineage. Although the predictions are overall correlated, STEMNET predicts more uniform levels across a larger fraction of the multipotent cell population. In (a-g) and (i-n) for 2,370 cells from four independent experiments with n = 4 mice are shown.

1. Paul, F. et al. Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors. Cell 163, 1663–1677 (2015).

2. Velten, L. et al. Human haematopoietic stem cell lineage commitment is a continuous process. Nat. Cell Biol. 19, 271–281 (2017).

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