Supplementary MaterialsS1 Fig: Manually curated style of gene regulatory network governing fate decision of CMP. during differentiation. Expression profiles of 17 transcription factors and control genes (rows) in individual cells (columns) are visualized as a heatmap. Cell columns are arranged for days d1, d3 and d6 with respect to different treatments where grey shades correspond to untreated progenitors (d0), red shades to EPO treatment, blue shades indicate cells treated with GM-CSF/IL-3 and purple shades to combined treatment EPO+GM-CSF/IL-3 cytokines. The various shades of every color indicate the various Sca1 marker manifestation amounts Sca1Low (L), Sca1Mid (M) and Sca1High (H) established during FACS sorting where darker tones denote higher Sca1 manifestation. Gene rows had been ordered according with their natural part as indicated for the remaining.(JPG) pbio.2000640.s002.jpg (218K) GUID:?D66091C6-3802-4E86-A418-6A3F8E20A0EA S3 Fig: Complex noise connected with single-cell RT-qPCR is significantly smaller sized than natural cell-cell variability. (A) Quantification cycles (Cq) of 80 person EML cells for GATA1 manifestation can be reported. Ideals are means STD for to 128 complex replicates up. (B) Quantification cycles (Cq) as high as 110 specialized replicates are shown for 3 chosen single-cells. Single-cell Cqs of natural examples display a broader distribution in accordance with that of complex replicates clearly. (C) Package plots represent the variability with regards to CV for specialized replicates averaged over 110 realizations from the real-time PCR-steps for the ds-cDNA as well as the distribution of CV across all 80 specific EML progenitor cells for the GATA1 manifestation. The biological variation was bigger than the technical noise (p-value 2 significantly.2e-28, Mann-Whitney U check). Similar outcomes were acquired for PU.1 (not shown).(JPG) pbio.2000640.s003.jpg (160K) GUID:?9B7BA818-4DAD-4A37-8846-A124C8A79CC6 S4 Fig: Distinct trajectories of cell differentiation are found upon stimulation of progenitor cells with cytokines in the PCA state space. Primary element projections in a complete of ~1600 haematopoietic cells including progenitor (dark), single-EPO treated (red-shades), Clonixin single-IL3/GM-CSF treated (blue-shades) and combined-treated (purple-shades) in the 1st three components established from manifestation of most 17 transcription elements and endogenous control genes. (B) Primary element loadings for Personal computer 2 and 3 indicate the degree to which each gene plays a part in the parting of cells along each element. (C) PCA weights of genes for the 1st three Personal computers reveals the need for the Clonixin average person genes to describe the difference between your different remedies and corresponding cell Clonixin fate. (D) Cells in their attractor states still exhibit heterogeneous transcription profiles that can be traced back to individual genes. Cells treated with GM-CSF/IL-3 for 6 days are clearly located within the state space defined by the myeloid genes and cells treated by EPO exhibit 2 clusters where the lower one is governed by erythroid genes and the higher one by stemness genes. (E) Variance explained by principal components Clonixin show that the first three components jointly explain more than 70% of variation in the data.(JPG) pbio.2000640.s004.jpg (192K) GUID:?305CCD8E-949A-4982-9B79-209137895D39 S5 Fig: Gene expression in individual cells from the progenitor population and the , , and subpopulations. (A-D) Heatmap representation of gene expression profiles for the set of 17 genes of the curated network and 2 endogenous genes as control in total 216 single cells including 72 progenitor cells (panel A) and 48 single cells from each of the three subpopulations in the tri-modal Sca-1 population distribution on day 3 after GM-CSF/IL-3 CALN treatment (Fig 3 in main text), (B) (C) and (D). Genes are ordered according to their reported biological role, as erythroid-associated (red box), stemness (green box), myloid-associated (blue box) and endogenous genes in all subplots. Based on the expressed genes, the subpopulation seems to be committed to the myeloid lineage while the subpopulation is committed to the.