Extended Data Figure 10: Putative markers for iCMs and pre-iCMs. | Nature

Extended Data Figure 10: Putative markers for iCMs and pre-iCMs.

From: Single-cell transcriptomics reconstructs fate conversion from fibroblast to cardiomyocyte

Extended Data Figure 10

Analysis using an ANOVA identified 7,624 differentially expressed genes among fibroblasts, intermediate fibroblasts, pre-iCMs and iCMs. There were 954 and 285 candidates for negative and positive selection markers of iCMs and 55 candidates for positive markers of pre-iCMs. These candidates were expressed the lowest and highest in iCMs and highest in pre-iCMs, respectively. No gene passed the selection criteria for negative markers of pre-iCMs. Top candidates were selected by largest fold change in expression in the cell population of interest compared to the expression in fibroblasts. a, Violin plots showing the expression of non-surface genes in top 30 candidates for negative markers of iCMs. Related to Fig. 4d. be, Top 30 candidates for positive selection markers of iCMs (b, c) or pre-iCMs (d, e). b, d, Fold change in gene expression in iCM/fibroblast (b) or pre-iCM/fibroblast (d). c, e, Violin plots of the same genes in four cell populations. f, Top 30 genes showing largest expression fold change in pre-iCMs and iCMs. gn, Effect of Cd200 knockdown (gj) or overexpression (kn) on iCM reprogramming. Cardiac fibroblasts were untransduced (mock) or simultaneously transduced with MGT and lentiviral shNT or shCd200 or LacZ and OE-Cd200 for 14 days. Knockdown or overexpression efficiency was verified by qRT–PCR (g, k). Data are mean ± s.d. n = 3 samples. Percentages of α-MHC–GFP+, cTnT+ and Cx43+ cells were determined by immunostaining followed by imaging and blinded quantification (h, i, l, m) with representative 20× images in h, l. Scale bars, 200 μm. n = 20 (i) or 10 (m) images. Data are mean ± s.e.m. Percentages of α-MHC–GFP+, cTnT+ and double-positive cells were also quantified by flow cytometry (j, n). Data are mean ± s.d. n = 3 samples. Two-sided Student’s t-test was used. ***P < 0.001; ns, not significant.

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