Figure 2.

Upregulated genes and cell enrichment analyses of undifferentiated and differentiated datasets

(A–C) The datasets were obtained by using BMP4-based protocols of (A) Io (pH9 versus H9_pBAP_D3), (B) Krendl (H9_BMP4 versus H9_BMP4_D3), and (C) Yabe (H1_Yabe versus H1_BAP_D8_>70).

In the volcano plot, the darker shade is undifferentiated, showing upregulated genes of pH9 (purple), H9_BMP4 (darker pink), and H1_Yabe (darker green). The lighter shade is their differentiated counterpart, H9_pBAP_D3 (lighter blue), H9_BMP4_D3 (lighter pink), and H1_BAP_D8_>70 (lighter green). Only genes with |log2fold| ≥ 1 and adjusted p value (padj) ≤ 0.05 are colored. The cell enrichment results of the upregulated genes are depicted as bar plots (color coordinated), with the top chart using the Vento-Tormo et al. (2018) dataset for enrichment analyses, the middle using the Xiang et al. (2020) dataset, and the bottom using the combined Zhou et al. (2019) and Petropoulos et al. (2016) datasets (curated by Castel et al., 2020). Only the three most-enriched fetal cell types are shown here (see Figure S1 for the full cell enrichment results).