Figure 3

The endogenous Tal1 and Lmo2 genes were differentially expressed in i5TFs V⁺CD⁺ compared to i5TFs V⁺CD⁻ cells. (A) PCA plots of ATAC-seq results (n = 2) (left panel) and RNA-seq (n = 4) results (right panel). Parent eVSM = FLK1⁻CD41⁻ cells sorted at day 1 of hemangioblast culture; late eVSM = VE-CAD⁻CD41⁻ cells sorted at day 1.5 of HE culture; V⁺CD⁻ = VE-CAD⁺CD41⁻ cells sorted at day 1.5 of HE culture; V⁺CD⁺  = VE-CAD⁺CD41⁺ cells sorted at day 1.5 of HE culture; dox = cultured in HE medium with doxycycline; unt = cultured in HE medium without doxycycline. (B) Results of diffTF analysis for the indicated cell lines. TFs identified as more active in i5TFs V⁺CD⁺ are displayed in the blue quadrant, TFs identified as more active in i5TFs V⁺CD^- are displayed in the red quadrant. TFs classified as activators are labeled in green, TFs classified as repressors are labeled in red, differentially active TFs that couldn’t be clearly classified as either are labeled in black. 5% of TFs were classified as activators or repressors (TF class stringency: 0.05) based on the Pearson correlation index. The x axis (weighted mean difference) shows the difference in TF activity between the two conditions. The y axis displays the significance of the TFs. The significance threshold is indicated with a dotted line (FDR adjusted p-value < 0.05). TFs are indicated as a dot. The size of each dot is proportional to the number of predicted genomic TFBS for each (TFBS). (C) Venn diagrams comparing the DEGs in i5TFs V⁺CD⁺ and i5TFs V⁺CD^- . A subset of hematopoietic genes differentially expressed in V⁺CD⁺ but not V⁺CD^- cells is shown. (D) Bar plots showing the differential expression (log2FC) of Tal1, Lmo2 and Lyl1 in i5TFs V⁺CD⁺ and i5TFs V⁺CD⁻ cells compared to untreated eVSM cells, identified by RNA-seq.