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. Author manuscript; available in PMC: 2013 Apr 26.
Published in final edited form as: Cell. 2012 Oct 18;151(3):559–575. doi: 10.1016/j.cell.2012.09.032

Figure 4. iVEC global gene transcriptome reveals vascular genes are turned on while non-vascular genes are silenced, matching expression profile of mature ECs.

Figure 4

a) ETS-TF transduced ACs (‘iVEC’) as well as two iVEC clones (‘iVEC Clone-3’ and ‘iVEC Clone-4’) cultured for two months with TGFβ inhibition underwent RNA-seq analysis. (iVEC Clone-4 has a similar ETS-TF expression profile to that of iVEC Clone-3 – data not shown). The expression profile of these iVEC samples were compared to human umbilical cord-blood derived CD34+ cells (‘CD34+’), human bone marrow stromal cells (‘BMS’), naïve human ACs (‘Amni ctrl’), ‘HUVEC’ and ‘LSEC’. Heat-maps of relative transcription levels are shown. b) Three dimensional MDS plots (3D MDS) was generated based on all pairwise distances between the global transcriptome-wide RNA-seq profiles of the samples shown here, including adult lung airway epithelial cells (Hackett et al., 2012). Distances were defined as one minus the Pearson correlation between two profiles. Multidimensional scaling (MDS) was used to identify the set of points in 3D space such that the distances between the points are approximately equal to the true distances between samples. This analysis shows a tight colocalization of clonal and nonconal iVECs with HUVECs and LSECs, thus indicating that their genome-wide expression profiles are highly similar. Contrarily, non-vascular cell types, such as BMS, epithelial cells, and CD34+ hematopoietic cells manifest no similarities to iVECs. This analysis was not biased towards any gene set or processes: all >30,000 RefSeq transcripts whose expression was quantified by RNA-seq were used to calculate distances between samples. c) Hierarchical clustering of iVEC and non-iVEC samples. The same samples and pairwise distances between global transcriptome-wide RNA-seq profiles were used as those used for 3D-MDS, by performing average linkage clustering. Like the 3D-MDS analysis, hierarchical clustering shows that clonal and non-clonal iVECs, but not non-vascular cells cluster closely with HUVECs and LSECs. See also 3D-MDS Movie.