Figure 2

Hox status defines SSC identity. (A) Comparison of 4 groups, unique in their embryonic origin and Hox status, allow for transcriptome comparison with RNAseq. (B) Hierarchical clustering analysis of top 1000 most divergent genes. For each gene, we calculated its coefficient of variation (CV) based on its log-transformed FPKM values across all RNAseq samples. The genes were then ranked based on their CV values. The heatmap was generated by hierarchical clustering of the top 1000 genes with the largest CV values. (C) Principal component analysis (PCA) of frontal (F), parietal (P), hyoid (H) bone and the tibia (T). (D) MA plot comparing differential gene expression between neural crest and mesoderm derived SSCs, and between (E) Hox-positive and Hox-negative SSCs. (F,G) Integration of both RNAseq and ATACseq data sets reveals genes that were differentially regulated (differential expression by RNAseq and differential open chromatin by ATACseq). Again, Hox⁺ vs. Hox⁻ best described their differences, as 6.5% of the genes were differentially regulated in this comparison (RNAseq: p < 0.05, ATACseq: p < 0.05).