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. 2015 Dec 14;4:e10567. doi: 10.7554/eLife.10567

Figure 3. Unbiased RNA-seq analysis reveals factors that define the hair peg niche.

(A) Diagram of the FACS experiments using Nfatc1- and Shh-CreER::Rosa-stop tdTomato::K14H2BGFP mice. (B) FACS isolation of distinct GFP+RFP+ populations to obtain Shh+ and Nfatc1+ epithelial cells. (C) Unsupervised hierarchical clustering and heat map display of genes that were differentially expressed between Shh+ cells and Nfatc1+ cells. N=2 (D) Gene Ontology analysis of ≥2-fold up-regulated genes in Shh+ cells compared to Nfatc1+ cells. The Wnt signaling pathway is highlighted. (E) Validation of differentially expressed genes using qPCR. N=3. (F–G) In situ staining of Axin2 (F) and Wnt10b (G) in developing hair follicles. (H) Shh+ cells are Wnt/β-catenin signal responsive cells. Shh expression was represented by tdTomato in Shh-CreER::Rosa-stop-tdTomato mice. Wnt/β-catenin-responsive cells were detected by β-gal staining in TOPGAL mice. Scale bars: 50 μm.

DOI: http://dx.doi.org/10.7554/eLife.10567.008

Figure 3—source data 1. RNA-seq results of differentially expressed genes between Nfatc1+ and Shh+ cells.
Genes with significantly different expression levels (p<0.01 and log2FC>1) between the Nfatc1+ and Shh+ cells were chosen for further analysis. N=2.
DOI: http://dx.doi.org/10.7554/eLife.10567.009
elife-10567-fig3-data1.xlsx (358.4KB, xlsx)
DOI: 10.7554/eLife.10567.009

Figure 3.

Figure 3—figure supplement 1. RNA seq results of representative genes from different populations.

Figure 3—figure supplement 1.

(A) RNA seq results of Nfact1 and Shh from different populations. N=2 (B) Fold enrichment of canonical Wnt pathway genes from the RNA-seq results. N=2.
DOI: http://dx.doi.org/10.7554/eLife.10567.010