Table 2.
Gene abundance analysis of ligand mRNAs in the combined 3 and 9 DPI nerve scRNA-seq dataset
| Gene abundance (%) | |||||||
|---|---|---|---|---|---|---|---|
| Gene | Epineurial/perineurial | Endoneurial | Combinedmesenchymal | VSM/pericytes | Endothelialcells | Schwanncells | Immune |
| Adm* * | 11.6 | 34.2 | 17.4 | 2.8 | BT | BT | BT |
| Agt* | 2.2 | 10.4 | 4.2 | 13.2 | BT | BT | BT |
| Angpt1* * | 17.3 | 23.7 | 18.9 | 21.1 | 2.1 | BT | BT |
| Angpt2* | 3.2 | BT | 2.6 | 29.0 | 18.5 | BT | BT |
| Angpt4** | 2.6 | BT | 2.0 | BT | BT | BT | BT |
| Apln* | 2.0 | 6.0 | 3.0 | BT | 11.2 | BT | BT |
| Artn | BT | BT | BT | BT | BT | 3.3 | BT |
| Bdnf* | 2.6 | BT | 2.3 | 2.2 | BT | 9.5 | BT |
| Bmp1** | 53.1 | 35.7 | 48.7 | 14.8 | 10.8 | 50.6 | 2.7 |
| Bmp2* | BT | 3.0 | 2.1 | 24.6 | 3.3 | BT | BT |
| Bmp4* | 2.8 | BT | 2.3 | BT | 16.6 | BT | BT |
| Bmp5* | BT | 3.8 | BT | 11.7 | BT | BT | BT |
| Bmp7** | 2.2 | 31.1 | 9.5 | BT | BT | BT | BT |
| Btc* | BT | 2.0 | 2.0 | BT | BT | 60.4 | BT |
| Cck | BT | BT | BT | 5.0 | BT | BT | BT |
| Ccl11** | 29.4 | 87.0 | 44.0 | 34.1 | 7.5 | 6.2 | 4.7 |
| Ccl19 | BT | BT | BT | 2.5 | BT | BT | BT |
| Ccl2** | 27.0 | 81.5 | 40.9 | 21.1 | 12.9 | 13.8 | 15.2 |
| Ccl24 | BT | BT | BT | BT | BT | BT | 2.4 |
| Ccl25 | BT | BT | BT | BT | BT | 2.2 | BT |
| Ccl3* | 3.0 | 4.2 | 3.3 | 3.2 | 2.3 | 3.1 | 13.7 |
| Ccl5* | 3.0 | 2.8 | 2.9 | BT | BT | BT | 6.4 |
| Ccl7** | 21.8 | 78.0 | 36.1 | 10.4 | 7.7 | 6.6 | 7.7 |
| Ccl9** | 11.8 | 75.0 | 27.9 | 4.1 | 6.1 | 5.9 | 22.5 |
| Clcf1* | 3.7 | 4.5 | 3.9 | BT | 4.3 | 16.0 | BT |
| Crlf1* | 3.2 | 25.9 | 9.0 | BT | BT | 35.2 | BT |
| Csf1** | 32.3 | 31.2 | 32.0 | 13.9 | 11.7 | 11.6 | 3.3 |
| Ctgf** | 25.7 | 36.9 | 28.5 | 25.6 | 33.3 | 3.5 | 2.2 |
| Cx3cl1** | 4.0 | 14.4 | 6.7 | BT | 5.3 | BT | BT |
| Cxcl1** | 27.4 | 59.3 | 35.5 | 38.2 | 29.0 | 11.7 | 9.5 |
| Cxcl10** | 2.6 | 9.8 | 4.4 | 3.2 | 4.1 | 6.6 | 2.0 |
| Cxcl12** | 46.6 | 52.6 | 48.1 | 33.8 | 44.0 | 5.9 | 5.0 |
| Cxcl13** | 6.7 | BT | 5.1 | BT | BT | BT | BT |
| Cxcl16* | 6.3 | 4.2 | 5.7 | 2.8 | 3.7 | BT | 15.7 |
| Cxcl2* | 12.3 | 22.9 | 15.0 | 7.3 | 10.4 | 7.2 | 22.9 |
| Cxcl9** | 5.3 | 2.7 | 4.6 | BT | 4.6 | BT | BT |
| Dhh | BT | BT | BT | BT | 6.3 | 30.1 | BT |
| Dll1 | BT | BT | BT | BT | 6.4 | BT | BT |
| Dll4 | BT | BT | BT | BT | 10.0 | BT | BT |
| Ebi3 | BT | BT | BT | BT | BT | BT | 2.5 |
| Eda** | 6.0 | 9.7 | 7.0 | BT | BT | 3.7 | BT |
| Edn3** | 3.1 | BT | 2.3 | BT | BT | BT | BT |
| Efna1* | 3.4 | 8.0 | 4.5 | BT | 24.9 | BT | BT |
| Efna2** | 3.3 | 3.8 | 3.4 | 2.5 | BT | 3.5 | BT |
| Efna4** | 4.8 | 6.2 | 5.2 | 3.2 | BT | 4.0 | BT |
| Efna5** | 5.1 | 6.7 | 5.5 | BT | BT | BT | BT |
| Efnb1** | 22.5 | 39.2 | 26.8 | 9.5 | 11.4 | 11.4 | 2.3 |
| Efnb2** | 13.0 | 42.4 | 20.4 | 4.1 | 16.4 | 4.0 | BT |
| Fgf1* | 7.1 | 4.8 | 6.5 | 9.8 | BT | 2.2 | BT |
| Fgf10** | 7.5 | BT | 5.8 | BT | BT | BT | BT |
| Fgf18** | 8.5 | BT | 6.8 | BT | BT | BT | BT |
| Fgf5 | BT | BT | BT | BT | BT | 19.4 | BT |
| Fgf7** | 26.1 | 37.7 | 29.1 | 3.2 | BT | 12.5 | BT |
| Figf** | 15.8 | 11.2 | 14.6 | BT | BT | BT | BT |
| Fstl1** | 96.8 | 96.5 | 96.7 | 85.8 | 56.5 | 33.4 | 19.6 |
| Gas6** | 44.3 | 2.3 | 35.9 | 13.6 | 22.5 | 2.2 | 6.2 |
| Gdf10** | 24.5 | 4.7 | 19.5 | BT | 3.3 | 2.0 | BT |
| Gdf11** | 4.3 | 10.4 | 5.9 | 10.1 | 3.4 | 3.9 | BT |
| Gdnf | BT | BT | BT | BT | BT | 21.8 | BT |
| Gmfb** | 23.4 | 34.6 | 26.3 | 10.7 | 17.5 | 27.9 | 11.6 |
| Gmfg | BT | BT | BT | BT | 5.7 | BT | 17.9 |
| Gnrh1** | BT | 2.3 | BT | BT | BT | BT | BT |
| Grp | BT | BT | BT | BT | 3.4 | BT | BT |
| Hbegf* | 6.5 | 5.2 | 6.2 | 10.7 | 19.2 | 43.9 | BT |
| Hgf** | 4.0 | BT | 3.1 | BT | BT | BT | BT |
| Igf1** | 76.6 | 84.3 | 78.6 | 15.8 | 31.7 | 16.7 | 13.8 |
| Igf2* | 15.5 | 8.2 | 13.6 | 16.4 | 6.1 | 2.4 | BT |
| Il15** | 2.2 | 9.0 | 3.9 | BT | 7.4 | BT | BT |
| Il16* | BT | 3.0 | BT | BT | 2.3 | BT | 7.9 |
| Il18** | 6.4 | 5.3 | 6.1 | BT | BT | BT | 2.5 |
| Il1b* | 5.6 | 7.3 | 6.1 | 5.0 | 5.7 | 5.0 | 18.6 |
| Il33** | 39.1 | 63.3 | 45.3 | 2.5 | 3.6 | 6.4 | 2.2 |
| Il6* | 7.2 | 7.0 | 7.1 | 12.6 | 15.2 | BT | BT |
| Inha** | BT | 2.0 | BT | BT | BT | BT | BT |
| Inhba** | 12.6 | 11.9 | 12.4 | 9.8 | BT | BT | 1.9 |
| Inhbb** | BT | 12.7 | 4.5 | BT | 9.2 | BT | BT |
| Jag1* | 20.3 | 17.2 | 19.5 | 33.1 | 17.8 | 8.4 | 2.8 |
| Jag2 | BT | BT | BT | BT | 8.4 | BT | BT |
| Lif** | 2.6 | 13.2 | 5.3 | BT | BT | 5.9 | BT |
| Ltb | BT | BT | BT | BT | BT | BT | 12.2 |
| Mdk** | 39.0 | 51.1 | 42.1 | 9.1 | 4.0 | 25.1 | BT |
| Metrn* | 7.1 | 14.5 | 9.0 | 8.5 | 3.0 | 57.8 | 2.6 |
| Mif** | 32.7 | 40.2 | 34.6 | 26.5 | 31.4 | 29.5 | 26.0 |
| Nenf** | 54.7 | 59.1 | 55.8 | 42.6 | 29.4 | 50.8 | 8.4 |
| Ngf* | 2.4 | 6.7 | 3.5 | 10.4 | BT | BT | BT |
| Nov** | 25.0 | 11.4 | 21.5 | 6.0 | 5.4 | 5.0 | BT |
| Nppc** | 2.2 | 5.3 | 3.0 | BT | BT | BT | BT |
| Ntf3* | 3.4 | BT | 2.9 | 4.4 | 4.8 | BT | BT |
| Ntn1** | 19.2 | 25.5 | 20.8 | BT | 6.0 | 4.6 | BT |
| Osm | BT | BT | BT | BT | BT | BT | 8.3 |
| Pdgfa* | 12.1 | 7.8 | 11.0 | 49.5 | 6.8 | 50.6 | 5.7 |
| Pdgfb | BT | BT | BT | 2.5 | 22.3 | BT | 2.4 |
| Pdgfc** | 7.2 | BT | 5.8 | 6.0 | 4.3 | BT | BT |
| Pf4* | 2.3 | 4.3 | 2.8 | BT | BT | BT | 10.0 |
| Pgf** | 2.0 | 12.2 | 4.6 | 7.6 | BT | BT | BT |
| Pomc** | BT | 3.3 | BT | BT | 3.3 | 2.2 | BT |
| Pthlh** | 10.4 | 13.7 | 11.2 | BT | BT | 2.4 | BT |
| Ptn* | 35.9 | 10.4 | 29.4 | 2.2 | 19.9 | 52.5 | BT |
| Rspo1** | 2.2 | BT | BT | BT | BT | BT | BT |
| Rspo3** | 6.0 | BT | 4.7 | BT | 2.4 | BT | BT |
| Rtn4* | 57.9 | 68.3 | 60.5 | 51.7 | 47.1 | 73.6 | 28.3 |
| Sema3b* | 7.7 | 12.4 | 8.9 | BT | BT | 53.8 | BT |
| Sema3c** | 35.4 | 9.0 | 28.7 | BT | BT | 25.1 | BT |
| Sema3d** | 9.6 | 2.0 | 7.6 | BT | BT | BT | BT |
| Sema3e* | 2.0 | BT | BT | BT | BT | 31.0 | BT |
| Sema3f* | 2.3 | 4.5 | 2.9 | 2.8 | 14.5 | 2.9 | BT |
| Sema3g* | BT | 3.0 | BT | BT | 11.8 | 9.0 | BT |
| Sema4a* | BT | 3.7 | 2.0 | BT | BT | BT | 6.9 |
| Sema4b* | 2.0 | 3.2 | 2.3 | 3.5 | BT | 7.7 | BT |
| Sema4c* | 8.4 | 12.0 | 9.3 | 6.3 | 10.2 | 16.0 | BT |
| Sema4d | BT | BT | BT | BT | BT | BT | 14.5 |
| Sema4f | BT | BT | BT | BT | BT | 18.3 | BT |
| Sema5a* | 4.3 | 3.5 | 4.1 | 13.2 | BT | BT | BT |
| Sema5b | BT | BT | BT | 10.4 | BT | BT | BT |
| Sema6a* | 4.0 | 14.5 | 6.7 | BT | 35.6 | 9.4 | BT |
| Sema6b* | 3.1 | 7.0 | 4.1 | BT | 18.1 | BT | BT |
| Sema6c** | 7.2 | 4.0 | 6.4 | BT | BT | 2.0 | BT |
| Sema6d* | 5.9 | 11.7 | 7.3 | 18.9 | 9.5 | 16.7 | BT |
| Sema7a* | 7.5 | 19.5 | 10.5 | BT | 17.4 | 20.0 | BT |
| Sfrp1** | 42.3 | 31.9 | 39.6 | 4.1 | 3.4 | 8.8 | BT |
| Sfrp2** | 29.6 | 6.5 | 23.8 | 2.2 | 3.3 | BT | 2.4 |
| Sfrp4** | 61.5 | 51.9 | 59.1 | 8.5 | 9.4 | 11.0 | 6.3 |
| Sfrp5** | 8.8 | 3.2 | 7.4 | BT | 2.1 | 8.1 | BT |
| Shh | BT | BT | BT | BT | BT | 12.8 | BT |
| Tgfa | BT | BT | BT | BT | 2.6 | BT | BT |
| Tgfb1* | 6.5 | 12.0 | 7.9 | 6.0 | 13.4 | 10.3 | 12.4 |
| Tgfb2* | 13.3 | 2.7 | 10.6 | 16.4 | 5.1 | 6.2 | BT |
| Tgfb3* | 26.3 | 8.7 | 21.8 | 27.4 | 2.3 | 4.6 | BT |
| Tnf* | BT | 2.2 | BT | BT | BT | BT | 7.7 |
| Tnfrsf11b** | 6.6 | BT | 5.0 | BT | BT | BT | BT |
| Tnfsf10 | BT | BT | BT | BT | 22.8 | 1.1 | BT |
| Tnfsf12** | 15.0 | 16.7 | 15.4 | 11.4 | 9.1 | 6.8 | 7.3 |
| Tnfsf14 | BT | BT | BT | BT | BT | BT | 2.3 |
| Tnfsf8** | 3.8 | 2.0 | 3.3 | BT | BT | BT | BT |
| Tnfsf9** | 2.8 | 5.8 | 3.6 | 5.4 | BT | BT | BT |
| Tslp** | 2.5 | 4.8 | 3.1 | 2.8 | 2.4 | BT | BT |
| Ucn2 | BT | BT | BT | BT | BT | 15.0 | BT |
| Vegfa** | 28.2 | 18.7 | 25.8 | 3.8 | 4.1 | 2.6 | 7.0 |
| Vegfb* | 7.1 | 7.0 | 7.0 | 7.3 | 6.0 | 8.4 | 3.3 |
| Vegfc* | 2.0 | BT | BT | BT | 5.5 | BT | BT |
| Wnt11** | 2.7 | BT | 2.2 | BT | BT | BT | BT |
| Wnt2** | 6.5 | BT | 5.3 | BT | BT | BT | BT |
| Wnt5a** | 15.9 | 14.4 | 15.5 | 4.4 | BT | BT | BT |
The combined 3 and 9 DPI scRNA-seq dataset (Fig. 1E) was analyzed for the percentage of cells within the defined nerve cell types that expressed ligand mRNAs as identified by microarray analysis (Table 1). Ligand mRNAs were only considered to be detected if they were expressed in at least 2% of cells within at least one cell type. BT = below threshold and indicates that <2% of cells detectably expressed the ligand mRNA. Ligands annotated with one asterisk in the leftmost column were expressed in ≥2% Pdgfra-positive mesenchymal cells and two asterisks indicate ligands with the highest expression in either the epineurial/perineurial or endoneurial Pdgfra-positive mesenchymal cells.
* >2% expression in Pdgfra-positive cells.
** >2% expression and highest expression in Pdgfra-positive cells.