Table 6.
Gene abundance of injured nerve ligand mRNAs in the combined injured, uninjured and neonatal mesenchymal cell scRNA-seq dataset
| Gene abundance (%) | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Neonatal | Inj/uninjured | Injured/uninjured/neonatal | Uninjured | Injured | Neonatal/injured | Fold change | |||
| Gene | Epineurial | Endoneurial | Epineurial | Perineurial | Endoneurial | Endoneurial | Differentiating | Proliferating | Injured:uninjuredendoneurial |
| Adm | 5.2 | 4.8 | 17.3 | 17.0 | 9.0 | 35.1 | 7.6 | 10.1 | 3.9 |
| Agt | BT (1.7) | BT (0.5) | 3.3 | BT (0.0) | BT (1.9) | 10.7 | BT (1.7) | 3.9 | 5.6 |
| Angpt1 | 3.7 | BT (0.5) | 11.6 | 5.2 | BT (0.7) | 23.9 | 24.6 | 20.8 | 33.6 |
| Angpt2 | 3.4 | BT (0.0) | 2.0 | BT (1.3) | BT (0.5) | BT (1.0) | 5.1 | 2.9 | 2.0 |
| Angpt4 | BT (0.5) | BT (0.0) | 4.9 | BT (1.3) | BT (0.2) | BT (0.4) | 2.0 | 2.6 | 1.7 |
| Apln | BT (0.7) | 2.1 | BT (0.5) | BT (0.7) | BT (0.7) | 5.3 | BT (1.9) | 6.5 | 7.5 |
| Bdnf | BT (0.6) | BT (1.1) | BT (0.2) | BT (0.7) | BT (0.0) | BT (1.9) | 5.2 | BT (1.6) | >1.9 |
| Bmp1 | 34.3 | 12.7 | 51.4 | 52.9 | 16.4 | 37.2 | 52.3 | 47.6 | 2.3 |
| Bmp2 | BT (0.2) | BT (0.0) | 2.9 | BT (0.7) | BT (0.9) | 3.1 | BT (0.7) | 3.9 | 3.3 |
| Bmp4 | 2.6 | 2.6 | 11.7 | BT (0.7) | 6.6 | BT (1.0) | BT (0.3) | BT (1.0) | 0.1 |
| Bmp5 | BT (0.4) | BT (1.6) | BT (1.8) | BT (1.3) | 6.6 | 4.0 | BT (1.1) | BT (1.6) | 0.6 |
| Bmp7 | BT (1.7) | 6.3 | BT (1.5) | 8.5 | 12.1 | 30.1 | BT (1.2) | 5.9 | 2.5 |
| Btc | BT (0.4) | BT (0.0) | BT (1.1) | BT (0.0) | BT (0.2) | BT (1.6) | BT (1.5) | 4.6 | 6.9 |
| Ccl11 | 18.0 | 70.9 | 42.6 | 19.0 | 89.3 | 85.9 | 21.4 | 40.4 | 1.0 |
| Ccl19 | BT (0.1) | BT (0.0) | 4.9 | BT (0.0) | BT (0.0) | BT (0.0) | BT (0.5) | BT (0.0) | - |
| Ccl2 | BT (0.7) | 19.8 | 14.4 | 10.5 | 16.1 | 81.6 | 25.6 | 49.5 | 5.1 |
| Ccl3 | BT (0.1) | BT (0.0) | 2.0 | 2.0 | BT (0.0) | 5.2 | 5.8 | 3.6 | >5.2 |
| Ccl5 | BT (0.2) | BT (0.0) | 2.2 | BT (1.3) | BT (0.2) | 3.0 | 2.5 | 3.3 | 12.7 |
| Ccl7 | 6.0 | 29.1 | 12.7 | 10.5 | 36.0 | 77.3 | 23.8 | 44.6 | 2.1 |
| Ccl9 | BT (0.2) | 2.9 | 5.2 | 2.6 | 16.8 | 72.1 | 12.0 | 26.1 | 4.3 |
| Clcf1 | BT (0.8) | BT (0.5) | BT (1.6) | BT (1.3) | BT (0.9) | 4.4 | 5.0 | 5.2 | 4.6 |
| Crlf1 | BT (0.2) | BT (0.0) | BT (1.1) | 5.2 | BT (0.0) | 26.1 | 3.4 | 11.1 | >26.1 |
| Csf1 | 12.2 | 3.4 | 40.9 | 11.8 | 10.9 | 31.0 | 24.0 | 30.9 | 2.8 |
| Ctgf | 7.3 | BT (1.9) | 18.9 | 19.0 | 2.4 | 37.2 | 29.2 | 25.4 | 15.7 |
| Cx3cl1 | BT (0.0) | BT (0.8) | BT (0.9) | BT (0.7) | BT (1.7) | 14.3 | 8.6 | 4.2 | 8.6 |
| Cxcl1 | 1.9 | 23.3 | 20.1 | 17.6 | 53.1 | 60.7 | 35.9 | 37.8 | 1.1 |
| Cxcl10 | BT (0.4) | BT (1.3) | BT (0.9) | BT (0.7) | BT (1.7) | 9.6 | 3.5 | 6.5 | 5.8 |
| Cxcl12 | 17.3 | 63.2 | 42.8 | 10.5 | 61.1 | 52.9 | 50.2 | 48.5 | 0.9 |
| Cxcl13 | BT (0.0) | BT (0.3) | 17.6 | BT (0.0) | BT (1.2) | BT (0.4) | BT (1.0) | BT (0.7) | 0.3 |
| Cxcl16 | BT (0.8) | BT (1.3) | 10.3 | 3.9 | BT (1.7) | 5.1 | 8.2 | 4.6 | 3.0 |
| Cxcl2 | BT (0.1) | BT (1.3) | 7.1 | 6.5 | BT (0.5) | 24.7 | 12.8 | 20.2 | 52.2 |
| Cxcl9 | BT (1.0) | BT (1.9) | BT (1.4) | BT (0.0) | BT (0.5) | 2.2 | 7.6 | 7.5 | 4.6 |
| Dhh | BT (1.3) | 2.4 | BT (0.0) | BT (0.7) | BT (0.2) | BT (0.5) | BT (0.8) | 2.3 | 2.3 |
| Eda | 8.2 | 10.6 | 4.0 | 19.6 | 7.8 | 9.4 | 7.7 | 7.5 | 1.2 |
| Edn3 | 5.3 | BT (0.5) | 6.6 | 6.5 | BT (1.7) | BT (0.3) | BT (1.6) | BT (1.0) | 0.2 |
| Efna1 | 4.1 | 3.7 | 3.2 | 5.9 | 4.0 | 7.8 | 3.9 | 4.2 | 1.9 |
| Efna2 | 3.6 | 3.7 | 2.4 | BT (1.3) | BT (1.2) | 4.4 | 4.9 | 5.2 | 3.7 |
| Efna4 | 4.2 | BT (1.9) | 2.5 | 6.5 | BT (0.7) | 6.1 | 9.0 | 3.9 | 8.6 |
| Efna5 | 6.1 | 4.2 | 4.7 | 11.1 | BT (1.2) | 5.2 | 2.0 | 4.9 | 4.4 |
| Efnb1 | 27.0 | 25.9 | 9.5 | 39.2 | 14.2 | 37.8 | 31.7 | 32.6 | 2.7 |
| Efnb2 | 9.5 | 17.2 | 3.4 | 23.5 | 10.9 | 41.9 | 19.7 | 20.5 | 3.8 |
| Fgf1 | 7.0 | 3.7 | 5.7 | 15.7 | BT (0.9) | 4.6 | 9.9 | 7.2 | 4.9 |
| Fgf10 | 4.0 | BT (0.0) | 13.6 | BT (0.0) | BT (0.0) | BT (0.7) | 3.9 | BT (1.6) | - |
| Fgf18 | 6.6 | BT (0.0) | 11.7 | 4.6 | BT (1.9) | BT (1.5) | 5.9 | 6.2 | 0.8 |
| Fgf5 | BT (1.9) | BT (0.0) | BT (0.5) | BT (0.0) | BT (0.2) | BT (0.1) | 2.1 | 2.0 | 0.6 |
| Fgf7 | 21.3 | 4.0 | 27.8 | 23.5 | 6.6 | 35.9 | 24.2 | 25.1 | 5.4 |
| Figf | 6.1 | BT (0.8) | 21.2 | 5.9 | 2.1 | 9.7 | 10.2 | 15.6 | 4.5 |
| Fstl1 | 96.2 | 92.3 | 96.9 | 86.3 | 76.1 | 94.7 | 96.1 | 90.6 | 1.2 |
| Gas6 | 26.6 | BT (0.5) | 51.4 | 88.2 | 9.7 | 11.1 | 38.7 | 20.5 | 1.1 |
| Gdf10 | 5.0 | BT (0.3) | 42.0 | 3.3 | 4.3 | 4.5 | 17.8 | 12.1 | 1.1 |
| Gdf11 | 4.0 | 7.1 | BT (1.6) | 3.3 | 4.3 | 9.8 | 5.3 | 4.6 | 2.3 |
| Gmfb | 13.7 | 18.3 | 15.2 | 28.1 | 9.2 | 34.4 | 25.9 | 30.6 | 3.7 |
| Gnrh1 | BT (0.8) | BT (0.8) | BT (1.9) | 3.3 | BT (0.5) | 2.2 | BT (1.5) | BT (1.6) | 4.6 |
| Hbegf | 2.3 | 2.1 | BT (1.4) | BT (1.3) | 2.4 | 4.9 | 9.3 | 13.4 | 2.1 |
| Hgf | BT (0.4) | BT (0.0) | BT (1.2) | BT (0.7) | BT (0.2) | BT (0.8) | 6.0 | 6.2 | 3.5 |
| Igf1 | 44.2 | 82.8 | 75.8 | 17.6 | 45.0 | 85.1 | 84.1 | 63.8 | 1.9 |
| Igf2 | 91.9 | 92.3 | 4.7 | 20.9 | 8.8 | 9.0 | 26.1 | 25.1 | 1.0 |
| Il15 | BT (0.6) | BT (1.3) | BT (1.4) | 9.8 | 4.7 | 9.3 | 4.2 | 2.6 | 2.0 |
| Il16 | BT (0.4) | BT (0.5) | 2.2 | BT (0.7) | BT (1.2) | 3.1 | BT (1.3) | BT (1.0) | 2.7 |
| Il18 | BT (0.3) | BT (0.3) | 9.4 | BT (0.7) | 4.0 | 5.5 | 5.2 | 5.2 | 1.4 |
| Il1b | BT (0.0) | BT (0.0) | 2.3 | BT (0.7) | BT (0.0) | 7.4 | 5.9 | 7.2 | >7.4 |
| Il33 | 17.2 | 13.8 | 32.7 | 56.2 | 72.7 | 63.7 | 40.8 | 44.6 | 0.9 |
| Il6 | BT (0.2) | 2.1 | 3.7 | BT (0.0) | 2.8 | 8.1 | 10.0 | 8.8 | 2.8 |
| Inha | 2.0 | BT (1.3) | BT (1.9) | 2.0 | BT (1.2) | 2.3 | 2.3 | 2.3 | 2.0 |
| Inhba | 3.4 | BT (0.5) | 2.1 | 6.5 | BT (1.4) | 12.8 | 15.8 | 23.5 | 9.0 |
| Inhbb | BT (0.0) | BT (0.0) | BT (1.3) | 2.6 | BT (0.0) | 12.8 | BT (1.6) | 2.3 | >12.8 |
| Jag1 | 22.3 | 13.8 | 13.4 | 25.5 | 4.5 | 16.7 | 23.4 | 23.1 | 3.7 |
| Lif | BT (1.3) | BT (1.1) | 2.4 | BT (0.0) | 3.1 | 11.6 | 2.1 | 6.2 | 3.8 |
| Mdk | 58.8 | 70.9 | 16.1 | 30.1 | 16.4 | 54.6 | 65.9 | 45.6 | 3.3 |
| Metrn | 5.2 | 10.3 | 3.1 | 5.9 | BT (1.2) | 13.3 | 5.1 | 23.5 | 11.2 |
| Mif | 21.1 | 30.4 | 18.6 | 15.0 | 14.9 | 42.2 | 42.5 | 54.7 | 2.8 |
| Nenf | 54.7 | 62.7 | 55.7 | 49.0 | 49.8 | 59.7 | 60.5 | 59.6 | 1.2 |
| Ngf | 2.3 | 13.5 | BT (1.2) | 8.5 | 2.6 | 7.7 | BT (1.7) | 6.8 | 2.9 |
| Nov | 16.7 | 5.6 | 30.0 | BT (0.7) | 8.1 | 9.7 | 17.6 | 22.5 | 1.2 |
| Nppc | 2.1 | 7.7 | BT (0.3) | BT (0.0) | 2.6 | 6.3 | 8.3 | 4.2 | 2.4 |
| Ntf3 | BT (1.3) | BT (0.5) | 4.6 | BT (0.0) | BT (0.7) | BT (1.4) | 5.3 | 3.6 | 1.9 |
| Ntn1 | 21.7 | BT (0.5) | 24.8 | 61.4 | 12.8 | 25.0 | 11.1 | 18.6 | 2.0 |
| Pdgfa | 4.0 | 2.6 | 6.5 | 9.8 | BT (1.7) | 7.9 | 11.0 | 25.1 | 4.8 |
| Pdgfc | BT (0.7) | BT (0.3) | 6.0 | BT (0.0) | BT (0.2) | BT (1.4) | 7.2 | 8.1 | 5.8 |
| Pf4 | BT (0.8) | BT (1.1) | 2.0 | BT (1.3) | BT (0.0) | 4.0 | 3.7 | 4.9 | >4.0 |
| Pgf | BT (1.4) | BT (1.1) | 2.0 | 3.3 | 5.0 | 12.7 | 2.5 | 3.9 | 2.6 |
| Pomc | BT (0.3) | BT (1.1) | BT (0.9) | BT (0.7) | BT (1.4) | 3.1 | BT (1.2) | BT (1.3) | 2.2 |
| Pthlh | 5.7 | 6.3 | 9.8 | 20.3 | 7.6 | 13.8 | 13.4 | 11.1 | 1.8 |
| Ptn | 21.1 | 21.7 | 15.5 | 2.6 | 4.0 | 11.1 | 56.8 | 45.6 | 2.7 |
| Rspo1 | 11.5 | BT (0.0) | 3.2 | 20.9 | BT (1.2) | BT (0.5) | BT (0.5) | BT (0.3) | 0.5 |
| Rspo3 | BT (0.4) | BT (0.0) | 3.1 | BT (1.3) | BT (0.0) | BT (0.7) | 11.6 | 6.2 | - |
| Rtn4 | 35.1 | 36.2 | 47.9 | 43.8 | 33.9 | 68.6 | 60.5 | 72.3 | 2.0 |
| Sema3b | 5.2 | 9.3 | 14.0 | 11.1 | 33.4 | 11.3 | 5.0 | 6.5 | 0.3 |
| Sema3c | 43.0 | 14.8 | 50.5 | 18.3 | 9.2 | 8.6 | 23.0 | 27.7 | 0.9 |
| Sema3d | 18.0 | 3.7 | 11.4 | 45.1 | BT (0.7) | BT (1.8) | 6.3 | 7.8 | 2.5 |
| Sema3e | BT (0.7) | BT (0.3) | 3.7 | BT (0.0) | BT (0.2) | BT (0.1) | BT (1.0) | 2.9 | 0.6 |
| Sema3f | 2.2 | BT (0.5) | BT (1.1) | 2.6 | BT (0.7) | 4.5 | 2.0 | 3.3 | 6.3 |
| Sema3g | BT (0.3) | BT (1.3) | BT (0.6) | BT (0.0) | 3.1 | 2.7 | BT (1.0) | 2.0 | 0.9 |
| Sema4a | BT (0.8) | BT (1.9) | BT (0.6) | 4.6 | BT (1.7) | 3.3 | BT (1.3) | BT (1.6) | 2.0 |
| Sema4b | BT (1.7) | BT (0.3) | BT (1.5) | 2.0 | 2.1 | 2.9 | 2.6 | 2.3 | 1.3 |
| Sema4c | 5.8 | 5.8 | 5.9 | 13.1 | 6.4 | 11.7 | 9.3 | 10.1 | 1.8 |
| Sema5a | 4.7 | 7.4 | BT (1.8) | 4.6 | 3.6 | 3.6 | 6.1 | 5.9 | 1.0 |
| Sema5b | 5.6 | 9.5 | BT (0.2) | BT (0.0) | BT (1.2) | BT (1.1) | BT (1.6) | 5.2 | 0.9 |
| Sema6a | 6.2 | 9.8 | 3.1 | 7.8 | 19.0 | 14.6 | 3.2 | 7.5 | 0.8 |
| Sema6b | BT (0.1) | BT (0.3) | 2.5 | BT (0.0) | 2.8 | 7.1 | BT (1.3) | 7.8 | 2.5 |
| Sema6c | 4.3 | 4.8 | 5.4 | BT (1.3) | 3.3 | 3.4 | 8.0 | 6.2 | 1.0 |
| Sema6d | 2.2 | 3.2 | 3.7 | 7.8 | 3.6 | 11.2 | 3.7 | 9.4 | 3.2 |
| Sema7a | BT (0.3) | BT (0.5) | BT (1.3) | BT (0.7) | BT (0.9) | 19.4 | 11.0 | 21.5 | 20.5 |
| Sfrp1 | 60.0 | 29.1 | 40.0 | 54.2 | 15.2 | 32.9 | 50.0 | 32.6 | 2.2 |
| Sfrp2 | 11.4 | BT (0.3) | 47.8 | 3.9 | 5.5 | 7.1 | 21.7 | 18.6 | 1.3 |
| Sfrp4 | 33.6 | BT (1.9) | 72.4 | 32.7 | 9.0 | 50.7 | 56.8 | 39.1 | 5.6 |
| Sfrp5 | 26.7 | 2.6 | 2.6 | 94.8 | 5.9 | 2.6 | 6.3 | 10.4 | 0.4 |
| Tgfb1 | BT (0.6) | BT (0.3) | 2.4 | 3.3 | 3.3 | 11.1 | 10.0 | 15.3 | 3.3 |
| Tgfb2 | 10.3 | BT (1.1) | 10.5 | 3.3 | 2.8 | 3.7 | 17.0 | 12.1 | 1.3 |
| Tgfb3 | 20.6 | 3.4 | 16.8 | 19.0 | 2.4 | 9.0 | 36.1 | 19.2 | 3.8 |
| Tnf | BT (0.0) | BT (0.3) | BT (1.7) | BT (0.7) | BT (0.0) | 2.5 | BT (0.7) | 2.6 | >2.5 |
| Tnfrsf11b | BT (1.9) | BT (0.0) | 4.6 | 8.5 | BT (0.5) | BT (0.7) | 4.4 | 10.7 | 1.4 |
| Tnfsf10 | BT (0.0) | BT (0.0) | BT (0.4) | 2.0 | BT (1.7) | BT (0.7) | BT (0.2) | BT (1.0) | 0.4 |
| Tnfsf12 | 9.6 | 11.6 | 15.7 | 15.0 | 17.8 | 17.3 | 14.6 | 14.7 | 1.0 |
| Tnfsf8 | BT (0.3) | BT (0.0) | BT (0.8) | 10.5 | BT (0.0) | 2.2 | 5.7 | 3.3 | >2.2 |
| Tnfsf9 | BT (0.5) | BT (1.6) | BT (1.4) | BT (1.3) | 4.0 | 5.9 | 4.5 | 7.2 | 1.5 |
| Tslp | BT (1.2) | 2.4 | 4.0 | 2.6 | BT (0.2) | 4.8 | BT (1.2) | 2.9 | 20.2 |
| Vegfa | 11.0 | 4.8 | 25.0 | 3.9 | 8.3 | 18.2 | 29.6 | 27.0 | 2.2 |
| Vegfb | 5.2 | 9.0 | 5.4 | 9.8 | 4.7 | 7.1 | 8.3 | 11.4 | 1.5 |
| Vegfc | BT (0.7) | BT (0.0) | 2.2 | BT (0.7) | BT (0.2) | BT (0.7) | 2.2 | 5.5 | 2.9 |
| Wnt11 | BT (1.2) | BT (0.0) | 6.2 | BT (0.0) | BT (0.5) | BT (0.5) | BT (0.9) | 2.9 | 1.2 |
| Wnt2 | 6.0 | BT (0.3) | 9.1 | BT (0.0) | BT (0.2) | BT (1.5) | 4.6 | 4.9 | 6.3 |
| Wnt5a | 15.5 | 4.0 | 19.1 | 7.8 | 10.4 | 13.9 | 13.0 | 14.0 | 1.3 |
The combined mesenchymal cell dataset (Fig. 4A,B) was analyzed to determine the percentage of cells within the different mesenchymal cell clusters that detectably expressed (≥2%) the 143 injured nerve ligand mRNAs (Table 2). Also shown is the difference, expressed as fold change, in the percentage of positive cells in the injured versus uninjured endoneurial mesenchymal cells. BT = below threshold and indicates that <2% of cells detectably expressed the ligand mRNA. Also shown are the absolute values, since these were used to determine the fold changes. Neonatal epineurial includes cluster 1 cells, neonatal endoneurial includes cluster 6 cells, inj/uninjured epineurial includes clusters 2 and 5 cells, neonatal/uninjured/injured perineurial includes cluster 8 cells, uninjured endoneurial includes cluster 4 cells, injured endoneurial includes cluster 3 cells, injured differentiating includes cluster 0 cells, and neonatal/injured proliferating includes cluster 7 cells.