Table 5.
List of selected chemokines and relative levels expressed in the ONH in naïve, rAION-vehicle-induced and rAION-PGJ2-treated animals. Illumina sequence data for ONH are based on Deseq2-normalized (log2-fold relative levels) expressed in ONH RNA from individual naïve, mean naïve (n = 5), rAION-vehicle-induced and rAION-PGJ2-treated animals, using a cutoff of <3.4. Normalization is based on Trimmed Mean Values (TMM) and normalized by EdgeR-cpm function with a cutoff of 2. Naïve retina (retina-N) and ischemic retina (retina-Isch) are from [19] and expressed in counts per million (CPM). The ratio of expression in ischemic retina/sham retina values are shown in the last column. The two greatest ratio changes in retinal conditions are shown in bold. The total list is found in Supplemental Data Table S1. NF: not found. The total list is found in Supplemental Data Table S1.
| Gene Symbol | Gene Name | ONH-1 | ONH-2 | ONH-3 | ONH-4 | ONH-5 | Mean Naïve | Veh-rNAION | PGJ2-rNAION | Veh/Naïve | Veh/PGJ2 | Ret-Sham (CPM) | Ret-Isch (CPM) | Ret-Isch/Ret-Sham |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ccl17 | C-C motif chemokine ligand 17 | 3.66247 | 3.66247 | 3.66247 | 4.78510 | 5.99643 | 4.35379 | 6.34187 | 5.47966 | 1.45663 | 1.15735 | 0 | 0.58685 | 0 |
| Ccl9 | chemokine (C-C motif) ligand 9 | 3.66247 | 4.50516 | 3.66247 | 4.69013 | 5.72428 | 4.44890 | 6.24965 | 4.80497 | 1.40476 | 1.30066 | 0.22664 | 0.58685 | 2.589332 |
| Ccl17 | C-C motif chemokine ligand 17 | 3.66247 | 3.66247 | 3.66247 | 4.78510 | 5.99643 | 4.35379 | 6.34187 | 5.47966 | 1.45663 | 1.15735 | 0 | 0.58685 | 0.00000 |
| Ccl9 | chemokine (C-C motif) ligand 9 | 3.66247 | 4.50516 | 3.66247 | 4.69013 | 5.72428 | 4.44890 | 6.24965 | 4.80497 | 1.40476 | 1.30066 | 0.22664 | 0.58685 | 2.589332 |
| Cxcl11 | C-X-C motif chemokine ligand 11 | 4.55453 | 5.24570 | 3.66247 | 6.44499 | 6.62156 | 5.30585 | 7.10257 | 6.85985 | 1.33863 | 1.03538 | 1.17676 | 4.84968 | 4.121221 |
| Cxcl3 | chemokine (C-X-C motif) ligand 3 | 3.66247 | 3.66247 | 3.66247 | 3.66247 | 6.09578 | 4.14913 | 5.50131 | 5.32898 | 1.32589 | 1.03234 | 0 | 1.76055 | 1.76000 |
| Ccl22 | C-C motif chemokine ligand 22 | 4.91547 | 4.50516 | 3.66247 | 3.66247 | 6.03093 | 4.55530 | 5.94922 | 5.06457 | 1.30600 | 1.17468 | 0 | 0.44014 | 0.00000 |
| Cxcl10 | C-X-C motif chemokine ligand 10 | 6.91014 | 6.74324 | 7.41151 | 7.34027 | 8.74746 | 7.43052 | 9.62249 | 7.72673 | 1.29499 | 1.24535 | 2.30759 | 6.96402 | 3.017873 |
| Ccl3 | C-C motif chemokine ligand 3 | 6.10348 | 5.47653 | 3.66247 | 5.72976 | 7.46226 | 5.68690 | 7.36272 | 6.85985 | 1.29468 | 1.07331 | 0.22664 | 113.3327 | 500.0525 |
| Ccl4 | C-C motif chemokine ligand 4 | 5.11673 | 5.18679 | 3.66247 | 5.21148 | 7.04250 | 5.24399 | 6.75924 | 6.41225 | 1.28895 | 1.05411 | 0 | 7.18892 | 7.18000 |
| Ccl11 | C-C motif chemokine ligand 11 | 5.97773 | 5.99532 | 5.23550 | 6.27199 | 8.79818 | 6.45574 | 8.03063 | 7.15605 | 1.24395 | 1.12222 | 0.98315 | 0.13551 | 0.137835 |
| Ccl21 | C-C motif chemokine ligand 21 | 3.66247 | 3.66247 | 3.66247 | 3.66247 | 5.97860 | 4.12570 | 5.06042 | 4.90761 | 1.22656 | 1.03114 | 0.64187 | 0 | 0.00000 |
| Ccr8 | C-C motif chemokine receptor 8 | 3.66247 | 3.66247 | 3.66247 | 3.66247 | 3.66247 | 3.66247 | 4.48830 | 3.66247 | 1.22548 | 1.22548 | NF | NF | NF |
| Cxcl17 | C-X-C motif chemokine ligand 17 | 6.19527 | 5.80569 | 3.66247 | 5.83632 | 5.92253 | 5.48446 | 6.66235 | 6.27156 | 1.21477 | 1.06231 | 0.70292 | 0.68646 | 0.97658 |
| Cxcl6 | C-X-C motif chemokine ligand 6 | 5.26306 | 4.95893 | 6.17198 | 5.39903 | 6.61271 | 5.68114 | 6.80838 | 5.89380 | 1.19842 | 1.15518 | 0 | 6.45535 | 6.4 |
| Ccl7 | C-C motif chemokine ligand 7 | 6.10348 | 5.29929 | 7.40593 | 5.17358 | 8.71593 | 6.53964 | 7.78204 | 6.92987 | 1.18998 | 1.12297 | 0.42791 | 621.8639 | 1453.252 |
| Cxcl2 | C-X-C motif chemokine ligand 2 | 5.38041 | 5.34857 | 3.66247 | 4.69013 | 6.71428 | 5.15917 | 6.01198 | 5.83595 | 1.16530 | 1.03016 | 4.40896 | 408.5915 | 92.67299 |
| Ccl24 | C-C motif chemokine ligand 24 | 6.72505 | 6.37803 | 6.89992 | 6.51138 | 7.96817 | 6.89651 | 7.86946 | 6.45161 | 1.14108 | 1.21977 | 1.24787 | 164.22 | 131.5999 |
| Cxcl1 | C-X-C motif chemokine ligand 1 | 5.32453 | 5.43672 | 6.57287 | 5.34265 | 7.33875 | 6.00310 | 6.70378 | 6.47071 | 1.11672 | 1.03602 | 1.95483 | 817.0636 | 417.9714 |