Table 3.
List of arachidonic acid synthetic genes: phospholipase A2 genes and MAGL/MGLL. Illumina sequence data for ONH are based on Deseq2-normalized (log2-fold relative levels) expressed in ONH RNA from naïve, 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. Gene-mRNA quantification and differential expression can be equated between the two studies (ONH and retina) by comparing the relative expression of both standard housekeeping genes (Beta-Actin (Actb), cyclophilin a ((ppia), cyclophilin b (ppib), glyceraldehyde phosphate dehydrogenase (GAPDH) and PPARγ (pparg), as well as the expression of some of the highest expressing genes in each tissue (MBP in ONH; Rho in retina). NF: not found.
| Gene Symbol | Gene Name | ONH-N1 | ONH-N2 | ONH-N3 | ONH-N4 | ONH-N5 | Mean Naïve | Veh-rAION | PGJ2-rAION | Veh/Naïve | Vehicle/PGJ2 | Ret-Sham (CPM) | Ret-Isch (CPM) | Ret-Isch/Ret/Sham |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Pla2g7 | phospholipase A2 group VII | 15.10933 | 14.79132 | 12.94959 | 14.77261 | 12.82698 | 14.089966 | 13.003512 | 13.335868 | 0.9228917 | 0.975078036 | 0.35146081 | 33.993338 | 0.010339 |
| Pla2g16 | phospholipase A2, group XVI | 13.63818 | 12.91624 | 13.40673 | 12.66619 | 12.365 | 12.998467 | 12.1254154 | 12.018962 | 0.9328343 | 1.008857111 | 235.236921 | 297.265176 | 0.791337 |
| Pla2g6 | phospholipase A2 group VI | 10.18158 | 10.04404 | 10.07626 | 10.34514 | 9.786774 | 10.086759 | 10.0580887 | 10.407593 | 0.9971576 | 0.966418349 | 11.0373495 | 14.7100521 | 0.750327 |
| Pla2g4a | phospholipase A2 group IVA | 8.836592 | 8.972135 | 9.337722 | 9.232697 | 10.36593 | 9.3490153 | 10.1824257 | 9.5777503 | 1.0891442 | 1.063133338 | 9.53095284 | 20.7441067 | 0.459454 |
| Pla2g15 | phospholipase A2, group XV | 9.021099 | 9.191856 | 9.603836 | 9.060801 | 9.575812 | 9.2906808 | 9.86609055 | 9.9238729 | 1.0619341 | 0.994177444 | 30.7126327 | 33.3418939 | 0.921142 |
| Pla2g12a | phospholipase A2, group XIIA | 9.676339 | 9.435444 | 9.30206 | 9.447172 | 9.004778 | 9.3731584 | 9.41553769 | 9.7066862 | 1.0045213 | 0.970005369 | 5.15867823 | 4.19978952 | 1.228318 |
| Pla2g3 | phospholipase A2, group III | 8.88697 | 8.229182 | 6.696327 | 8.932058 | 6.585697 | 7.8660468 | 7.30830417 | 7.5213669 | 0.9290949 | 0.97167234 | NF | NF | NF |
| Pla2g2c | phospholipase A2, group IIC | 7.839402 | 7.646561 | 6.955483 | 7.387974 | 6.77704 | 7.321292 | 6.70783566 | 7.2020536 | 0.9162093 | 0.93137819 | 4.15672828 | 2.80687237 | 1.480911 |
| Pla2g4b | phospholipase A2 group IVB | 7.73606 | 8.229182 | 8.981785 | 8.117569 | 8.634831 | 8.3398853 | 8.46154825 | 8.4582903 | 1.0145881 | 1.000385178 | 3.29683962 | 9.62216053 | 0.34263 |
| Pla2g5 | phospholipase A2, group V | 6.704759 | 8.235359 | 3.662474 | 7.034882 | 6.198245 | 6.3671437 | 6.56962921 | 6.4612068 | 1.0318016 | 1.016780527 | 3.76985453 | 5.81568605 | 0.648222 |
| Pla2g2a | phospholipase A2 group IIA | 7.158225 | 6.601056 | 6.469342 | 5.929593 | 6.384064 | 6.5084562 | 7.37481481 | 7.4208545 | 1.1331128 | 0.993795911 | 0.98906215 | 0.54023288 | 1.830807 |
| Pla2g2e | phospholipase A2, group IIE | 7.240552 | 7.280109 | 5.870084 | 6.790849 | 6.548524 | 6.7460235 | 6.10158817 | 6.3282454 | 0.9044718 | 0.964183242 | 0 | 0.27011644 | 0 |
| Pla2g1b | phospholipase A2 group IB | 5.640167 | 5.121023 | 3.662474 | 5.173576 | 3.662474 | 4.6519426 | 5.48358443 | 4.9921317 | 1.178773 | 1.098445474 | 4.35437038 | 4.03998796 | 1.077818 |
| Pla2g4f | phospholipase A2, group IVF | 5.906466 | 5.995318 | 5.571123 | 5.891002 | 5.64408 | 5.8015978 | 5.70985447 | 6.172554 | 0.9841865 | 0.925039216 | NF | NF | NF |
| Pla2g2d | phospholipase A2, group IID | 6.501938 | 5.046214 | 7.169554 | 5.729765 | 6.126362 | 6.1147665 | 6.48782433 | 5.8557298 | 1.0610093 | 1.107944629 | 0 | 1.90726317 | 0 |
| Pnpla2 | patatin-like phospholipase domain containing 2 | 5.708367 | 5.995318 | 5.607421 | 6.579621 | 5.584945 | 5.8951345 | 6.33600637 | 6.8198346 | 1.0747857 | 0.929055717 | 20.634368 | 21.9832379 | 0.938641 |
| Pla2g10 | phospholipase A2, group X | 3.662474 | 3.662474 | 3.662474 | 4.690134 | 3.662474 | 3.8680059 | 3.66247389 | 3.6624739 | 0.9468636 | 1 | 0 | 1.08409959 | 0 |
| Pla2r1 | phospholipase A2 receptor 1 | 5.977731 | 6.193288 | 6.550772 | 6.304503 | 6.548524 | 6.3149638 | 6.84479358 | 6.5347544 | 1.0839007 | 1.047444655 | 67.6342502 | 74.59747 | 0.906656 |
| Mgll/MAGL | monoglyceride lipase | 10.45186 | 10.21227 | 9.67473 | 10.12171 | 8.472095 | 9.7865318 | 9.61457884 | 10.15996 | 0.9824296 | 0.946320558 | 99.503189 | 74.4858603 | 1.335867 |
| Gene expression controls | ||||||||||||||
| Ppia | peptidylprolyl isomerase A | 14.88068 | 14.21798 | 15.31686 | 14.29613 | 15.27559 | 14.935534 | 14.8897368 | 14.79745 | 1.0062367 | 0.996933659 | 15.5049789 | 17.7037818 | 0.8758 |
| Ppib | peptidylprolyl isomerase B | 13.29631 | 12.87667 | 13.54295 | 12.97108 | 13.79579 | 13.421187 | 13.3416644 | 13.296562 | 1.003392 | 0.994074854 | 56.1145906 | 102.154809 | 0.549309 |
| Actb | actin, beta | 17.01179 | 16.81788 | 17.20874 | 16.96558 | 17.38982 | 17.599677 | 17.4216397 | 17.078761 | 1.0200763 | 0.989884031 | 631.922522 | 2276.3337 | 0.277605 |
| Gapdh | glyceraldehyde-3-phosphate dehydrogenase | 14.429 | 13.95914 | 14.01805 | 14.01042 | 15.03571 | 15.000118 | 14.9295525 | 14.290462 | 1.0447214 | 0.995295699 | 78.0188393 | 65.4709231 | 1.191656 |
| Pparg | peroxisome proliferator-activated receptor gamma | 5.564472 | 4.852943 | 3.662474 | 5.041199 | 6.095778 | 4.9076087 | 5.89109898 | 5.0433732 | 1.1680871 | 1.200401111 | 0 | 1.01533353 | 0 |
| Mbp | myelin basic protein | 18.37768 | 18.23455 | 17.80142 | 18.32891 | 17.65172 | 18.175157 | 17.9969671 | 18.078857 | 0.9954704 | 0.99019598 | 7.4746679 | 2.33938774 | 3.195139 |
| Rho | rhodopsin | 6.177695 | 7.738614 | 7.482357 | 8.943992 | 7.457686 | 7.8474819 | 6.45206772 | 7.5600688 | 0.8534403 | 0.822183193 | 5309.71918 | 3564.86423 | 1.489459 |