Supplementary Materials
Regeneration Rosetta: An interactive web application to explore regeneration-associated gene expression and chromatin accessibility
Andrea Rau, Sumona P. Dhara, Ava J. Udvadia, Paul L. Auer
1. Table S1. List of cholesterol metabolic genes from MGI database 2. Table S2. List of differentially expressed transcripts during optic nerve regeneration in zebrafish using the MGI cholesterol metabolic gene queries in the Regeneration Rosetta app 3. Table S3. List of transcription factor encoding genes from brain cell bodies following spinal cord injury in lamprey over a course of 12 weeks 4. Table S4. List of transcription factor encoding genes from spinal cell bodies following spinal cord injury in lamprey over a course of 12 weeks
Ensembl ID MGI Gene ID Symbol Name
ENSMUSG00000015243 MGI:99607 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1
ENSMUSG00000026944 MGI:99606 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2
ENSMUSG00000024030 MGI:107704 Abcg1 ATP binding cassette subfamily G member 1
ENSMUSG00000026003 MGI:87866 Acadl acyl-Coenzyme A dehydrogenase, long-chain
ENSMUSG00000018574 MGI:895149 Acadvl acyl-Coenzyme A dehydrogenase, very long chain
ENSMUSG00000038641 MGI:2384785 Akr1d1 aldo-keto reductase family 1, member D1
ENSMUSG00000028553 MGI:1353627 Angptl3 angiopoietin-like 3
ENSMUSG00000031996 MGI:88047 Aplp2 amyloid beta (A4) precursor-like protein 2
ENSMUSG00000032083 MGI:88049 Apoa1 apolipoprotein A-I
ENSMUSG00000005681 MGI:88050 Apoa2 apolipoprotein A-II
ENSMUSG00000032080 MGI:88051 Apoa4 apolipoprotein A-IV
ENSMUSG00000032079 MGI:1913363 Apoa5 apolipoprotein A-V
ENSMUSG00000020609 MGI:88052 Apob apolipoprotein B
ENSMUSG00000042759 MGI:2176230 Apobr apolipoprotein B receptor
ENSMUSG00000040564 MGI:88053 Apoc1 apolipoprotein C-I
ENSMUSG00000032081 MGI:88055 Apoc3 apolipoprotein C-III
ENSMUSG00000002985 MGI:88057 Apoe apolipoprotein E
ENSMUSG00000047631 MGI:104539 Apof apolipoprotein F
ENSMUSG00000022892 MGI:88059 App amyloid beta (A4) precursor protein
ENSMUSG00000031982 MGI:1916115 Arv1 ARV1 homolog, fatty acid homeostasis modulator
ENSMUSG00000027187 MGI:88271 Cat catalase
ENSMUSG00000034957 MGI:99480 Cebpa CCAAT/enhancer binding protein (C/EBP), alpha ENSMUSG00000026818 MGI:88374 Cel carboxyl ester lipase
ENSMUSG00000056973 MGI:2148202 Ces1d carboxylesterase 1D
ENSMUSG00000041301 MGI:88388 Cftr cystic fibrosis transmembrane conductance regulator
ENSMUSG00000050370 MGI:1333869 Ch25h cholesterol 25-hydroxylase
ENSMUSG00000032245 MGI:2159324 Cln6 ceroid-lipofuscinosis, neuronal 6
ENSMUSG00000026317 MGI:1349447 Cln8 ceroid-lipofuscinosis, neuronal 8
ENSMUSG00000026726 MGI:1931256 Cubn cubilin (intrinsic factor-cobalamin receptor)
ENSMUSG00000018042 MGI:94893 Cyb5r3 cytochrome b5 reductase 3
ENSMUSG00000028240 MGI:106091 Cyp7a1 cytochrome P450, family 7, subfamily a, polypeptide 1
ENSMUSG00000039519 MGI:104978 Cyp7b1 cytochrome P450, family 7, subfamily b, polypeptide 1
Cyp11a ENSMUSG00000032323 MGI:88582 1 cytochrome P450, family 11, subfamily a, polypeptide 1
Cyp11b ENSMUSG00000075604 MGI:88583 1 cytochrome P450, family 11, subfamily b, polypeptide 1
Cyp11b ENSMUSG00000022589 MGI:88584 2 cytochrome P450, family 11, subfamily b, polypeptide 2
Cyp27a ENSMUSG00000026170 MGI:88594 1 cytochrome P450, family 27, subfamily a, polypeptide 1
Cyp39a ENSMUSG00000023963 MGI:1927096 1 cytochrome P450, family 39, subfamily a, polypeptide 1
Cyp46a ENSMUSG00000021259 MGI:1341877 1 cytochrome P450, family 46, subfamily a, polypeptide 1
ENSMUSG00000001467 MGI:106040 Cyp51 cytochrome P450, family 51
ENSMUSG00000030747 MGI:1915050 Dgat2 diacylglycerol O-acyltransferase 2
ENSMUSG00000004815 MGI:102918 Dgkq diacylglycerol kinase, theta
ENSMUSG00000058454 MGI:1298378 Dhcr7 7-dehydrocholesterol reductase
ENSMUSG00000034926 MGI:1922004 Dhcr24 24-dehydrocholesterol reductase ENSMUSG00000041544 MGI:2444403 Disp3 dispatched RND transporter family member 3
ENSMUSG00000031168 MGI:107822 Ebp phenylalkylamine Ca2+ antagonist (emopamil) binding protein
ENSMUSG00000022040 MGI:99500 Ephx2 epoxide hydrolase 2, cytoplasmic
ENSMUSG00000025198 MGI:2387613 Erlin1 ER lipid raft associated 1
ENSMUSG00000031483 MGI:2387215 Erlin2 ER lipid raft associated 2
ENSMUSG00000021273 MGI:102706 Fdft1 farnesyl diphosphate farnesyl transferase 1
ENSMUSG00000059743 MGI:104888 Fdps farnesyl diphosphate synthetase
ENSMUSG00000032051 MGI:103224 Fdx1 ferredoxin 1
ENSMUSG00000018861 MGI:104724 Fdxr ferredoxin reductase
ENSMUSG00000024588 MGI:95513 Fech ferrochelatase
ENSMUSG00000036585 MGI:95515 Fgf1 fibroblast growth factor 1
ENSMUSG00000031594 MGI:102795 Fgl1 fibrinogen-like protein 1
ENSMUSG00000031400 MGI:105979 G6pdx glucose-6-phosphate dehydrogenase X-linked
ENSMUSG00000028048 MGI:95665 Gba glucosidase, beta, acid
ENSMUSG00000028467 MGI:2654325 Gba2 glucosidase beta 2
ENSMUSG00000021148 MGI:3704398 Gm9745 predicted gene 9745
ENSMUSG00000023439 MGI:95785 Gnb3 guanine nucleotide binding protein (G protein), beta 3
ENSMUSG00000034088 MGI:99256 Hdlbp high density lipoprotein (HDL) binding protein
ENSMUSG00000021670 MGI:96159 Hmgcr 3-hydroxy-3-methylglutaryl-Coenzyme A reductase
ENSMUSG00000093930 MGI:107592 Hmgcs1 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1
ENSMUSG00000027875 MGI:101939 Hmgcs2 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2
ENSMUSG00000029556 MGI:98504 Hnf1a HNF1 homeobox A
hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid ENSMUSG00000042289 MGI:2141879 Hsd3b7 delta-isomerase 7 Hsd17b ENSMUSG00000026675 MGI:1330808 7 hydroxysteroid (17-beta) dehydrogenase 7
ENSMUSG00000033520 MGI:2444315 Idi2 isopentenyl-diphosphate delta isomerase 2
ENSMUSG00000000869 MGI:96556 Il4 interleukin 4
ENSMUSG00000045294 MGI:1916289 Insig1 insulin induced gene 1
ENSMUSG00000003721 MGI:1920249 Insig2 insulin induced gene 2
ENSMUSG00000004880 MGI:2138281 Lbr lamin B receptor
ENSMUSG00000035237 MGI:96755 Lcat lecithin cholesterol acyltransferase
ENSMUSG00000032193 MGI:96765 Ldlr low density lipoprotein receptor
ENSMUSG00000037295 MGI:2140175 Ldlrap1 low density lipoprotein receptor adaptor protein 1
ENSMUSG00000059201 MGI:104663 Lep leptin
ENSMUSG00000057722 MGI:104993 Lepr leptin receptor
ENSMUSG00000023022 MGI:1920992 Lima1 LIM domain and actin binding 1
ENSMUSG00000032207 MGI:96216 Lipc lipase, hepatic
ENSMUSG00000003123 MGI:96790 Lipe lipase, hormone sensitive
ENSMUSG00000002279 MGI:1923733 Lmf1 lipase maturation factor 1
ENSMUSG00000040249 MGI:96828 Lrp1 low density lipoprotein receptor-related protein 1
ENSMUSG00000024913 MGI:1278315 Lrp5 low density lipoprotein receptor-related protein 5
ENSMUSG00000033105 MGI:1336155 Lss lanosterol synthase
ENSMUSG00000031835 MGI:1927235 Mbtps1 membrane-bound transcription factor peptidase, site 1
ENSMUSG00000031760 MGI:97173 Mt3 metallothionein 3
ENSMUSG00000028158 MGI:106926 Mttp microsomal triglyceride transfer protein
ENSMUSG00000006517 MGI:2179327 Mvd mevalonate (diphospho) decarboxylase
ENSMUSG00000041939 MGI:107624 Mvk mevalonate kinase ENSMUSG00000038615 MGI:99421 Nfe2l1 nuclear factor, erythroid derived 2,-like 1
ENSMUSG00000024413 MGI:1097712 Npc1 NPC intracellular cholesterol transporter 1
ENSMUSG00000020447 MGI:2685089 Npc1l1 NPC1 like intracellular cholesterol transporter 1
ENSMUSG00000021242 MGI:1915213 Npc2 NPC intracellular cholesterol transporter 2
ENSMUSG00000031349 MGI:1099438 Nsdhl NAD(P) dependent steroid dehydrogenase-like
ENSMUSG00000044254 MGI:2140260 Pcsk9 proprotein convertase subtilisin/kexin type 9
ENSMUSG00000020553 MGI:107375 Pctp phosphatidylcholine transfer protein
ENSMUSG00000040374 MGI:107486 Pex2 peroxisomal biogenesis factor 2
ENSMUSG00000018217 MGI:97631 Pmp22 peripheral myelin protein 22
ENSMUSG00000027952 MGI:1915853 Pmvk phosphomevalonate kinase
ENSMUSG00000002588 MGI:103295 Pon1 paraoxonase 1
ENSMUSG00000005514 MGI:97744 Por P450 (cytochrome) oxidoreductase
MGI:104573 Pphc2 polyunsaturated fat induced postprandial hypercholesterolemia
ENSMUSG00000050697 MGI:2145955 Prkaa1 protein kinase, AMP-activated, alpha 1 catalytic subunit
ENSMUSG00000028518 MGI:1336173 Prkaa2 protein kinase, AMP-activated, alpha 2 catalytic subunit
ENSMUSG00000074115 MGI:98221 Saa1 serum amyloid A 1
ENSMUSG00000032018 MGI:1353611 Sc5d sterol-C5-desaturase
ENSMUSG00000032485 MGI:2135958 Scap SREBF chaperone
ENSMUSG00000037936 MGI:893578 Scarb1 scavenger receptor class B, member 1
ENSMUSG00000028603 MGI:98254 Scp2 sterol carrier protein 2, liver
ENSMUSG00000003585 MGI:1915065 Sec14l2 SEC14-like lipid binding 2
Serpina serine (or cysteine) peptidase inhibitor, clade A (alpha-1 ENSMUSG00000041567 MGI:1915304 12 antiproteinase, antitrypsin), member 12
ENSMUSG00000037049 MGI:98325 Smpd1 sphingomyelin phosphodiesterase 1, acid lysosomal ENSMUSG00000026600 MGI:104665 Soat1 sterol O-acyltransferase 1
ENSMUSG00000023045 MGI:1332226 Soat2 sterol O-acyltransferase 2
ENSMUSG00000022982 MGI:98351 Sod1 superoxide dismutase 1, soluble
ENSMUSG00000049313 MGI:1202296 Sorl1 sortilin-related receptor, LDLR class A repeats-containing
ENSMUSG00000022351 MGI:109296 Sqle squalene epoxidase
ENSMUSG00000020538 MGI:107606 Srebf1 sterol regulatory element binding transcription factor 1
ENSMUSG00000022463 MGI:107585 Srebf2 sterol regulatory element binding factor 2
ENSMUSG00000003271 MGI:1926342 Sult2b1 sulfotransferase family, cytosolic, 2B, member 1
ENSMUSG00000021779 MGI:98743 Thrb thyroid hormone receptor beta
ENSMUSG00000024799 MGI:1920416 Tm7sf2 transmembrane 7 superfamily member 2
ENSMUSG00000026700 MGI:104511 Tnfsf4 tumor necrosis factor (ligand) superfamily, member 4
ENSMUSG00000038172 MGI:1917113 Ttc39b tetratricopeptide repeat domain 39B
ENSMUSG00000024924 MGI:98935 Vldlr very low density lipoprotein receptor
Table S1. List of cholesterol metabolic genes from MGI database and their associated ensembl ID for user-provided gene set queries in the Regeneration Rosetta app.
2dpi- 4dpi- 7dpi- 12dpi- 2dpi- 4dpi- 7dpi- 12dpi- Zebrafish_g Zebrafish Ensembl ID Cluster 0dpi_qva 0dpi_qva 0dpi_qva 0dpi_qva 0dpi_LF 0dpi_LF 0dpi_LF 0dpi_LF ene symbol l l l l C C C C - - growth towards the 0.055674 0.928325 0.690320 0.473554 0.246228 0.028007 0.118288 ENSDART00000113093 midline gba 1.11E-05 455 691 273 928 233 284 896 - growth towards the 0.000166 0.430723 0.942817 0.699523 0.404585 0.130204 0.022544 0.113079 ENSDART00000148582 midline smpd1 524 334 089 141 024 031 887 466 - - growth towards the 0.001556 0.384822 0.914551 0.499923 0.729567 0.287798 0.063690 0.310097 ENSDART00000050399 midline npc2 765 365 548 782 353 394 935 689 - - growth towards the 0.009322 0.034493 0.905158 0.730001 0.315070 0.266918 0.034640 0.111553 ENSDART00000126978 midline acadl 914 954 839 037 362 423 916 388
growth towards the 0.058427 0.406017 0.994465 1.578129 0.684715 0.389649 0.031719 ENSDART00000124663 midline npc2 7.69E-08 541 406 692 482 762 636 264 - growth towards the 0.133882 0.458914 0.033282 0.710864 0.214033 0.130340 0.268396 0.115766 ENSDART00000167514 midline abca1a 254 664 403 259 988 273 538 571 - growth towards the 0.016923 0.016316 0.298424 0.979874 0.315023 0.311610 0.172590 0.026031 ENSDART00000023089 midline acadvl 89 201 368 802 187 409 27 8 - growth towards the 0.017944 0.011533 0.247377 0.845818 0.652859 0.675562 0.386488 0.183988 ENSDART00000103982 midline nfe2l1a 516 123 553 106 432 602 33 16
growth towards the NPC2 (1 of 0.001644 0.069931 0.990790 3.182180 2.136779 1.408480 0.095015 ENSDART00000002945 midline many) 4.68E-07 856 219 12 208 184 393 31 - growth towards the 0.001218 0.089741 0.655177 0.745138 0.962705 0.587027 0.239926 0.279230 ENSDART00000051556 midline abca1b 945 646 301 148 135 009 413 387 - growth towards the 0.000342 0.017176 0.099987 0.946538 0.446892 0.322223 0.244841 0.050194 ENSDART00000011863 midline hdlbpa 284 287 389 75 02 522 165 137
growth towards the 0.000856 0.762949 0.720319 0.625239 0.526452 ENSDART00000104616 midline lepr 2.96E-08 1.39E-07 1.05E-05 073 533 043 528 567
growth towards the 0.000959 1.173965 1.129708 0.920018 0.667267 ENSDART00000079173 midline lepr 5.12E-12 2.43E-11 1.74E-07 999 688 824 098 8
growth towards the 0.000724 4.559547 4.778234 4.366752 2.765663 ENSDART00000170572 midline lepa 6.60E-11 3.13E-12 3.73E-10 181 685 325 593 683
growth towards the 0.044142 0.006783 0.087130 0.336803 2.880332 3.535090 2.510243 2.078786 ENSDART00000132146 midline hsd17b7 616 76 748 167 402 877 514 507
growth towards the 0.025410 0.014154 0.262740 0.773370 0.465985 0.491501 0.281421 0.167335 ENSDART00000131019 midline acadvl 864 149 666 237 818 242 395 906 - - growth towards the 0.991120 0.028094 0.668275 0.988897 0.007306 0.381217 0.125471 0.024425 ENSDART00000148540 midline fech 974 033 11 802 354 581 62 403 - - - growth towards the si:ch211- 0.694031 0.782937 0.396603 0.049871 0.158550 0.117683 0.256320 0.510696 ENSDART00000165342 midline 93f2.1 347 688 565 554 393 559 731 237 - growth towards the 0.356612 0.003458 0.865218 0.721963 0.249947 0.551180 0.073389 0.183272 ENSDART00000166496 midline cat 354 029 019 852 463 864 354 25 - - - growth towards the 0.993779 0.970779 0.337822 0.013674 0.006114 0.023577 0.261635 0.555062 ENSDART00000173143 midline lrp1aa 498 906 232 414 382 911 578 861
midline crossing and 0.074429 0.000294 0.007243 0.674291 0.350368 0.588496 0.465895 0.178939 ENSDART00000172441 target selection lima1a 082 565 269 587 785 789 41 257
midline crossing and 0.199387 0.001411 0.007386 0.268361 0.688085 1.301360 1.138008 0.729999 ENSDART00000153227 target selection nfe2l1b 901 736 091 164 235 444 541 096 - midline crossing and 0.964439 0.001225 0.028894 0.878598 0.037650 0.839125 0.622258 0.165134 ENSDART00000148601 target selection insig1 289 581 275 548 91 818 944 159
midline crossing and 0.930089 0.279139 0.025426 0.904498 0.033270 0.191352 0.318689 0.072412 ENSDART00000056376 target selection tmem55ba 381 056 181 872 73 043 436 325
midline crossing and 0.059415 0.022855 0.005780 0.057643 2.392110 2.697063 3.119814 2.653468 ENSDART00000012247 target selection dhcr24 464 025 851 5 544 662 675 904 - - midline crossing and 0.365520 0.996650 0.048662 0.947964 0.273134 0.003097 0.452734 0.079225 ENSDART00000125019 target selection dhcr24 03 965 488 979 055 208 37 052
midline crossing and 0.764108 0.133189 0.000131 0.250779 0.717953 2.106714 1.525845 ENSDART00000163680 target selection hmgcs1 136 833 2.92E-09 252 539 967 123 318 - midline crossing and 0.937890 0.779964 0.000788 0.087843 0.061825 0.154559 0.893983 0.609306 ENSDART00000167613 target selection hmgcs1 417 462 936 59 835 892 325 628 - midline crossing and 0.018553 0.009655 0.821048 0.488876 0.314769 0.517151 0.148788 ENSDART00000113097 target selection hsd17b7 036 0.193448 684 076 774 091 777 215 - midline crossing and 0.993271 0.041801 0.094390 0.007030 0.441941 0.773565 0.436893 ENSDART00000092690 target selection srebf2 251 32 3.17E-05 79 288 306 631 785 - midline crossing and 0.990591 0.013899 0.170571 0.013482 0.739364 1.301376 0.568328 ENSDART00000151899 target selection ldlrb 906 649 7.32E-07 211 381 147 15 03
midline crossing and 0.910233 0.013059 0.001717 0.364812 0.177821 1.524901 1.830059 0.927790 ENSDART00000159316 target selection mvda 515 122 471 696 409 044 782 622
midline crossing and 0.384843 0.023273 0.018395 0.176504 1.591273 3.017393 3.100136 2.442907 ENSDART00000172241 target selection nsdhl 025 55 08 925 733 364 405 405
midline crossing and 0.397142 0.510664 1.875874 2.415595 1.866281 ENSDART00000110994 target selection sqlea 33 3.20E-07 9.24E-12 1.23E-06 466 264 993 513
midline crossing and 0.979247 0.023589 0.018772 0.850105 1.080881 0.554137 ENSDART00000062551 target selection cyp51 733 9.84E-06 5.63E-09 747 193 191 624 375 - midline crossing and 0.841975 0.036626 0.003204 0.345217 0.125607 0.619273 0.802648 0.437253 ENSDART00000065600 target selection sc5d 729 452 598 784 15 704 489 012
midline crossing and 0.881675 0.007445 0.000381 0.409104 0.105064 0.758038 0.952561 0.413786 ENSDART00000042162 target selection tm7sf2 472 135 185 478 5 931 873 8 - midline crossing and 0.986325 0.000831 0.001919 0.292356 0.034972 1.767545 1.673143 0.929274 ENSDART00000164585 target selection mvda 295 764 902 93 011 823 467 175 - midline crossing and 0.835503 0.008946 0.000357 0.608557 0.148803 0.843708 1.082868 0.366540 ENSDART00000013785 target selection insig1 343 432 987 059 263 665 772 247 midline crossing and 0.764048 0.028249 0.004200 0.715415 0.080932 0.304370 0.372374 0.127047 ENSDART00000143723 target selection idi1 984 076 79 577 725 095 682 939 - - - 0.498388 0.041236 0.649213 0.785459 0.129978 0.268802 0.097227 0.102143 ENSDART00000156995 brain reinnervation sorl1 186 995 893 062 292 979 509 372 - - 0.032429 0.253527 0.929493 0.988391 3.646800 2.308559 0.370802 0.243200 ENSDART00000168276 brain reinnervation scarb1 793 644 191 815 721 886 474 954 - - - 0.008047 0.010309 0.886937 0.832588 0.467410 0.450218 0.057865 0.125768 ENSDART00000166508 brain reinnervation fdft1 735 603 095 895 589 58 823 039 - - 0.002979 0.086540 0.641240 0.988391 0.417658 0.274360 0.114636 0.022214 ENSDART00000092665 brain reinnervation srebf1 303 633 969 815 309 919 817 824 - - 0.000159 0.006239 0.775755 0.277169 0.473539 0.363304 0.075744 0.226987 ENSDART00000125536 brain reinnervation appb 341 429 973 566 223 525 005 466 - - 0.172515 0.990728 0.020916 0.019457 0.282814 0.006298 0.401417 0.446278 ENSDART00000149553 brain reinnervation hmgcra 058 292 779 872 218 507 4 745 - 0.513462 0.883704 0.027647 0.027858 0.174557 0.058201 0.389886 0.431312 ENSDART00000097460 brain reinnervation hmgcra 124 521 1 225 714 434 63 576 - - - - downregulated during 0.047590 0.068454 0.586932 0.952347 0.446677 0.413500 0.183093 0.072200 ENSDART00000151246 regeneration- early gnb3b 012 739 58 61 088 571 758 588 - - - - downregulated during 0.014660 0.020052 0.006566 0.202181 0.742372 0.705345 0.793489 0.543448 ENSDART00000168089 regeneration- early cyp27a7 346 881 642 822 496 887 907 957 - - - - downregulated during si:dkey- 0.002244 0.017235 0.559735 0.547517 0.696070 0.446988 0.222080 ENSDART00000063703 regeneration- early 71h2.2 442 2.81E-05 395 938 928 326 451 286 - - - - downregulated during 0.000255 0.132055 0.461666 0.843899 0.618559 0.314869 0.194806 0.125519 ENSDART00000155397 regeneration- early soat2 322 603 394 86 497 95 138 338 - - - - downregulated during 0.001745 0.036362 0.000171 0.611271 0.360057 0.265096 0.439594 ENSDART00000012673 regeneration- early gnb3a 4.75E-09 536 031 819 729 677 652 606 - - - - downregulated during 0.017565 0.035207 0.548529 0.236825 0.359432 0.324487 0.138175 0.257634 ENSDART00000083359 regeneration- early sec14l8 987 725 037 006 343 355 947 1 - - - - downregulated during 0.152465 0.239900 0.002035 0.014580 0.248477 0.212122 0.427881 0.390078 ENSDART00000064376 regeneration- late sod1 986 86 646 321 917 084 094 569 - - - downregulated during 0.995047 0.987832 0.003415 0.049780 0.005358 0.010211 0.591626 0.490299 ENSDART00000008326 regeneration- late pon2 727 72 892 891 778 923 082 784 - - - - downregulated during 0.884739 0.268210 0.014771 0.080531 0.087554 0.343001 0.600108 0.533488 ENSDART00000058965 regeneration- late apoeb 777 448 435 125 29 804 968 23 - - - - downregulated during 0.001075 0.116786 0.292758 0.363769 0.208045 0.481848 0.192036 ENSDART00000127656 regeneration- late cln6b 392 127 3.48E-06 327 389 101 131 43 - - - - downregulated during 0.999179 0.435223 0.007394 0.862611 0.000462 0.183644 0.434826 0.105981 ENSDART00000131286 regeneration- late erlin2 255 795 961 454 383 452 094 059 - - - downregulated during 0.744548 0.958508 0.033766 0.848896 0.079210 0.018544 0.273202 0.083540 ENSDART00000109872 regeneration- late cln6a 765 113 616 483 86 414 82 486 - - - - downregulated during 0.498401 0.011858 0.029905 0.641189 0.205328 0.495702 0.443190 0.211013 ENSDART00000170790 regeneration- late thrb 525 621 089 377 436 017 893 858 - - - - downregulated during 0.324180 0.002664 0.004383 0.716261 0.193382 0.415286 0.400030 0.136855 ENSDART00000166313 regeneration- late thrb 982 973 897 895 381 369 228 946 - - - - downregulated during 0.973866 0.052104 0.010717 0.980915 0.019793 0.383158 0.468203 0.036502 ENSDART00000058093 regeneration- late ldlrap1b 391 373 03 101 679 495 159 488 - - - - downregulated during 0.915448 0.219287 0.009101 0.829465 0.036215 0.196356 0.337053 0.094153 ENSDART00000029774 regeneration- late tmem55bb 584 437 012 951 71 812 328 869 - - - - downregulated during 0.569323 0.133658 0.010230 0.849977 0.185553 0.343974 0.508555 0.134197 ENSDART00000005547 regeneration- late gnb3b 344 566 328 196 204 986 347 91 Table S2. List of differentially expressed transcripts during optic nerve regeneration in zebrafish using the MGI cholesterol metabolic gene queries in the Regeneration Rosetta app. The result table includes the zebrafish ensembl ID, DE genes based on an FDR adjusted p-value <0.05 compared to 0dpi control and log2 fold change for each regenerating timepoints 2, 4, 7, 12 dpi.
Brain Official Gene Symbol Lamprey Gene ID DNA Binding Domain
Tfap2b PMZ_0018996-RA AP-2
Ash1l PMZ_0005066-RA AT hook
AKNA PMZ_0011406-RA AT hook
ZBED1 PMZ_0016473-RA BED ZF
Sgsm2 PMZ_0017332-RA BED ZF
Mlxip PMZ_0011574-RA bHLH
NCOA3 PMZ_0005855-RA bHLH
ARNTL PMZ_0022526-RA bHLH
Mlxipl PMZ_0011572-RA bHLH
NEUROD1 PMZ_0005582-RA bHLH
TWIST1 PMZ_0008383-RA bHLH TWIST2 PMZ_0004583-RA bHLH
BHLHE40 PMZ_0015665-RA bHLH
ptf1a PMZ_0023241-RA bHLH
AHR PMZ_0009169-RA bHLH
CLOCK PMZ_0006274-RA bHLH
SCX PMZ_0011122-RA bHLH
Atf3 PMZ_0005968-RA bZIP
Jun PMZ_0015901-RA bZIP
CEBPA PMZ_0019312-RA bZIP
FOSL2 PMZ_0023077-RA bZIP
Crem PMZ_0012457-RA bZIP
fos PMZ_0001200-RA bZIP
mafb PMZ_0014543-RA bZIP
NFIL3 PMZ_0019135-RA bZIP
Nfe2 PMZ_0014947-RA bZIP
ZNF219 PMZ_0000147-RA C2H2 ZF
ZNF217 PMZ_0000126-RA C2H2 ZF
EEA1 PMZ_0012072-RA C2H2 ZF
Osr2 PMZ_0006091-RA C2H2 ZF
ZBTB42 PMZ_0017837-RA C2H2 ZF
ZNF704 PMZ_0017942-RA C2H2 ZF
KLF1 PMZ_0020730-RA C2H2 ZF
Klf7 PMZ_0008885-RA C2H2 ZF
PRDM8 PMZ_0005757-RA C2H2 ZF Sall3 PMZ_0012241-RA C2H2 ZF
ZNF22 PMZ_0011057-RA C2H2 ZF
ZNF676 PMZ_0019476-RA C2H2 ZF
ZNF841 PMZ_0002784-RA C2H2 ZF
KLF15 PMZ_0002919-RA C2H2 ZF
dzip1 PMZ_0013304-RA C2H2 ZF
ikzf5 PMZ_0001000-RA C2H2 ZF
PRDM5 PMZ_0005403-RA C2H2 ZF
REST PMZ_0007778-RA C2H2 ZF
Klf10 PMZ_0012571-RA C2H2 ZF
PEG3 PMZ_0002813-RA C2H2 ZF
Prdm1 PMZ_0020972-RA C2H2 ZF
ZNF135 PMZ_0019928-RA C2H2 ZF
Znf239 PMZ_0018206-RA C2H2 ZF
ZEB2 PMZ_0017801-RA C2H2 ZF; Homeodomain
TRERF1 PMZ_0003066-RA C2H2 ZF; Myb/SANT
Rbpjl PMZ_0019954-RA CSL
kdm2b PMZ_0005926-RA CxxC
KDM2A PMZ_0023537-RA CxxC
EHF PMZ_0011596-RA Ets
ETV7 PMZ_0019267-RA Ets
ETS1 PMZ_0023551-RA Ets
Foxb2 PMZ_0010602-RA Forkhead
FOXG1 PMZ_0000494-RA Forkhead FOXK1 PMZ_0012299-RA Forkhead
Foxk2 PMZ_0009477-RA Forkhead
FOXL2 PMZ_0010037-RA Forkhead
gata2 PMZ_0008156-RA GATA
GCM2 PMZ_0010350-RA GCM
SOX10 PMZ_0020526-RA HMG/Sox
Sry PMZ_0006678-RA HMG/Sox
otx2 PMZ_0000784-RA Homeodomain
Adnp PMZ_0015678-RA Homeodomain
DLX5 PMZ_0012874-RA Homeodomain
HOXB6 PMZ_0019528-RA Homeodomain
Hoxb8 PMZ_0019779-RA Homeodomain
hoxc9 PMZ_0002315-RA Homeodomain
Hoxd8 PMZ_0006066-RA Homeodomain
Hoxd9 PMZ_0001980-RA Homeodomain
IRX3 PMZ_0019709-RA Homeodomain
Lhx1 PMZ_0018111-RA Homeodomain
MKX PMZ_0013726-RA Homeodomain
PHOX2B PMZ_0023008-RA Homeodomain
SIX1 PMZ_0022507-RA Homeodomain
SIX3 PMZ_0017270-RA Homeodomain
SIX6 PMZ_0015477-RA Homeodomain
TPRX1 PMZ_0023099-RA Homeodomain
Dbx1 PMZ_0001656-RA Homeodomain Nkx6-1 PMZ_0024089-RA Homeodomain
Pou4f2 PMZ_0005302-RA Homeodomain; POU
POU6F2 PMZ_0004395-RA Homeodomain; POU
PIN1 PMZ_0005768-RA MBD
Mecp2 PMZ_0011998-RA MBD; AT hook
Nr1d1 PMZ_0012318-RA Nuclear receptor
ESR1 PMZ_0002173-RA Nuclear receptor
Hnf4a PMZ_0002236-RA Nuclear receptor
ppara PMZ_0011032-RA Nuclear receptor
RORC PMZ_0011373-RA Nuclear receptor
Nr1d2 PMZ_0018839-RA Nuclear receptor
PROX1 PMZ_0012095-RA Prospero
REL PMZ_0002455-RA Rel
Nfatc3 PMZ_0011590-RA Rel
RUNX1 PMZ_0019080-RA Runt
DEAF1 PMZ_0007366-RA SAND
NFIA PMZ_0005871-RA SMAD
tbx20 PMZ_0017953-RA T-box
Tbr1 PMZ_0005862-RA T-box
Dr1 PMZ_0012187-RA Unknown
LTF PMZ_0007403-RA Unknown
Son PMZ_0022239-RA Unknown Table S3. List of transcription factor encoding genes from brain cell bodies following spinal cord injury in lamprey over a course of 12 weeks (derived from Herman et al., 2018). This table includes the official gene symbol corresponding to lamprey gene ID for the transcription factors with known DNA binding domain for user-provided gene set queries in the Regeneration Rosetta app.
Spinal cord Official Gene Symbol Lamprey Gene ID DNA binding domain
Adnp PMZ_0015678-RA Homeodomain
ARNTL PMZ_0022526-RA bHLH
Ash1l PMZ_0005066-RA AT hook
ATF3 PMZ_0021004-RA bZIP
Bhlhe41 PMZ_0006661-RA bHLH
CEBPA PMZ_0019312-RA bZIP
Crem PMZ_0012457-RA bZIP
Deaf1 PMZ_0007365-RA SAND
DLX5 PMZ_0012874-RA Homeodomain
Dr1 PMZ_0004286-RA Unknown
EEA1 PMZ_0012072-RA C2H2 ZF
EHF PMZ_0011596-RA Ets
ESR1 PMZ_0002173-RA Nuclear receptor
ETV7 PMZ_0019267-RA Ets
FOS PMZ_0019104-RA bZIP
FOSL2 PMZ_0023077-RA bZIP Foxb2 PMZ_0010602-RA Forkhead
FOXG1 PMZ_0000494-RA Forkhead
Gcm2 PMZ_0003269-RA GCM
Hnf4a PMZ_0002236-RA Nuclear receptor
HOXB6 PMZ_0019528-RA Homeodomain
Hoxb8 PMZ_0019779-RA Homeodomain
hoxc9 PMZ_0002315-RA Homeodomain
Hoxd8 PMZ_0006066-RA Homeodomain
Hoxd9 PMZ_0001980-RA Homeodomain
IRX3 PMZ_0019709-RA Homeodomain
Jun PMZ_0015901-RA bZIP
kdm2b PMZ_0005926-RA CxxC
KLF1 PMZ_0020730-RA C2H2 ZF
Klf7 PMZ_0013729-RA C2H2 ZF
Lhx1 PMZ_0018111-RA Homeodomain
mafb PMZ_0014543-RA bZIP
max PMZ_0008167-RA bHLH
Mecp2 PMZ_0011998-RA MBD; AT hook
MKX PMZ_0013726-RA Homeodomain
Mlxip PMZ_0011574-RA bHLH
Mlxipl PMZ_0011572-RA bHLH
NCOA3 PMZ_0005855-RA bHLH
NEUROD1 PMZ_0005582-RA bHLH
NFIA PMZ_0005872-RA SMAD Nr1d1 PMZ_0012318-RA Nuclear receptor
Osr2 PMZ_0006091-RA C2H2 ZF
otx2 PMZ_0000784-RA Homeodomain
PHOX2B PMZ_0023008-RA Homeodomain
PIN1 PMZ_0005768-RA MBD
Pou4f2 PMZ_0005302-RA Homeodomain; POU
Pou6f2 PMZ_0004393-RA Homeodomain; POU
ppara PMZ_0011032-RA Nuclear receptor
PRDM8 PMZ_0005757-RA C2H2 ZF
PROX1 PMZ_0012095-RA Prospero
REL PMZ_0002455-RA Rel
RUNX1 PMZ_0019080-RA Runt
Sall3 PMZ_0012241-RA C2H2 ZF
SIX1 PMZ_0022507-RA Homeodomain
SIX3 PMZ_0017270-RA Homeodomain
SIX6 PMZ_0015477-RA Homeodomain
Tbr1 PMZ_0005862-RA T-box
tbx20 PMZ_0009881-RA T-box
Tfap2b PMZ_0018996-RA AP-2
TPRX1 PMZ_0023099-RA Homeodomain
TWIST1 PMZ_0003348-RA bHLH
TWIST2 PMZ_0004583-RA bHLH
ZBED1 PMZ_0016473-RA BED ZF
ZBTB42 PMZ_0017837-RA C2H2 ZF ZFAT PMZ_0006891-RA C2H2 ZF
ZNF217 PMZ_0000126-RA C2H2 ZF
ZNF219 PMZ_0000147-RA C2H2 ZF
ZNF22 PMZ_0011057-RA C2H2 ZF
Znf385b PMZ_0005569-RA C2H2 ZF
ZNF676 PMZ_0019476-RA C2H2 ZF
ZNF704 PMZ_0019042-RA C2H2 ZF
ZNF841 PMZ_0002784-RA C2H2 ZF
Table S4. List of transcription factor encoding genes from spinal cell bodies following spinal cord injury in lamprey over a course of 12 weeks (derived from Herman et al., 2018). This table includes the official gene symbol corresponding to lamprey gene ID for the transcription factors with known DNA binding domain for user-provided gene set queries in the Regeneration Rosetta app.