Supplementary table 1. Significantly modulated genes by C1q in rat immature primary cortical neurons

GenBank Accession number mRNA_assignment Log2 fold-change C1q p-value over untreated

ENSRNOT00000040062 cdna:known chromosome:RGSC3.4:X:145746425:145862162:-1 3.2 6.29E-05 ENSRNOT00000004262 cdna:novel chromosome:RGSC3.4:X:123283542:123284430:1 3.01 1.73E-04 gene:ENSRNOG00000003194 NM_031124 syntaxin 3 (Stx3), mRNA. 3.01 1.19E-04 ENSRNOT00000053082 ncrna:snoRNA chromosome:RGSC3.4:11:45561199:45561336:1 2.84 1.28E-06 gene:ENSRNOG00000034959

ENSRNOT00000036156 similar to golgi-specific brefeldin A-resistance factor 1 2.81 2.39E-04 gene:ENSRNOG00000026048 ENSRNOT00000040039 similar to nucleoporin 62 gene:ENSRNOG00000030223 2.8 1.63E-04 ENSRNOT00000060755 similar to Glucosamine 6-phosphate N-acetyltransferase 2.78 2.52E-04 gene:ENSRNOG00000039626 ENSRNOT00000053003 ncrna:snRNA chromosome:RGSC3.4:12:21759559:21759663:-1 2.71 3.68E-05 gene:ENSRNOG00000034880 NM_053645 interleukin 5 receptor, alpha (Il5ra), mRNA. 2.66 2.62E-04 NM_001033896 transmembrane protein 79 (Tmem79), mRNA. 2.59 2.67E-04 NM_001009506 vomeronasal V1r-type receptor V1rf1 (V1rf1), mRNA. 2.59 2.14E-06 NM_022695.1 neurotensin receptor 2 (Ntsr2), mRNA 2.58 8.21E-06 GENSCAN00000065878 cdna:Genscan chromosome:RGSC3.4:10:108608582:108608884:-1 2.53 2.39E-04

NM_001024333 cell death-inducing DFFA-like effector c (Cidec), mRNA. 2.52 1.53E-04 ENSRNOT00000033017 cdna:novel chromosome:RGSC3.4:15:26865443:26869448:-1 2.48 3.15E-04 gene:ENSRNOG00000025868 ENSRNOT00000017834 similar to stearoyl-CoA desaturase 4 gene:ENSRNOG00000032554 2.48 8.12E-05

BC091230 neuropathy target esterase like 1, mRNA (cDNA clone MGC:108975 2.46 2.02E-04 IMAGE:7321805), complete cds. NM_001107620 ubiquitin associated and SH3 domain containing, A (predicted) 2.44 1.97E-04 (Ubash3a_predicted), mRNA. NM_001108814 Norrie disease homolog (Ndph), mRNA. 2.44 2.38E-04 NM_001025415 cholesterol 25-hydroxylase (Ch25h), mRNA. 2.43 4.90E-06 NM_022605 heparanase (Hpse), mRNA. 2.42 1.86E-04 ENSRNOT00000022475 cdna:novel chromosome:RGSC3.4:17:93278206:93348360:1 2.42 3.05E-04 gene:ENSRNOG00000016716 ENSRNOT00000020036 similar to emopamil binding related protein, delta8-delta7 sterol isomerase 2.39 1.84E-04 related protein gene:ENSRNOG00000014659 NM_013028 short stature homeobox 2 (Shox2), mRNA. 2.39 3.22E-05 ENSRNOT00000030167 cdna:novel chromosome:RGSC3.4:18:77151106:77151432:-1 2.37 2.17E-04 gene:ENSRNOG00000026317 ENSRNOT00000034522 cdna:novel chromosome:RGSC3.4:3:134559161:134597603:1 2.37 1.89E-04 gene:ENSRNOG00000026377 NM_001024351 apolipoprotein F (Apof), mRNA. 2.35 2.45E-04 NM_001108195 kelch repeat and BTB (POZ) domain containing 5 (predicted) 2.35 6.00E-05 (Kbtbd5_predicted), mRNA. rno-mir-28 MI0000861 miR-28 stem-loop 2.33 8.44E-05 NM_022396 guanine nucleotide binding protein (G protein), gamma 11 (Gng11), 2.33 1.71E-04 mRNA. ENSRNOT00000060447 cdna:novel chromosome:RGSC3.4:4:55012417:55014352:1 2.33 2.52E-04 gene:ENSRNOG00000039446 ENSRNOT00000059794 cdna:novel chromosome:RGSC3.4:16:26444081:26444302:1 2.3 6.97E-05 gene:ENSRNOG00000039096 NM_001035252 myosin, light polypeptide 2, regulatory, cardiac, slow (Myl2), mRNA. 2.25 1.14E-05

ENSRNOT00000030658 hypothetical protein gene:ENSRNOG00000025796 2.25 9.32E-06 XM_001081377 PREDICTED: hypothetical protein LOC692042 (LOC692042), mRNA. 2.24 1.90E-04

ENSRNOT00000037540 cdna:pseudogene chromosome:RGSC3.4:1:58871274:58872523:1 2.24 1.90E-04 gene:ENSRNOG00000030444

ENSRNOT00000037540 cdna:pseudogene chromosome:RGSC3.4:1:58871274:58872523:1 2.24 1.90E-04 gene:ENSRNOG00000030444

GENSCAN00000085492 cdna:Genscan chromosome:RGSC3.4:13:15794551:15801465:-1 2.24 1.90E-04

ENSRNOT00000041594 cdna:novel chromosome:RGSC3.4:4:43462118:43462585:-1 2.23 7.46E-05 gene:ENSRNOG00000030995 ENSRNOT00000022700 similar to transcription elongation regulator 1-like 2.22 2.47E-04 gene:ENSRNOG00000016737 NM_173312 glucosaminyl (N-acetyl) transferase 3, mucin type (Gcnt3), mRNA. 2.2 2.37E-04

ENSRNOT00000055308 cdna:pseudogene chromosome:RGSC3.4:3:145941387:145941635:-1 2.2 1.16E-04 gene:ENSRNOG00000036853

ENSRNOT00000010441 similar to Homeobox protein Hox-A13 gene:ENSRNOG00000007928 2.16 2.46E-04

BC083694 small nuclear ribonucleoprotein polypeptides B and B1, mRNA (cDNA 2.15 5.30E-05 clone IMAGE:7189534), complete cds. NM_001107253 potassium channel tetramerisation domain containing 6 (predicted) 2.14 2.83E-04 (Kctd6_predicted), mRNA. XM_001058175 PREDICTED: similar to N-formylpeptide receptor-like 2 (predicted) 2.13 1.13E-04 (RGD1566044_predicted), mRNA. NM_001001970 lymphocyte antigen 6 complex, locus G6D (Ly6g6d), mRNA. 2.09 2.81E-04 ENSRNOT00000025290 cdna:novel chromosome:RGSC3.4:1:201626472:201631260:-1 2.08 1.08E-04 gene:ENSRNOG00000018710 GENSCAN00000082163 cdna:Genscan chromosome:RGSC3.4:3:116835858:116876799:1 2.05 1.59E-04

ENSRNOT00000001147 cdna:pseudogene chromosome:RGSC3.4:X:143394456:143394930:-1 2.05 1.32E-04 gene:ENSRNOG00000000859

ENSRNOT00000043247 cdna:novel chromosome:RGSC3.4:4:70606277:70606676:1 1.99 8.89E-06 gene:ENSRNOG00000031483 NM_013062.1 kinase insert domain protein receptor (Kdr), mRNA 1.98 1.63E-04 NM_022524 sushi-repeat-containing protein (Srpx), mRNA. 1.95 1.34E-05 ENSRNOT00000034886 similar to glycerophosphodiester phosphodiesterase domain containing 4 1.94 2.37E-05 gene:ENSRNOG00000028470 ENSRNOT00000015349 cdna:novel chromosome:RGSC3.4:9:64828542:64830614:-1 1.94 2.50E-04 gene:ENSRNOG00000023290 NM_021696 serine (or cysteine) peptidase inhibitor, clade B, member 2 (Serpinb2), 1.93 1.32E-04 mRNA. ENSRNOT00000030332 hypothetical protein gene:ENSRNOG00000039141 1.93 7.07E-05 ENSRNOT00000045110 Ott protein (Fragment) gene:ENSRNOG00000000620 1.92 1.08E-04 NM_058213.1 ATPase, Ca++ transporting, cardiac muscle, fast twitch 1 (Atp2a1), 1.92 2.96E-04 mRNA ENSRNOT00000015113 similar to integrin alpha 9 gene:ENSRNOG00000029910 1.91 2.57E-04 GENSCAN00000046588 cdna:Genscan chromosome:RGSC3.4:11:81011385:81012192:1 1.9 1.69E-04 NM_001108945 tripartite motif-containing 59 (predicted) (Trim59_predicted), mRNA. 1.84 4.98E-05

NM_001013245 tubulin cofactor a (Tbca), mRNA. 1.78 1.72E-04 ENSRNOT00000029821 cdna:novel chromosome:RGSC3.4:9:59947827:60108665:-1 1.77 1.46E-04 gene:ENSRNOG00000024469 NM_031689.1 crystallin, beta A4 (Cryba4), mRNA 1.74 1.61E-04 ENSRNOT00000050013 similar to DnaJ (Hsp40) homolog, subfamily C, member 14 1.7 2.43E-04 gene:ENSRNOG00000030239 NM_001014162 similar to Aa2-174 (RGD1309578), mRNA. 1.69 1.64E-04 NM_053395 small muscle protein, X-linked (Smpx), mRNA. 1.68 9.07E-06 ENSRNOT00000016604 cdna:novel chromosome:RGSC3.4:13:31047506:31049268:-1 1.67 2.36E-05 gene:ENSRNOG00000012435 ENSRNOT00000049035 cdna:novel chromosome:RGSC3.4:16:72976875:73321943:1 1.65 3.03E-04 gene:ENSRNOG00000032766 ENSRNOT00000059884 similar to developmental pluripotency-associated 2 1.64 3.06E-04 gene:ENSRNOG00000039144 NM_013154.2 CCAAT/enhancer binding protein (C/EBP), delta (Cebpd), mRNA 1.63 1.11E-04

GENSCAN00000077289 cdna:Genscan chromosome:RGSC3.4:X:156998380:157005636:1 1.61 2.98E-04

ENSRNOT00000061944 similar to chromobox homolog 3 gene:ENSRNOG00000029143 1.56 1.59E-04

XM_001081771 PREDICTED: similar to chromosome 17 open reading frame 27 1.54 3.65E-05 (LOC688296), mRNA. ENSRNOT00000027344 similar to Interferon-inducible protein gene:ENSRNOG00000020164 1.54 5.73E-06

ENSRNOT00000041731 similar to testis expressed gene 11 gene:ENSRNOG00000025672 1.54 3.22E-05

NM_176856 septin 9 (Sept9), transcript variant 2, mRNA. 1.53 1.30E-04 ENSRNOT00000058671 cdna:pseudogene chromosome:RGSC3.4:14:73007051:73007402:1 1.52 3.54E-05 gene:ENSRNOG00000038494

ENSRNOT00000060121 similar to G protein-coupled receptor 31, D17Leh66c region 1.5 2.95E-04 gene:ENSRNOG00000039255 ENSRNOT00000001922 18 kDa protein gene:ENSRNOG00000001418 1.5 2.97E-04 NM_001106007 phosphoglucomutase 2 (Pgm2), mRNA. 1.47 1.92E-04 ENSRNOT00000041051 hypothetical protein gene:ENSRNOG00000026588 1.46 6.27E-05 NM_021576 5' nucleotidase, ecto (Nt5e), mRNA. 1.44 2.82E-04 NM_001009527 vomeronasal V1r-type receptor V1rc42 (V1rc42), mRNA. 1.44 2.08E-04 XM_001067609 PREDICTED: similar to interleukin 23 receptor (LOC683816), mRNA. 1.42 1.84E-04

NM_001109126 similar to RIKEN cDNA 1700065I17 (predicted) 1.38 1.52E-05 (RGD1561039_predicted), mRNA. NM_001107829 fibrinogen C domain containing 1 (predicted) (Fibcd1_predicted), mRNA. 1.38 2.97E-04

NM_001099486 similar to vomeronasal 2, receptor, 1 (LOC689670), mRNA. 1.37 1.29E-04 NM_001099477 similar to putative pheromone receptor (predicted) 1.37 1.29E-04 (RGD1562647_predicted), mRNA. NM_001099486 similar to vomeronasal 2, receptor, 1 (LOC689670), mRNA. 1.37 1.29E-04 NM_001099517 similar to vomeronasal 2, receptor, 1 (LOC689072), mRNA. 1.37 1.29E-04 NM_001099477 similar to putative pheromone receptor (predicted) 1.37 1.29E-04 (RGD1562647_predicted), mRNA. NM_001099517 similar to vomeronasal 2, receptor, 1 (LOC689072), mRNA. 1.37 1.29E-04 NM_001008821 keratin 40 (Krt40), mRNA. 1.37 1.30E-04 ENSRNOT00000060751 cdna:known chromosome:RGSC3.4:16:12063956:12065311:1 1.35 5.08E-05 gene:ENSRNOG00000039624 ENSRNOT00000028442 similar to U2(RNU2) small nuclear RNA auxiliary factor 1-like 4 1.35 1.83E-04 gene:ENSRNOG00000020957 NM_001012217 slingshot homolog 3 (Drosophila) (Ssh3), mRNA. 1.32 2.47E-04 GENSCAN00000042355 cdna:Genscan chromosome:RGSC3.4:8:41109476:41109833:1 1.32 1.48E-04 ENSRNOT00000042447 similar to CD200 cell surface glycoprotein receptor 1.31 2.86E-04 gene:ENSRNOG00000002046 NM_022606 integrin-linked kinase-associated serine/threonine phosphatase 2C (Ilkap), 1.31 2.93E-05 mRNA. ENSRNOT00000055046 cdna:pseudogene chromosome:RGSC3.4:10:103097578:103097891:1 1.31 1.10E-04 gene:ENSRNOG00000036731

ENSRNOT00000054295 ncrna:snRNA chromosome:RGSC3.4:8:50054490:50054596:-1 1.3 1.96E-04 gene:ENSRNOG00000036172 ENSRNOT00000014449 cdna:known chromosome:RGSC3.4:8:84809074:84817572:1 1.3 2.08E-04 gene:ENSRNOG00000010657 ENSRNOT00000008854 similar to methyl-CpG binding domain protein 6 1.28 2.90E-04 gene:ENSRNOG00000006209 NM_001002288 MAS-related GPR, member E (Mrgpre), mRNA. 1.28 2.48E-04 NM_001024234 WSC domain containing 1 (Wscd1), mRNA. 1.27 3.90E-05 NM_133527 folate receptor 1 (adult) (Folr1), mRNA. 1.26 1.80E-04 NM_212508 nurim (nuclear envelope membrane protein) (Nrm), mRNA. 1.26 3.42E-05 ENSRNOT00000013501 similar to polymerase (RNA) III (DNA directed) polypeptide A, 155kDa 1.23 3.13E-05 gene:ENSRNOG00000010008 ENSRNOT00000030458 similar to essential meiotic endonuclease 1 homolog 2 1.22 1.21E-04 gene:ENSRNOG00000024867 NM_001013954 Leber congenital amaurosis 5 (human) (Lca5), mRNA. 1.2 3.13E-04 NM_130408 cytochrome P450, family 26, subfamily A, polypeptide 1 (Cyp26a1), 1.19 2.78E-04 mRNA. ENSRNOT00000059628 similar to Agouti-related protein precursor gene:ENSRNOG00000039001 1.19 2.03E-04

ENSRNOT00000005369 similar to Protein C14orf102 homolog gene:ENSRNOG00000004004 1.19 3.13E-04

XR_005624 PREDICTED: similar to Glyceraldehyde-3-phosphate dehydrogenase 1.18 1.52E-04 (GAPDH) (LOC503131), mRNA. NM_001014199.1 ATPase, H+ transporting, V1 subunit C, isoform 2 (Atp6v1c2), mRNA 1.18 1.34E-04

NM_001047958 LRRGT00162 (LOC500594), mRNA. 1.16 2.20E-04 NM_001106484 fidgetin (predicted) (Fign_predicted), mRNA. 1.14 2.85E-04 NM_001107904 trimethylguanosine synthase homolog (S. cerevisiae) (Tgs1), mRNA. 1.13 2.52E-04

NM_001108495 RELT tumor necrosis factor receptor (Relt), mRNA. 1.08 1.89E-04 NM_017316 solute carrier family 23 (nucleobase transporters), member 2 (Slc23a2), 1.06 2.31E-04 mRNA. NM_001008848 RT1 class II, locus Ha (RT1-Ha), mRNA. 1.01 1.44E-04 NM_001108061 amnionless (predicted) (Amn_predicted), mRNA. 1.01 4.60E-05 ENSRNOT00000056715 cdna:pseudogene chromosome:RGSC3.4:7:104532167:104532459:-1 1 2.40E-04 gene:ENSRNOG00000037469

NM_178091 insulin induced gene 2 (Insig2), mRNA. 1 2.15E-04 ENSRNOT00000028733 cdna:pseudogene chromosome:RGSC3.4:2:190479652:190479907:1 1 1.57E-04 gene:ENSRNOG00000021159

ENSRNOT00000047563 similar to alpha 3 type VI collagen isoform 1 precursor -1.02 2.81E-04 NM_001013252 signal recognition particle receptor, B subunit (Srprb), mRNA. -1.03 1.55E-04 ENSRNOT00000031496 similar to zinc finger protein 488 gene:ENSRNOG00000024597 -1.04 2.18E-04 ENSRNOT00000027298 cdna:novel chromosome:RGSC3.4:16:44701347:44792412:1 -1.07 2.32E-04 gene:ENSRNOG00000020128 BC079269 similar to RIKEN cDNA 4933417A18, mRNA (cDNA clone MGC:94380 -1.09 2.11E-04 IMAGE:7133712), complete cds. NM_172073 trophoblast specific protein alpha (Tpbpa), mRNA. -1.11 2.70E-04 ENSRNOT00000061605 cdna:novel chromosome:RGSC3.4:11:28817802:28818008:-1 -1.12 2.17E-04 gene:ENSRNOG00000040063 ENSRNOT00000004559 similar to coagulation factor IX gene:ENSRNOG00000003430 -1.12 7.21E-05 ENSRNOT00000043603 similar to large subunit ribosomal protein L36a -1.16 7.35E-05 gene:ENSRNOG00000032062 NM_001030034 rhomboid family 1 (Drosophila) (Rhbdf1), mRNA. -1.16 1.02E-05 ENSRNOT00000036132 28 kDa protein gene:ENSRNOG00000026039 -1.19 1.98E-04 NM_001109618 transmembrane 4 L six family member 20 (Tm4sf20), mRNA. -1.2 1.80E-04 NM_001011916 REC8 homolog (yeast) (Rec8), mRNA. -1.23 2.95E-04 NM_030851 bradykinin receptor, beta 1 (Bdkrb1), mRNA. -1.24 1.38E-04 NM_001109257 kelch domain containing 5 (Klhdc5), mRNA. -1.25 1.55E-04 NM_001001504 general transcription factor II I repeat domain-containing 1 (Gtf2ird1), -1.26 7.43E-05 mRNA. ENSRNOT00000052280 cdna:known chromosome:RGSC3.4:6:11747486:11747857:-1 -1.26 1.79E-04 gene:ENSRNOG00000031564 NM_053356 collagen, type I, alpha 2 (Col1a2), mRNA. -1.27 2.98E-04 ENSRNOT00000059229 cdna:novel chromosome:RGSC3.4:2:98170167:98174341:1 -1.28 1.51E-04 gene:ENSRNOG00000038768 ENSRNOT00000022799 cdna:known chromosome:RGSC3.4:5:166836753:166861368:-1 -1.29 4.07E-05 gene:ENSRNOG00000016949 NM_057206 pancreatic lipase-related protein 2 (Pnliprp2), mRNA. -1.3 2.53E-04 XM_226468 PREDICTED: hydrocephalus-inducing protein (LOC292017), mRNA. -1.33 1.78E-05

NM_001107648 pentatricopeptide repeat domain 2 (predicted) (Ptcd2_predicted), mRNA. -1.34 2.02E-06

NM_031058 mutS homolog 2 (E. coli) (Msh2), mRNA. -1.35 2.73E-04 NM_001025144 protein arginine N-methyltransferase 2 (Prmt2), mRNA. -1.39 2.46E-04 ENSRNOT00000034891 cdna:pseudogene chromosome:RGSC3.4:5:151555174:151555714:1 -1.4 1.15E-04 gene:ENSRNOG00000026561

NM_001113366 connector enhancer of kinase suppressor of Ras 2 (Cnksr2), transcript -1.41 8.94E-05 variant 1, mRNA. NM_173292 killer cell lectin-like receptor subfamily B member 1B (Klrb1b), mRNA. -1.41 1.72E-04

NM_001039588.1 autogenous vein graft remodeling associated protein 1 (Avgr1), mRNA -1.41 1.38E-05

ENSRNOT00000057956 similar to Protein diaphanous homolog 3 gene:ENSRNOG00000008986 -1.41 6.12E-05

NM_138825 serine (or cysteine) peptidase inhibitor, clade A (alpha-1 antiproteinase, -1.43 2.14E-04 antitrypsin), member 12 (Serpina12), mRNA. ENSRNOT00000019955 cdna:known chromosome:RGSC3.4:15:32933274:32935243:-1 -1.43 3.20E-05 gene:ENSRNOG00000014810 NM_001107330 Iroquois related homeobox 4 (Drosophila) (predicted) (Irx4_predicted), -1.44 1.63E-04 mRNA. NM_001106573 crystallin, gamma N (predicted) (Crygn_predicted), mRNA. -1.44 2.51E-04 ENSRNOT00000015469 similar to CG7332-PA gene:ENSRNOG00000011530 -1.45 3.05E-04 ENSRNOT00000061772 similar to Greb1 protein gene:ENSRNOG00000040149 -1.45 1.56E-04 NM_001105786 B9 protein domain 1 (B9d1), mRNA. -1.46 1.48E-04 NM_138522 chemokine (C-X-C motif) ligand 3 (Cxcl3), mRNA. -1.46 1.60E-04 NM_181638 T-box 3 (Tbx3), mRNA. -1.47 1.86E-04 ENSRNOT00000052766 ncrna:misc_RNA chromosome:RGSC3.4:2:202402878:202402973:1 -1.48 2.23E-04 gene:ENSRNOG00000034643

NM_001126082 anaphase promoting complex subunit 11 homolog (yeast) (Anapc11), -1.51 7.73E-05 mRNA. NM_001005382 kallikrein 1 (Klk1), mRNA. -1.52 2.33E-04 NM_023987 baculoviral IAP repeat-containing 3 (Birc3), mRNA. -1.52 2.28E-04 BC082003 hypothetical protein LOC499980, mRNA (cDNA clone MGC:94246 -1.52 1.51E-04 IMAGE:7131395), complete cds. NM_001107349 similar to D0H6S2654E protein (predicted) (RGD1563458_predicted), -1.53 2.97E-04 mRNA. NM_001039377 arachidonate 12-lipoxygenase, 12R type (Alox12b), mRNA. -1.53 2.69E-04 BC086566 similar to testes development-related NYD-SP18, mRNA (cDNA clone -1.55 1.64E-04 MGC:105845 IMAGE:7112589), complete cds. ENSRNOT00000021140 similar to mitochondrial methionyl-tRNA synthetase -1.55 1.99E-04 gene:ENSRNOG00000015648 ENSRNOT00000061266 cdna:novel chromosome:RGSC3.4:X:12297176:12297507:1 -1.55 6.90E-05 gene:ENSRNOG00000039889 XR_009543 PREDICTED: similar to L-lactate dehydrogenase A chain (LDH-A) (LDH -1.56 7.43E-05 muscle subunit) (LDH-M) (LOC502349), mRNA.

NM_001037220 KIAA0415 protein (Kiaa0415), mRNA. -1.57 2.10E-05 ENSRNOT00000048958 cdna:novel chromosome:RGSC3.4:2:41934583:41935379:-1 -1.57 7.58E-05 gene:ENSRNOG00000029084 ENSRNOT00000021300 similar to bone specific CMF608 gene:ENSRNOG00000015887 -1.58 1.07E-04

NM_181082 sperm protein 3111 (Sp3111), mRNA. -1.59 4.85E-05 NM_181091 glia maturation factor, gamma (Gmfg), mRNA. -1.6 2.29E-05 NM_001108548 ribosomal protein L22 like 1 (predicted) (Rpl22l1_predicted), mRNA. -1.61 3.17E-05

NM_012488 alpha-2-macroglobulin (A2m), mRNA. -1.61 1.94E-04 ENSRNOT00000053142 ncrna:snRNA chromosome:RGSC3.4:8:63482866:63482976:1 -1.61 2.77E-04 gene:ENSRNOG00000035019 NM_001105752 processing of precursor 5, ribonuclease P/MRP family (S. cerevisiae) -1.62 2.01E-04 (predicted) (Pop5_predicted), mRNA. ENSRNOT00000061666 similar to CG14483-PA gene:ENSRNOG00000040092 -1.62 2.98E-04 NM_001106046 ADAM-like, decysin 1 (predicted) (Adamdec1_predicted), mRNA. -1.63 2.42E-05

NM_053525 DEAD (Asp-Glu-Ala-Asp) box polypeptide 52 (Ddx52), mRNA. -1.66 2.37E-04

XR_008624 PREDICTED: similar to hypothetical protein FLJ37396 (predicted) -1.66 1.39E-04 (RGD1561147_predicted), mRNA. NM_001106625 endoplasmic reticulum protein 27 (Erp27), mRNA. -1.66 1.93E-04 NM_001025280 solute carrier family 10 (sodium/bile acid cotransporter family), member 5 -1.67 1.72E-04 (Slc10a5), mRNA. ENSRNOT00000052682 ncrna:snRNA chromosome:RGSC3.4:1:250001661:250001767:1 -1.67 1.23E-04 gene:ENSRNOG00000034559

ENSRNOT00000020162 similar to testis expressed gene 13 gene:ENSRNOG00000015032 -1.68 2.85E-04

ENSRNOT00000018476 Sodium/myo-inositol cotransporter 2 gene:ENSRNOG00000013407 -1.68 2.43E-04

NM_001109341 similar to divalent cation tolerant protein CUTA (predicted) -1.69 2.75E-04 (RGD1564854_predicted), mRNA. XR_007777 PREDICTED: similar to glyceraldehyde-3-phosphate dehydrogenase -1.7 1.82E-04 (phosphorylating) (EC 1.2.1.12) (predicted) (RGD1564390_predicted), mRNA. NM_203470 MAS-related GPR, member G (Mrgprg), mRNA. -1.7 1.47E-04 BC097383 similar to GLI-Kruppel family member GLI4, mRNA (cDNA clone -1.7 1.67E-04 MGC:114422 IMAGE:7446306), complete cds. ENSRNOT00000053114 ncrna:snoRNA chromosome:RGSC3.4:10:48948092:48948225:1 -1.7 1.29E-04 gene:ENSRNOG00000034991

ENSRNOT00000010296 similar to ring finger protein 43 gene:ENSRNOG00000007606 -1.7 2.80E-05 NM_001013043 secreted and transmembrane 1A (Sectm1a), mRNA. -1.7 2.09E-04 ENSRNOT00000050210 hypothetical protein gene:ENSRNOG00000039483 -1.71 2.89E-04 NM_012528 cholinergic receptor, nicotinic, beta polypeptide 1 (muscle) (Chrnb1), -1.71 2.07E-04 mRNA. NM_012767 gonadotropin-releasing hormone 1 (Gnrh1), mRNA. -1.71 7.98E-05 NM_134379 integral membrane transport protein UST4r (UST4r), mRNA. -1.71 1.28E-04 ENSRNOT00000016684 cdna:novel chromosome:RGSC3.4:4:68287242:68296614:1 -1.72 2.30E-04 gene:ENSRNOG00000038989 NM_001106027 oncoprotein induced transcript 1 (Oit1), mRNA. -1.72 2.51E-04 ENSRNOT00000060734 cdna:novel chromosome:RGSC3.4:5:58064285:58270061:1 -1.73 2.44E-04 gene:ENSRNOG00000039613 NM_001007150.1 staufen, RNA binding protein, homolog 2 (Drosophila) (Stau2), transcript -1.73 5.52E-05 variant SS, mRNA NM_001001519 lipocalin 6 (Lcn6), mRNA. -1.73 1.10E-04 NM_019231 mitogen activated protein kinase 13 (Mapk13), mRNA. -1.74 4.55E-05 ENSRNOT00000058540 cdna:novel chromosome:RGSC3.4:6:101107988:101108050:1 -1.74 1.52E-04 gene:ENSRNOG00000038431 ENSRNOT00000055436 cdna:known chromosome:RGSC3.4:4:186842411:186843542:1 -1.75 2.47E-04 gene:ENSRNOG00000036912

ENSRNOT00000011467 similar to ATP/GTP binding protein-like 2 gene:ENSRNOG00000008467 -1.75 8.89E-06

NM_012940 cytochrome P450, family 1, subfamily b, polypeptide 1 (Cyp1b1), mRNA. -1.76 2.89E-04

NM_173321.1 hemiferrin, transferrin-like protein (LOC286987), mRNA -1.77 2.56E-04 ENSRNOT00000049083 similar to Protein CXorf48 gene:ENSRNOG00000027952 -1.77 1.59E-04 ENSRNOT00000049083 similar to Protein CXorf48 gene:ENSRNOG00000027952 -1.77 1.59E-04 NM_020656 parvin, alpha (Parva), mRNA. -1.77 1.72E-05 ENSRNOT00000018526 similar to Meiotic recombination protein DMC1/LIM15 homolog -1.78 1.81E-04 gene:ENSRNOG00000013807 NM_001108740 cytoskeleton-associated protein 4 (predicted) (Ckap4_predicted), mRNA. -1.78 1.79E-04

ENSRNOT00000016662 cdna:known chromosome:RGSC3.4:1:62539390:62540310:-1 -1.79 1.07E-04 gene:ENSRNOG00000012492 NM_001009962 meteorin, glial cell differentiation regulator (Metrn), mRNA. -1.79 2.09E-04 NM_001106061 Rho guanine nucleotide exchange factor (GEF) 3 (predicted) -1.8 1.99E-04 (Arhgef3_predicted), mRNA. NM_001105745 POU domain, class 2, transcription factor 3 (Pou2f3), mRNA. -1.8 1.14E-04 NM_133522 somatostatin receptor 3 (Sstr3), mRNA. -1.81 1.92E-04 XR_008014 PREDICTED: similar to 60S ribosomal protein L21 (LOC364597), -1.82 2.83E-04 mRNA. NM_001108553 transmembrane protein 154 (Tmem154), mRNA. -1.82 7.55E-05 ENSRNOT00000035580 hypothetical protein gene:ENSRNOG00000023352 -1.83 3.09E-04 ENSRNOT00000060360 hypothetical protein gene:ENSRNOG00000039386 -1.84 3.11E-06 ENSRNOT00000060358 13 kDa protein gene:ENSRNOG00000039386 -1.84 3.11E-06 NM_019199.1 fibroblast growth factor 18 (Fgf18), mRNA -1.86 2.80E-04 NM_134393 polyamine modulated factor 1 binding protein 1 (Pmfbp1), mRNA. -1.86 9.90E-05

NM_001012176 radial spoke head 1 homolog (Chlamydomonas) (Rsph1), mRNA. -1.88 5.48E-05 NM_001106375 3'-phosphoadenosine 5'-phosphosulfate synthase 2 (predicted) -1.88 3.47E-05 (Papss2_predicted), mRNA. NM_001105882 transmembrane serine protease 7 (predicted) (Tmprss7_predicted), -1.88 2.02E-04 mRNA. NM_001006962 TERF1 (TRF1)-interacting nuclear factor 2 (Tinf2), mRNA. -1.88 1.77E-04 NM_001037359 G protein-coupled receptor 35 (Gpr35), mRNA. -1.89 2.55E-04 ENSRNOT00000032278 406 kDa protein gene:ENSRNOG00000023803 -1.89 2.74E-05 ENSRNOT00000058373 similar to M phase phosphoprotein 6 gene:ENSRNOG00000038335 -1.9 1.46E-04

XR_008494 PREDICTED: similar to sorbitol dehydrogenase (LOC363732), mRNA. -1.9 3.60E-05

XM_001064593 PREDICTED: similar to Contactin associated protein-like 3 precursor -1.9 1.09E-04 (Cell recognition molecule Caspr3) (predicted) (RGD1563615_predicted), mRNA. XM_001063911 PREDICTED: similar to RIKEN cDNA B430306N03 gene (predicted) -1.9 2.04E-04 (RGD1311406_predicted), mRNA. XR_007811 PREDICTED: similar to SWI/SNF-related matrix-associated actin- -1.9 1.19E-04 dependent regulator of chromatin e1 (LOC500467), mRNA.

ENSRNOT00000047751 similar to keratin Kb40 gene:ENSRNOG00000024909 -1.91 4.05E-05 NM_057209 myosin light chain kinase 2, skeletal muscle (Mylk2), mRNA. -1.92 1.62E-04 NM_001108088 epiphycan (Epyc), mRNA. -1.93 4.70E-05 ENSRNOT00000022369 similar to Protein C6orf146 homolg gene:ENSRNOG00000016672 -1.93 1.72E-04

ENSRNOT00000006809 hypothetical protein gene:ENSRNOG00000005100 -1.94 2.66E-04 NM_023976 periaxin (Prx), mRNA. -1.94 6.63E-06 NM_001008345 mesoderm development candidate 2 (Mesdc2), mRNA. -1.94 1.41E-04 NM_012605 myosin light chain, phosphorylatable, fast skeletal muscle (Mylpf), -1.94 5.64E-05 mRNA. ENSRNOT00000059282 cdna:novel chromosome:RGSC3.4:15:41700388:41720938:-1 -1.95 1.96E-04 gene:ENSRNOG00000038799 NM_053303 Burkitt lymphoma receptor 1 (Blr1), mRNA. -1.95 1.58E-04 NM_001106371 helicase, lymphoid specific (Hells), mRNA. -1.95 6.26E-05 XR_007814 PREDICTED: similar to 60S ribosomal protein L26 (LOC364390), -1.96 1.99E-04 mRNA. NM_013198 monoamine oxidase B (Maob), nuclear gene encoding mitochondrial -1.96 4.96E-05 protein, mRNA. BC101877 dedicator of cytokinesis 2, mRNA (cDNA clone IMAGE:5599905), -1.97 1.76E-04 complete cds. ENSRNOT00000042335 similar to Protocadherin 19 precursor gene:ENSRNOG00000003929 -1.97 2.34E-05

NM_001012135 melanophilin (Mlph), mRNA. -1.97 1.43E-04 ENSRNOT00000055614 cdna:novel chromosome:RGSC3.4:1:137706616:137708253:-1 -1.97 9.07E-05 gene:ENSRNOG00000036981 ENSRNOT00000007485 similar to ADP-ribosyltransferase 4 gene:ENSRNOG00000005670 -1.97 6.69E-05

ENSRNOT00000002333 similar to type V P-type ATPase isoform 4 gene:ENSRNOG00000001714 -1.97 1.73E-04

GENSCAN00000044060 cdna:Genscan chromosome:RGSC3.4:3:22668:22864:-1 -1.98 2.09E-04 ENSRNOT00000023114 similar to C32D5.6 gene:ENSRNOG00000027343 -1.98 2.01E-04 ENSRNOT00000043048 similar to Carbonic anhydrase 6 precursor gene:ENSRNOG00000021355 -1.98 9.71E-05

NM_001105789 Rho guanine nucleotide exchange factor (GEF) 15 (predicted) -1.98 6.35E-05 (Arhgef15_predicted), mRNA. NM_139335 taste receptor, type 2, member 126 (Tas2r126), mRNA. -1.98 2.34E-04 NM_053587 S100 calcium binding protein A9 (calgranulin B) (S100a9), mRNA. -1.98 2.58E-04 NM_001025768 DSN1, MIND kinetochore complex component, homolog (S. cerevisiae) -1.98 1.66E-05 (Dsn1), mRNA. NM_001012068 uroporphyrinogen III synthase (Uros), mRNA. -1.98 2.31E-04 ENSRNOT00000055521 cdna:pseudogene chromosome:RGSC3.4:3:139859556:139859864:1 -1.98 1.60E-04 gene:ENSRNOG00000036950

NM_017047 solute carrier family 10 (sodium/bile acid cotransporter family), member 1 -1.99 4.35E-05 (Slc10a1), mRNA. NM_001108880 BarH-like homeobox 1 (predicted) (Barx1_predicted), mRNA. -1.99 9.57E-05 ENSRNOT00000045278 similar to CD33 antigen gene:ENSRNOG00000033588 -1.99 2.33E-04 NM_001031825 glycoprotein 9 (platelet) (Gp9), mRNA. -2 2.23E-06 ENSRNOT00000038984 cdna:known chromosome:RGSC3.4:4:31650840:31651278:1 -2 2.06E-05 gene:ENSRNOG00000024270 ENSRNOT00000032267 67 kDa protein gene:ENSRNOG00000033340 -2.01 1.16E-04 ENSRNOT00000011337 cdna:known chromosome:RGSC3.4:7:22394024:22394988:-1 -2.01 3.03E-04 gene:ENSRNOG00000008576 NM_212505 immediate early response 3 (Ier3), mRNA. -2.01 2.87E-04 ENSRNOT00000049474 similar to Lymphoid-restricted membrane protein -2.01 2.44E-04 gene:ENSRNOG00000029308 XR_008613 PREDICTED: similar to nuclear RNA export factor 2 (predicted) -2.01 6.49E-05 (RGD1559530_predicted), mRNA. ENSRNOT00000054244 ncrna:snRNA chromosome:RGSC3.4:15:17506440:17506542:-1 -2.01 1.13E-04 gene:ENSRNOG00000036121 NM_022218 chemokine-like receptor 1 (Cmklr1), mRNA. -2.01 2.19E-04 NM_001013167 WAS protein family, member 2 (Wasf2), mRNA. -2.02 1.74E-04 NM_001109361 IQ motif containing F1 (Iqcf1), mRNA. -2.02 4.25E-05 NM_020094 Kv channel-interacting protein 2 (Kcnip2), transcript variant a, mRNA. -2.03 2.24E-04

ENSRNOT00000046038 similar to ATPase inhibitor, mitochondrial precursor -2.04 2.78E-04 gene:ENSRNOG00000032924 NM_033237 galanin (Gal), mRNA. -2.06 2.49E-04 ENSRNOT00000051159 similar to Collagen alpha-1(XII) chain precursor -2.07 2.00E-04 gene:ENSRNOG00000010510 NM_001107237 similar to DNA-binding protein Ikaros form 1 - mouse (predicted) -2.07 4.22E-05 (RGD1562979_predicted), mRNA. ENSRNOT00000008721 similar to pleckstrin homology domain containing, family G, member 3 -2.08 2.76E-04 gene:ENSRNOG00000006570 NM_001012345 diacylglycerol O-acyltransferase 2 (Dgat2), mRNA. -2.09 2.73E-04 ENSRNOT00000017602 cdna:novel chromosome:RGSC3.4:7:90184446:90184826:1 -2.09 2.76E-05 gene:ENSRNOG00000013191 ENSRNOT00000037899 cdna:pseudogene chromosome:RGSC3.4:11:15547326:15548091:1 -2.09 3.03E-04 gene:ENSRNOG00000028223

NM_012955 centromere protein I (Cenpi), mRNA. -2.09 4.02E-05 NM_001107623 transmembrane protein 26 (predicted) (Tmem26_predicted), mRNA. -2.1 1.44E-04

NM_001109229 monooxygenase, DBH-like 2 (Moxd2), mRNA. -2.1 2.46E-04 NM_001109424 keratin associated protein 16-5 (Krtap16-5), mRNA. -2.1 1.02E-04 BC091257 gamma-2a immunoglobulin heavy chain, mRNA (cDNA clone -2.1 1.56E-04 MGC:109083 IMAGE:7375893), complete cds. ENSRNOT00000045677 similar to Lethal gene:ENSRNOG00000007044 -2.1 9.92E-05 ENSRNOT00000020846 cdna:known chromosome:RGSC3.4:3:106023867:106024961:1 -2.13 2.69E-04 gene:ENSRNOG00000015542

ENSRNOT00000000901 hypothetical protein gene:ENSRNOG00000000711 -2.14 1.20E-04 XM_001081768 PREDICTED: similar to chromosome 17 open reading frame 27 -2.15 1.04E-05 (predicted) (RGD1308168_predicted), mRNA. ENSRNOT00000028079 similar to CG11760-PB, isoform B gene:ENSRNOG00000020692 -2.16 2.80E-04

NM_017131 calsequestrin 2 (Casq2), mRNA. -2.16 1.78E-05 NM_001109009 aquaporin 12 (Aqp12), mRNA. -2.16 2.19E-04 NM_001007010 dyslexia susceptibility 1 candidate 1 homolog (human) (Dyx1c1), mRNA. -2.16 2.08E-04 rno-mir-410 MI0006143 miR-410 stem-loop -2.17 1.82E-04 ENSRNOT00000003441 5-hydroxytryptamine receptor 5B gene:ENSRNOG00000002549 -2.19 1.54E-04

ENSRNOT00000008011 similar to guanine nucleotide binding protein (G protein), gamma -2.2 1.46E-04 transducing activity polypeptide 2 gene:ENSRNOG00000006108

NM_199082 secreted and transmembrane 1B (Sectm1b), mRNA. -2.21 1.78E-05 XR_005907 PREDICTED: similar to galectin 8 (LOC501599), mRNA. -2.23 2.78E-04 ENSRNOT00000015296 similar to CXXC finger 6 gene:ENSRNOG00000011387 -2.24 8.67E-05 NM_001108823 similar to Prostatic spermine-binding protein precursor (SBP) (predicted) -2.24 1.69E-05 (RGD1562673_predicted), mRNA. NM_030993 dendrin (Ddn), mRNA. -2.25 4.97E-05 NM_001037528 defensin beta 43 (Defb43), mRNA. -2.26 1.18E-04 GENSCAN00000067624 cdna:Genscan chromosome:RGSC3.4:3:86338744:86338815:-1 -2.27 3.27E-06 NM_133590.1 RAB7, member RAS oncogene family-like 1 (Rab7l1), mRNA -2.28 2.57E-04 ENSRNOT00000061598 cdna:novel chromosome:RGSC3.4:11:28911604:28911750:-1 -2.28 2.36E-05 gene:ENSRNOG00000040057 NM_022610.1 inducible T-cell co-stimulator (Icos), mRNA -2.28 2.14E-04 NM_012705 CD4 antigen (Cd4), mRNA. -2.29 2.08E-05 ENSRNOT00000046348 similar to serine/threonine kinase gene:ENSRNOG00000031056 -2.29 1.18E-04

ENSRNOT00000048286 similar to TD and POZ domain containing 3 -2.29 3.78E-05 gene:ENSRNOG00000029298 NM_001004246 tetratricopeptide repeat domain 12 (Ttc12), mRNA. -2.3 5.54E-05 NM_001107629 radial spokehead-like 3 (predicted) (Rshl3_predicted), mRNA. -2.3 3.97E-05 ENSRNOT00000008848 cdna:novel chromosome:RGSC3.4:4:94733118:94733840:-1 -2.31 7.74E-05 gene:ENSRNOG00000006765 NM_001106751 G-protein coupled receptor 65 (predicted) (Gpr65_predicted), mRNA. -2.33 1.37E-04

ENSRNOT00000052899 ncrna:snRNA chromosome:RGSC3.4:10:4369721:4369880:1 -2.34 1.75E-05 gene:ENSRNOG00000034776 ENSRNOT00000038249 cdna:known chromosome:RGSC3.4:20:33382408:33383408:-1 -2.34 2.12E-05 gene:ENSRNOG00000026207 ENSRNOT00000000623 cdna:novel chromosome:RGSC3.4:20:7225694:7226754:-1 -2.36 3.13E-04 gene:ENSRNOG00000000516 NM_022547.1 formyltetrahydrofolate dehydrogenase (Fthfd), mRNA -2.36 8.85E-06 NM_022679.1 trispanning orphan (Tore), mRNA -2.37 1.58E-04 ENSRNOT00000033300 similar to Homeobox protein Hox-C13 gene:ENSRNOG00000028679 -2.37 1.32E-04

ENSRNOT00000058804 cdna:novel chromosome:RGSC3.4:6:97599046:97599550:-1 -2.39 1.83E-05 gene:ENSRNOG00000038548 ENSRNOT00000054423 ncrna:snRNA chromosome:RGSC3.4:1:82810914:82811020:-1 -2.41 1.16E-04 gene:ENSRNOG00000036302 rno-mir-497 MI0003724 miR-497 stem-loop -2.42 2.86E-04 ENSRNOT00000030186 57 kDa protein gene:ENSRNOG00000027067 -2.42 4.06E-05 ENSRNOT00000054456 ncrna:miRNA chromosome:RGSC3.4:11:13104242:13104321:-1 -2.43 2.77E-05 gene:ENSRNOG00000036334 NM_001106341 methylmalonyl CoA epimerase (predicted) (Mcee_predicted), mRNA. -2.43 1.52E-04 ENSRNOT00000047045 cdna:pseudogene chromosome:RGSC3.4:7:12683750:12684356:1 -2.45 8.41E-06 gene:ENSRNOG00000029851

ENSRNOT00000000651 similar to dynein, axonemal, heavy chain 8 -2.46 1.31E-04 gene:ENSRNOG00000000542 NM_001025420 lymphocyte specific 1 (Lsp1), mRNA. -2.47 3.05E-04 NM_001109398 similar to Bifunctional methylenetetrahydrofolate -2.47 7.82E-05 dehydrogenase/cyclohydrolase, mitochondrial precursor (LOC680308), nuclear gene encoding mitochondrial protein, mRNA.

NM_001106497 signal recognition particle 14 (predicted) (Srp14_predicted), mRNA. -2.49 1.51E-04

NM_001047919 similar to RIKEN cDNA 2900055D03 (LOC367117), mRNA. -2.49 1.49E-04 ENSRNOT00000055830 29 kDa protein gene:ENSRNOG00000007961 -2.5 1.11E-04 NM_001034935 protein phosphatase with EF hand calcium-binding domain 1 (Ppef1), -2.51 2.33E-04 mRNA. ENSRNOT00000044038 similar to ubiquitin specific protease 12 gene:ENSRNOG00000033411 -2.51 4.39E-05

ENSRNOT00000061131 cdna:novel chromosome:RGSC3.4:12:8809819:8810695:1 -2.51 4.39E-05 gene:ENSRNOG00000029046 XM_001069848 PREDICTED: similar to ubiquitin specific protease 12 (LOC684318), -2.51 4.39E-05 mRNA. ENSRNOT00000044038 similar to ubiquitin specific protease 12 gene:ENSRNOG00000033411 -2.51 4.39E-05

NM_001077646 CD3 antigen, gamma polypeptide (Cd3g), mRNA. -2.55 2.99E-04 NM_001012232 ribonuclease 17 (Rnase17), mRNA. -2.56 5.35E-06 NM_001012232 ribonuclease 17 (Rnase17), mRNA. -2.56 5.35E-06 NM_001108072 pleckstrin homology domain containing, family J member 1 (Plekhj1), -2.56 1.06E-04 mRNA. NM_020071 fibrinogen, B beta polypeptide (Fgb), mRNA. -2.56 1.73E-04 NM_001109483 peptidylprolyl isomerase (cyclophilin) like 5 (Ppil5), mRNA. -2.56 5.98E-05 ENSRNOT00000045740 cdna:novel chromosome:RGSC3.4:15:59622091:59624917:1 -2.57 2.31E-04 gene:ENSRNOG00000031693 AY059383 HES-related repressor protein 2 HERP2 mRNA, partial cds. -2.57 9.48E-06 NM_199085 serine (or cysteine) peptidase inhibitor, clade B, member 6a (Serpinb6a), -2.59 1.07E-05 mRNA. NM_053318 hemopexin (Hpx), mRNA. -2.59 6.81E-06 NM_022515 ribosomal protein L24 (Rpl24), mRNA. -2.61 1.00E-04 XR_005593 PREDICTED: similar to glyceraldehyde-3-phosphate dehydrogenase -2.61 2.77E-04 (LOC364896), mRNA. NM_022291 neuropeptide FF receptor 1 (Npffr1), mRNA. -2.63 3.72E-06 ENSRNOT00000039316 cdna:known chromosome:RGSC3.4:4:88376454:88378742:-1 -2.64 1.94E-04 gene:ENSRNOG00000023657 rno-let-7c-1 MI0000830 let-7c-1 stem-loop -2.66 6.47E-05 GENSCAN00000012532 cdna:Genscan chromosome:RGSC3.4:10:92630659:92638577:-1 -2.67 2.81E-04

NM_001047946 LRRGT00038 (LOC499565), mRNA. -2.68 5.43E-05 NM_001108968 PTK6 protein tyrosine kinase 6 (predicted) (Ptk6_predicted), mRNA. -2.71 1.54E-05

NM_012702 carcinoembryonic antigen-related cell adhesion molecule 3 (Ceacam3), -2.73 9.23E-05 mRNA. XR_009465 PREDICTED: similar to chaperonin subunit 6a (zeta) (LOC688183), -2.74 2.37E-05 mRNA. XM_001075018 PREDICTED: RGD1559872 (predicted) (RGD1559872_predicted), -2.74 7.70E-05 mRNA. NM_001109256 similar to RIKEN cDNA 2210417D09 (predicted) -2.74 3.08E-04 (RGD1562899_predicted), mRNA. NM_001047866 similar to contactin associated protein-like 5 isoform 1 (predicted) -2.77 1.60E-05 (RGD1566343_predicted), mRNA. ENSRNOT00000004902 similar to zinc finger protein 354B gene:ENSRNOG00000029678 -2.78 1.15E-04

ENSRNOT00000061349 cdna:novel chromosome:RGSC3.4:15:10765477:10766100:1 -2.78 3.05E-05 gene:ENSRNOG00000039934 XM_001057963 PREDICTED: hypothetical protein LOC680606 (LOC680606), mRNA. -2.79 3.87E-05

ENSRNOT00000058750 cdna:novel chromosome:RGSC3.4:X:56021140:56021604:1 -2.79 8.53E-05 gene:ENSRNOG00000038521 XR_007628 PREDICTED: similar to Glyceraldehyde-3-phosphate dehydrogenase -2.79 2.92E-04 (GAPDH) (LOC361904), mRNA. NM_001037506 defensin beta 26 (Defb26), mRNA. -2.8 5.24E-05 NM_001034937 phosphoglycerate dehydrogenase like 1 (Phgdhl1), mRNA. -2.82 2.56E-04 AF164039 interferon-inducible protein variant 10 mRNA, complete cds. -2.84 8.08E-05 NM_001047864 developmental pluripotency-associated 3 (Dppa3), mRNA. -2.97 2.34E-04 NM_173294 cytochrome P450IIB3 (Cyp2b3), mRNA. -3.19 2.93E-07 ENSRNOT00000043809 cdna:novel chromosome:RGSC3.4:1:81230276:81230446:-1 -3.19 2.93E-07 gene:ENSRNOG00000032405 ENSRNOT00000024483 similar to dehydrogenase/reductase member 2 -3.43 1.46E-05 gene:ENSRNOG00000018177 Supplementary table 2. Sequence of primers used in PCR and qRT-PCR reactions

Gene Accession PCR type Targeted Forward sequence Reverse sequence symbol Number species (5’-3’) (5’-3’) CH25H BC039919 qRT-PCR Mouse cccactcaccatctttacctttc cccagcattttgtcccagt C/EBP-δ BC139293 qRT-PCR Mouse gaaggaacacgggaaagca gtagaggcaacgaggaatcaagt IER3 BC006950 qRT-PCR Mouse gaacactaccaccaagagacacc attacatacacccctccttcacc LY6G6D BC131990 qRT-PCR Mouse ctacaggcataaacgaacgtga ctccaccgcagtcatagca PNPLA7 BC027342 qRT-PCR Mouse atggctctctgtggaggtatgt gctgggaggttgttgatgtaa SEPT9 BC046524 qRT-PCR Mouse gccaggtaacaagagagggttt ggaaatagagcacagaggcaag SSTR3 BC137670 qRT-PCR Mouse ctctacggcttcctctcctacc tcttcttcttcatcctcctcctc STX3 BC024844 qRT-PCR Mouse cccctattaccataccatacctg ccatcctgagaccaactatcatc WASF2 AY135643 qRT-PCR Mouse tctacaccaacccctcatacttc ccattttcatcttctcccactc C/EBP-δ NM_013154 PCR Rat gcagacagtggtgagcttgg tatagcttctctcgcagtccagt GAPDH M17701 PCR Rat gtgttcctacccccaatgtatc gcctctctcttgctctcagtatc NGF J04154 PCR Rat ctaccagtcccaactcatcaaac gtctgctttcttgtccttctgtc NT-3 NM_031073 PCR Rat cacagaactactacggcaacaga acaaggcacacacacaggaagt A2M NM_012488 qRT-PCR Rat ctggaggaagagatgaatgtgtc gccgaagcagttagaaggattac AATF NM_053720 qRT-PCR Rat ctgaggaagtggaaaaaggaag tgaagacagggaaaacatctgg ALOX12B NM_001039377 qRT-PCR Rat ccgagcactggactgaagatag tctgtaactgggaacttgtctgg APOF NM_001024351 qRT-PCR Rat atgctctgtcctctgccctac cactctctgttcctgctcattct ARG2 NM_019168 qRT-PCR Rat cacgacagcattccagagttg gtgaccaaaatagagaaggggact ATN1 NM_017228 qRT-PCR Rat agggaagaagggacagacaag tacagaagaaaagcaggggatg C/EBP-δ NM_013154 qRT-PCR Rat tgctacagtttcttgggcact cgcagtctcttcctcttatctac CD9 NM_053018 qRT-PCR Rat cttccacagcaagttccacatc tagaccatttctcggctcctg CENPI NM_012955 qRT-PCR Rat gattctaaccacgctgacga gttccaagccacattttccac CH25H NM_001025415 qRT-PCR Rat aggttacgactttccgtggtc cattttgtcccagtgtgtgaag CLN3 NM_001006971 qRT-PCR Rat gcatctacctcatcttcatcgtc aaactctcggtgcttgtcact CREB-L1 NM_001002809 qRT-PCR Rat ctacctcaatcatccctgacttct acaccccaccttcctttacc CXCL3 NM_138522 qRT-PCR Rat cagtgctaagagacgggaatg agattgttcgctgatgcgtagt EIF3D NM_001004283 qRT-PCR Rat agggcaaatacctcatcctca tcttcttcttcctcctcttcctc GAL NM_033237 qRT-PCR Rat agtcctgagaccacacccac cagcatcaaagcagagaac GAP43 NM_017195 qRT-PCR Rat acaggatgagggtaaagaagacc gagcaggacaggagaggaaact GAPDH M17701 qRT-PCR Rat attctacccacggcaagttca agactccacgacatactcagcac GPR119 NM_181770 qRT-PCR Rat tattccagcagaccacctacca gaagaagacaaagaggagcacag IER3 NM_212505 qRT-PCR Rat taactcagaacactaccgccaag attacatacacccctccttcacc IL5RA NM_053645 qRT-PCR Rat tagccacacccacttcagg ggcattcttcagtccaaacact LY6G6D NM_001001970 qRT-PCR Rat ctacaggcataaacgaacgtga ctccaccgcagtcatagca MAOB NM_013198 qRT-PCR Rat cagatacacaggctctctcac ggacctaacacaccagaag MAP2K1 NM_031643 qRT-PCR Rat ctgcgattttggggtcag ggaggaggaatggggtatctt MXRA8 NM_001007002 qRT-PCR Rat gattcctttctgtccaatgctc cttcatcccatcctcagtcaa NDPH NM_001108814 qRT-PCR Rat gctcttcattcccttctccttt ccccacattttcccactaatac NGF J04154 qRT-PCR Rat caactccttcagcacctcaac ccctcctgtcctttattgtctct NT-3 NM_031073 qRT-PCR Rat gggattgatgacaaacactgg acaaggcacacacacaggaagt NTN1 NM_053731 qRT-PCR Rat gcgacgagaacgaagatga gcctacagtcacacaccagac NTRK2 NM_001163168 qRT-PCR Rat gaaccacctgccctttagaac ctttagactgctctcctgctcac PNPLA7 BC091230 qRT-PCR Rat gtctcctcagcattttggatg cctcaccagagtttcaggg PPM1A NM_017038 qRT-PCR Rat agggggctctgtgatgatt ctgctctgtgggaccttttc SEPT9 NM_176856 qRT-PCR Rat gggctcactcatcttctctca cgacctaactaacctcaccaaac SSTR3 NM_133522 qRT-PCR Rat ctctacggcttcctctcctacc tcttcttcttcatcctcctcctc STX1A NM_053788 qRT-PCR Rat catccacaggcaaggagtatg gtgacggggtaaagggaagt STX3 NM_031124 qRT-PCR Rat gcacgggatgaaactaaaagag ctaaaatgcccagcaacacaac SYN1 NM_019133 qRT-PCR Rat ttctccgactgacacctactctg gggttctcaagggatttgga TNFRSF5 NM_134360 qRT-PCR Rat ctacgggaaggaacaagtcag cacaaagatggtgatgaggatg TRP53INP1 NM_181084 qRT-PCR Rat agcagaagaagaggaggaagatg gacaggactcaaactgaaggaag WASF2 NM_001013167 qRT-PCR Rat gctctaccatccaagaccagaag cttttccgtcgtccctgtaa *qRT-PCR= quantitative real-time PCR