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