Kurrasch et al. Supplemental Table 1. Top VMH-enriched (≥1.51-fold).

Rank Symbol Name Accession # Fold Allen 1 Vgll2 Vestigial like 2 homolog NM_153786 8.42 0 * 2 Nr5a1 Nuclear receptor subfamily 5, group A, member 1 (SF1, Ad4BP) NM_139051 7.75 +++ * 3 Sox14 SRY-box containing gene 14 XM_284529 7.35 ++ 4 Nptx2 Neuronal pentraxin 2 NM_016789 6.85 +++ 5 RIKF11 RIKEN cDNA 9130024F11 AK020268 6.13 N/A * 6 Bdnf Brain derived neurotrophic factor NM_007540 5.37 ++ 7 Satb2 Special AT-rich sequence binding 2 AK035129 4.68 ++ 8 Gpr149 -coupled receptor 149 NM_177346 4.43 ++ 9 Fezf1 Fez family zinc finger 1 XM_133029 4.38 +++ 10 Ddn Dendrin AK122363 4.29 ++ * 11 Cbln1 Cerebellin 1 precursor protein NM_019626 4.28 N/A 12 RIKG08 RIKEN cDNA C130093G08 AK082001 4.27 N/A 13 Mst1r Macrophage stimulating 1 receptor NM_009074 3.83 0 14 Tnfrsf8 Tumor necrosis factor receptor superfamily, member 8 NM_009401 3.79 ++ 15 Nmbr Neuromedin B receptor NM_008703 3.30 + * 16 Adcyap1 Adenylate cyclase activating polypeptide 1 (PACAP) NM_009625 3.28 +++ * 17 Nr0b1 Nuclear receptor subfamily 0, group B, member 1 (Dax1) NM_007430 3.18 ++ 18 Pdyn Prodynorphin NM_018863 3.16 +++ 19 Amigo2 Adhesion molecule with Ig like domain 2 NM_178114 3.13 +++ 20 RIKK11 RIKEN cDNA 1700024K11 CN839877 3.12 N/A 21 Plp1 Proteolipid protein (myelin) 1 AK077564 3.05 +/0 22 Nkx2-2 NK2 transcription factor related, 2 NM_010919 2.94 + * 23 Gabra5 Gamma-aminobutyric acid receptor, subunit alpha 5 NM_176942 2.89 +++ * 24 Gda Guanine deaminase AK080065 2.81 +++ 25 RIKC22 RIKEN cDNA C230097C22 BB396351 2.74 N/A * 26 Nr2f2 Nuclear receptor subfamily 2, group F, member 2 (COUP-TFII) NM_009697 2.73 +++ 27 RIKB13 RIKEN cDNA E030019B13 BC064451 2.73 N/A 28 Camkv CaM kinase-like vesicle-associated NM_145621 2.70 +++ 29 Ldb2 LIM domain binding 2 NM_010698 2.65 ++ 30 Fbxw7 F-box and WD-40 domain protein 7, archipelago homolog NM_080428 2.62 +++ * 31 Cckbr Cholecystokinin B receptor NM_007627 2.60 ++ 32 Cdh4 4 NM_009867 2.58 0 33 Col6a3 Procollagen, type VI, alpha 3 XM_484897 2.53 + 34 Sema3a Sema domain, Ig, short basic domain, secreted, 3A NM_009152 2.52 ++ 35 RIKP06 RIKEN cDNA 1700007P06 AK005744 2.48 N/A 36 Rerg RAS-like, estrogen-regulated, growth-inhibitor NM_181988 2.46 ++ 37 Acvr1c Activin A receptor, type IC XM_194020 2.44 ++ 38 A2bp1 Ataxin 2 binding protein 1, transcript variant 2 (Fox-1) NM_021477 2.40 +++ * 39 Tac1 Tachykinin 1 (Substance P) NM_009311 2.36 +++ 40 Lcorl Ligand dependent nuclear receptor corepressor-like, transcript v.2 NM_172153 2.36 + 41 Card14 Caspase recruitment domain family, member 14 NM_130886 2.32 ++ 42 cDNA sequence BC034076 NM_177649 2.27 +++ * 43 Titf1 Thyroid transcription factor 1 (Nkx2.1) NM_009385 2.27 + 44 B3gnt3 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3 NM_028189 2.25 ++ 45 Tcfcp2l2 Transcription factor CP2-like 2 (Grhl1) NM_145890 2.24 + 46 Kcnj5 Potassium inwardly-rectifying channel, subfamily J, member 5 NM_010605 2.22 + 47 Ntn3 Netrin 3 NM_010947 2.21 + 48 Calb1 -28K AK038856 2.21 +++ 49 Tmem35 Transmembrane protein 35 NM_026239 2.20 +++ 50 RIKI05 RIKEN cDNA C030019I05 NM_177075 2.20 +

Kurrasch et al. Supplemental Table 1. Top VMH-enriched genes, continued Rank Symbol Gene Name Accession # Fold Allen 51 Cmbl Carboxymethylenebutenolidase-like (Pseudomonas) NM_181588 2.15 ++ 52 cDNA sequence BC027127 NM_145967 2.11 ++ 53 Abcc8 ATP-binding cassette, sub-family C (CFTR/MRP), member 8 NM_011510 2.11 + 54 Bid3 BH3 interacting (with BCL2 family) domain, agonist NM_007545 2.10 ++ 55 RIKP17 RIKEN cDNA 4930483P17 gene AK019653 2.09 N/A 56 Pvrl3 Poliovirus receptor-related 3 transcript variant alpha NM_021495 2.07 +++ 57 Cacna2d1 , voltage-dependent, alpha2/delta subunit 1 NM_009784 2.07 +++ 58 Ass1 Argininosuccinate synthetase 1 NM_007494 2.06 N/A 59 Htr1b 5-hydroxytryptamine (serotonin) receptor 1B NM_010482 2.06 + 60 RIKF16 RIKEN cDNA 2410137F16 AK038689 2.04 N/A 61 Rasgrf2 RAS protein-specific guanine nucleotide-releasing factor 2 NM_009027 2.03 +++ * 62 Slc17a6 Solute carrier family 17, member 6 (VGLUT2) AK013772 2.03 +++ 63 RIKM16 RIKEN cDNA 6430502M16 BC096609 2.03 +++ 64 Chrna4 Cholinergic receptor, nicotinic, alpha polypeptide 4 NM_015730 2.02 ++ 65 Clca1 calcium activated 1 NM_009899 2.01 + 66 Cda Cytidine deaminase NM_028176 2.00 + 67 Grrp1 Glycine/arginine rich protein 1 XM_485455 2.00 + 68 Prlr Prolactin receptor NM_011169 1.99 + 69 Rasa4 RAS p21 protein activator 4 XM_355650 1.99 + 70 Gng13 Guanine nucleotide binding protein 13, gamma NM_022422 1.99 ++ 71 RIKK07 RIKEN cDNA 2700055K07 (Tppp3) NM_026481 1 . 9 9 +++ 72 Cadps2 Ca2+-dependent activator protein for secretion 2 NM_153163 1.99 +++ 73 Nptx1 Neuronal pentraxin 1 NM_008730 1.98 0 74 RIKK08 RIKEN cDNA A830021K08 AK043702 1.97 0 75 Mapk15 Mitogen-activated 15 NM_177922 1.97 + * 76 Slit3 Slit homolog 3 (Drosophila) XM_203363 1.97 +++ 77 Kcnab1 Potassium voltage-gated channel, -related subfamily, beta 1 NM_010597 1.95 +++ 78 Adamts18 A disintegrin-like and metalloprotease with thrombospondin type1,18 AK036137 1.95 ++ 79 RIKD01 RIKEN cDNA E130006D01 NM_207252 1.93 + 80 Has3 Hyaluronan synthase 3 NM_008217 1.93 ++ 81 H2-D1 Histocompatibility 2, D region locus 1 NM_010380 1.93 ++ 82 Klhl4 Kelch-like 4 (Drosophila) NM_172781 1.92 + 83 Ugt1a7c UDP glucuronosyltransferase 1 family, polypeptide A7C NM_201642 1.91 + 84 RIKP15 RIKEN cDNA E530018P15 BB560451 1.89 N/A * 85 Cnr1 Cannabinoid receptor 1 NM_007726 1.88 +++ 86 RIKN13 RIKEN cDNA B830045N13 NM_153539 1.87 ++ 87 Neud4 Neuronal d4 domain family member NM_013874 1.87 ++ 88 RIKL19 RIKEN cDNA 1700001L19 XM_127414 1.86 ++ 89 Rasal1 RAS protein activator like 1 (GAP1 like) NM_013832 1.86 +++ 90 Rtn1 Reticulon 1, transcript variant 2 NM_001007596 1.85 ++ 91 Nell2 Nel-like 2 homolog (chicken) NM_016743 1.84 ++ 92 Myc Myelocytomatosis oncogene NM_010849 1.83 + 93 Pde8b Phosphodiesterase 8B NM_172263 1.82 ++ 94 Gcnt2 Glucosaminyl (N-acetyl) transferase 2, I-branching enzyme NM_008105 1.81 + 95 Arhgdig Rho GDP dissociation inhibitor (GDI) gamma NM_008113 1.81 ++ 96 Atp10a ATPase, class V, type 10A NM_009728 1.80 + 97 Ptchd2 Patched domain containing 2 XM_620145 1.80 +++ 98 Ntng1 Netrin G1 AK020842 1.80 + 99 RIKF12 RIKEN cDNA B830032F12 AK046858 1.78 N/A 100 Rtn4r Reticulon 4 receptor NM_022982 1.78 0

Kurrasch et al. Supplemental Table 1. Top VMH-enriched genes, continued Rank Symbol Gene Name Accession # Fold Allen 101 Cotl1 Coactosin-like 1 (Dictyostelium) BC010249 1.78 ++ 102 Ptpns1 Protein tyrosine phosphatase, non-receptor type substrate 1 NM_007547 1.78 ++ 103 Grm7 Glutamate receptor, metabotropic 7 NM_177328 1.78 N/A 104 Tmem132a Transmembrane protein 132A NM_133804 1.77 ++ 105 Itpr1 Inositol 1,4,5-triphosphate receptor 1 NM_010585 1.77 ++ * 106 Odz2 Odd Oz/ten-m homolog 2 (Drosophila) NM_011856 1.76 ++ 107 RIKK16 RIKEN cDNA 9330109K16 AK020364 1.76 N/A 108 Fxyd7 FXYD domain-containing ion transport regulator 7 NM_022007 1.75 ++ 109 RIKE08 RIKEN cDNA 9230112E08 NM_177264 1.74 + 110 RIKI19 RIKEN cDNA 1500031I19 BC053419 1.73 N/A 111 Baiap2 Brain-specific angiogenesis inhibitor 1-associated protein 2 AK083201 1.73 ++ 112 Tuba4 Tubulin, alpha 4 NM_009447 1.73 ++ 113 Isl1 ISL1 transcription factor, LIM/homeodomain NM_021459 1.72 ++ 114 Chst8 Carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 8 NM_175140 1.72 ++ 115 Fgd2 FYVE, RhoGEF and PH domain containing 2 NM_013710 1.71 0 116 Gcnt2 Glucosaminyl (N-acetyl) transferase 2, I-branching enzyme NM_133219 1.71 +++ 117 Car11 Carbonic anhydrase 11 NM_009800 1.71 +++ 118 Htr2a 5-hydroxytryptamine (serotonin) receptor 2 A NM_172812 1.71 0 119 RIKC02 RIKEN cDNA 2010300C02 XM_129808 1.70 + 120 Ppp3ca 3, catalytic subunit, alpha isoform NM_008913 1.70 +++ 121 Ntsr1 Neurotensin receptor 1 NM_018766 1.70 0 122 RIKH15 RIKEN cDNA D030054H15 XM_622235 1.69 N/A 123 Ush1c Usher syndrome 1C homolog (human), transcript variant a1 NM_023649 1.69 + 124 Doc2b Double C2, beta NM_007873 1.69 +++ 125 Hypothetical protein 9530064J02 XM_489200 1.69 0 126 Stx1a Syntaxin 1A NM_016801 1.69 ++ 127 Car10 Carbonic anhydrase 10 AK132222 1.69 +++ 128 RIKK04 RIKEN cDNA A130090K04 AK041335 1.68 N/A 129 Slitrk1 SLIT and NTRK-like family, member 1 AK173296 1.68 ++ 130 Lphn2 Latrophilin 2 XM_131258 1.68 ++ 131 RIKA10 RIKEN cDNA 1500001A10 NM_026886 1.68 + 132 RIKF05 RIKEN cDNA 1500004F05 AK158492 1.68 N/A 133 Isyna1 Myo-inositol 1-phosphate synthase A1 NM_023627 1.67 ++ 134 Large Like-glycosyltransferase NM_010687 1.67 ++ 135 RIKB11 RIKEN cDNA 4930568B11 AK016246 1.67 N/A 136 Camk2a Calcium/-dependent protein kinase II alpha NM_177407 1.67 ++ 137 Tpd52l1 Tumor protein D52-like 1 NM_009413 1.66 ++ 138 RIKB05 RIKEN cDNA E430005B05 BY762008 1.65 N/A 139 Igsf4b Immunoglobulin superfamily, member 4B NM_053199 1.65 +++ 140 Sez6l Seizure related 6 homolog like XM_132255 1.65 ++ 141 Lmo4 LIM domain only 4 AK159590 1.65 + 142 RIKH02 RIKEN cDNA 6530403H02 AK032656 1.65 N/A 143 RIKH04 RIKEN cDNA 1700037H04 NM_026091 1.65 ++ 144 Lba1 Lupus brain antigen 1 XM_135191 1.65 ++ 145 Nit1 Nitrilase 1 NM_012049 1.65 ++ 146 RIKM07 RIKEN cDNA 4930506M07 NM_175172 1.64 ++ 147 Hypothetical protein B230218O03 NM_183219 1.64 ++ 148 RIKB19 RIKEN cDNA C630007B19 NM_182808 1.64 N/A 149 Ndg2 Nur77 downstream gene 2 AK075746 1.63 ++ 150 Cacna1h Calcium channel, voltage-dependent, T type, alpha 1H subunit NM_021415 1.63 ++

Kurrasch et al. Supplemental Table 1. Top VMH-enriched genes, continued Rank Symbol Gene Name Accession # Fold Allen 151 Slitrk5 SLIT and NTRK-like family, member 5 NM_029273 1.63 ++ 152 Ankrd35 Ankyrin repeat domain 35 XM_143418 1.63 ++ 153 Gpr176 G protein-coupled receptor 176 NM_201367 1.62 +/0 154 Impdh1 Inosine 5'-phosphate dehydrogenase 1 NM_011829 1.62 ++ 155 Pam Peptidylglycine alpha-amidating monooxygenase NM_013626 1.61 +++ 156 Crip2 Cysteine rich protein 2 NM_024223 1.61 + 157 Ppp1r3d Protein phosphatase 1, regulatory subunit 3D AK011539 1.61 0 158 Sema3d Sema domain, Ig, short basic domain, secreted, 3D NM_028882 1.61 + 159 Nol4 Nucleolar protein 4 NM_199024 1.60 ++ 160 Pde2a Phosphodiesterase 2A, cGMP-stimulated BC057029 1.60 N/A 161 Enc1 Ectodermal-neural cortex 1 NM_007930 1.60 ++ 162 Ethe1 Ethylmalonic encephalopathy 1 NM_023154 1.60 + 163 Kctd13 tetramerisation domain containing 13 NM_172747 1.59 ++ 164 RIKN22 RIKEN cDNA 1500035N22 BY705531 1.59 ++ 165 Rtn1 Reticulon 1, transcript variant 1 NM_153457 1.59 ++ 166 Nnmt Nicotinamide N-methyltransferase NM_010924 1.59 0 167 Sorcs3 Sortilin-related VPS10 domain containing receptor 3 NM_025696 1.58 ++ 168 Gja9 protein alpha 9 NM_010290 1.58 ++ 169 Unc5c Unc-5 homolog C (C. elegans) NM_009472 1.58 + 170 Kcnv1 Potassium channel, subfamily V, member 1 NM_026200 1.58 0 171 Mif Macrophage migration inhibitory factor NM_010798 1.58 ++ 172 Shh Sonic hedgehog NM_009170 1.58 0 173 Pnma1 Paraneoplastic antigen MA1 NM_027438 1.58 + 174 Lrrn6c Leucine rich repeat neuronal 6C NM_175516 1.58 + 175 Nrgn Neurogranin NM_022029 1.57 +++ 176 H2-Q7 Histocompatibility 2, Q region locus 7 NM_010394 1.57 N/A 177 Mef2d Myocyte enhancer factor 2D BC040217 1.57 ++ 178 Pdzk3 PDZ domain containing 3 AK163415 1.57 0 179 Bcl11a B-cell CLL/lymphoma 11A NM_016707 1.56 + 180 Dlgap3 Discs, large (Drosophila) homolog-associated protein 3 NM_198618 1.55 + 181 Cdh13 Cadherin 13 NM_019707 1.55 +++ 182 Kcnq3 Potassium voltage-gated channel, subfamily Q, member 3 NM_152923 1.55 ++ 183 RIKG10 RIKEN cDNA 6330532G10 AK140181 1.55 N/A 184 RIKO10 RIKEN cDNA 2900024O10 XM_619130 1.54 + 185 Pcdh19 19 XM_205287 1.54 N/A 186 Usmg5 Upregulated during skeletal muscle growth 5 NM_023211 1.54 + 187 Ets2 E26 avian leukemia oncogene 2, 3' domain NM_011809 1.53 +++ 188 RIKK04 RIKEN cDNA 5033414K04 NM_001003948 1.53 + 189 Prkce Protein kinase C, epsilon NM_011104 1.53 ++ 190 Atp1a1 ATPase, Na+/K+ transporting, alpha 1 polypeptide NM_144900 1.51 +++ 191 B3galt5 UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5 NM_033149 1.51 ++ VMH candidates are ranked by fold expression relative to hypothalamus minus VMH. * denotes previously known genes. Symbol, gene name, and accession number are given, as well as fold expression. Allen refers to adult VMH enrichment using virtual analyses (Allen Brain Atlas, www.brain-map.org). +++, high VMH expression; +, low VMH expression; 0, no VMH expression; N/A, no data available.