Y+MCx upregulated over Y+SSCx (Change call ≥ 66%; average change p-value of all I/MI calls ≤0.001, P calls min. ≥2/3 in Y+MCx) 103 Probe Avg. Avg. Avg. Set ID Gene Title Gene Symbol SLR ± SD (n=9) SLR ± SD (n=4) SLR ± SD (n=9) Y+Cx ± SD Cx V ± SD Cx I-VI ± SD 1455913_x_at transthyretin Ttr 4.07 ± 0.54 1.92 ± 1.84 1.17 ± 1.83 1425466_at RIKEN cDNA 4930538C18 gene 4930538C18Rik 2.55 ± 1.36 -0.51 ± 0.76 0.00 ± 0.35 1434544_at RIKEN cDNA 1110025L05 gene 1110025L05Rik 1.18 ± 0.74 -0.01 ± 0.13 0.13 ± 0.33 1433570_s_at RIKEN cDNA C030004C14 gene C030004C14Rik 0.88 ± 0.88 -0.18 ± 0.44 0.12 ± 0.32 1424443_at transmembrane 6 superfamily member 1 Tm6sf1 0.72 ± 0.52 -0.11 ± 0.09 0.27 ± 0.28 1427183_at epidermal growth factor-containing fibulin-like extracellular matrix protein 1 Efemp1 0.72 ± 0.21 0.02 ± 0.23 0.40 ± 0.24 1454064_a_at ring finger protein 138 Rnf138 0.72 ± 0.53 0.19 ± 0.28 -0.04 ± 0.20 1417002_at RIKEN cDNA 0610012G03 gene 0610012G03Rik 0.71 ± 0.44 -0.13 ± 0.18 0.08 ± 0.22 1418188_a_at RIKEN cDNA 2210401K01 gene 2210401K01Rik 0.68 ± 0.37 0.31 ± 0.33 -0.90 ± 1.11 1451317_at RIKEN cDNA 9430020E02 gene 9430020E02Rik 0.68 ± 0.32 -0.14 ± 0.44 0.34 ± 0.40 1417972_s_at RIKEN cDNA 1500019J17 gene 1500019J17Rik 0.65 ± 0.34 0.09 ± 0.25 -0.04 ± 0.11 1436064_x_at ribosomal protein S24 Rps24 0.65 ± 0.39 -0.13 ± 0.09 -0.23 ± 0.22 1438403_s_at RIKEN cDNA 2210401K01 gene 2210401K01Rik 0.64 ± 0.36 0.90 ± 0.48 -1.42 ± 1.15 1424018_at histidine triad nucleotide binding protein Hint 0.63 ± 0.43 -0.06 ± 0.02 0.01 ± 0.25 1416427_at cyclin I Ccni 0.62 ± 0.28 0.44 ± 0.42 -0.15 ± 0.37 1433611_s_at Mus musculus expressed sequence C77604, mRNA (cDNA clone IMAGE:3594956), conta --- 0.61 ± 0.29 0.02 ± 0.29 -0.10 ± 0.08 1451780_at B-cell linker Blnk 0.61 ± 0.46 0.14 ± 0.35 0.29 ± 0.31 1428530_x_at ribosomal protein S24 Rps24 0.60 ± 0.45 -0.11 ± 0.07 -0.15 ± 0.26 1419441_at acidic ribosomal phosphoprotein P0 Arbp 0.59 ± 0.24 -0.04 ± 0.47 0.06 ± 0.14 1420502_at spermidine/spermine N1-acetyl transferase 1 Sat1 0.59 ± 0.42 0.07 ± 0.34 0.02 ± 0.25 1416245_at RIKEN cDNA 0610033H09 gene 0610033H09Rik 0.58 ± 0.30 -0.08 ± 0.28 -0.02 ± 0.16 1434543_a_at RIKEN cDNA 1110025L05 gene 1110025L05Rik 0.58 ± 0.30 0.25 ± 0.41 0.16 ± 0.19 1415753_at cDNA sequence BC005632 BC005632 0.56 ± 0.53 0.03 ± 0.41 0.34 ± 0.12 1416834_x_at NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2 Ndufb2 0.56 ± 0.33 -0.05 ± 0.10 -0.12 ± 0.39 1450150_a_at ribosomal protein L13 Rpl13 0.55 ± 0.32 -0.60 ± 0.56 -0.09 ± 0.36 1452184_at NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9 Ndufb9 0.55 ± 0.19 -0.13 ± 0.20 -0.02 ± 0.35 1453362_x_at ribosomal protein S24 Rps24 0.55 ± 0.45 -0.08 ± 0.20 -0.20 ± 0.36 1459890_s_at RIKEN cDNA 1110008P14 gene 1110008P14Rik 0.54 ± 0.33 -0.28 ± 0.28 -0.06 ± 0.16 1424698_s_at grancalcin Gca 0.53 ± 0.10 0.10 ± 0.38 -0.09 ± 0.30 1428322_a_at NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10 Ndufb10 0.53 ± 0.22 0.00 ± 0.14 -0.14 ± 0.13 1426271_at SMC5 structural maintenance of chromosomes 5-like 1 (yeast) Smc5l1 0.51 ± 0.38 0.05 ± 0.14 -0.19 ± 0.16 1426477_at RAS p21 protein activator 1 Rasa1 0.51 ± 0.24 -0.37 ± 0.32 -0.09 ± 0.20 1448540_a_at RIKEN cDNA 0610012G03 gene 0610012G03Rik 0.51 ± 0.32 -0.15 ± 0.11 0.20 ± 0.15 1416971_at cytochrome c oxidase, subunit VIIa 2 Cox7a2 0.50 ± 0.19 0.07 ± 0.06 -0.05 ± 0.31 1416026_a_at ribosomal protein L12 Rpl12 0.48 ± 0.37 0.05 ± 0.09 -0.02 ± 0.22 1449556_at histocompatibility 2, T region locus 23 H2-T23 0.48 ± 0.27 -0.75 ± 0.39 -0.05 ± 0.35 1416698_a_at CDC28 protein kinase 1 Cks1 0.47 ± 0.28 0.03 ± 0.45 0.38 ± 0.34 1427351_s_at immunoglobulin heavy chain 6 (heavy chain of IgM) Igh-6 0.47 ± 0.12 -0.18 ± 0.23 -0.25 ± 0.16 1428127_at Mus musculus LOC382423 (LOC382423), mRNA --- 0.47 ± 0.25 0.16 ± 0.58 0.21 ± 0.17 1430326_s_at RIKEN cDNA 1500040F11 gene 1500040F11Rik 0.47 ± 0.21 -0.07 ± 0.10 0.02 ± 0.24 1448274_at complement component 1, q subcomponent binding protein C1qbp 0.47 ± 0.32 -0.05 ± 0.22 0.05 ± 0.11 1448739_x_at ribosomal protein S18 Rps18 0.47 ± 0.15 0.30 ± 0.13 -0.06 ± 0.12 1438723_a_at RIKEN cDNA 2210402A09 gene Rps10 0.46 ± 0.24 -0.16 ± 0.10 -0.07 ± 0.22 1416269_at ATP synthase, H+ transporting, mitochondrial F0 complex, subunit f, isoform 2 Atp5j2 0.45 ± 0.23 -0.06 ± 0.12 -0.05 ± 0.18 1417879_at RIKEN cDNA 1110060M21 gene 1110060M21Rik 0.45 ± 0.44 -0.22 ± 0.08 -0.07 ± 0.17 1423442_a_at F-box and WD-40 domain protein 2 Fbxw2 0.45 ± 0.25 -0.35 ± 0.25 0.03 ± 0.29 1438001_x_at deleted in polyposis 1 Dp1 0.45 ± 0.15 0.01 ± 0.31 -0.02 ± 0.13 1448685_at RIKEN cDNA 2900010M23 gene 2900010M23Rik 0.45 ± 0.28 0.01 ± 0.14 -0.26 ± 0.14 1456497_x_at RIKEN cDNA 2210402A09 gene Rps10 0.45 ± 0.13 -0.19 ± 0.14 -0.12 ± 0.16 1415859_at RIKEN cDNA 3230401O13 gene 3230401O13Rik 0.44 ± 0.24 0.27 ± 0.44 -0.04 ± 0.31 1416719_a_at RIKEN cDNA 2210402A09 gene Rps10 0.44 ± 0.23 -0.15 ± 0.11 0.00 ± 0.38 1448952_at RIKEN cDNA A030009H04 gene A030009H04Rik 0.44 ± 0.16 -0.14 ± 0.33 -0.08 ± 0.18 1452919_a_at RIKEN cDNA 1700012G19 gene 1700012G19Rik 0.44 ± 0.16 -0.27 ± 0.18 0.06 ± 0.33 1416519_at ribosomal protein L36 Rpl36 0.43 ± 0.19 -0.21 ± 0.10 -0.01 ± 0.25 1418439_at RIKEN cDNA 2900055D03 gene 2900055D03Rik 0.43 ± 0.25 -0.09 ± 0.21 -0.20 ± 0.13 1419543_a_at Mus musculus similar to splicing factor, arginine/serine-rich (transformer 2 Drosophila homo--- 0.43 ± 0.25 0.06 ± 0.35 -0.04 ± 0.38 1423090_x_at Mus musculus transcribed sequence with strong similarity to protein sp:P38384 (H.sapiens --- 0.43 ± 0.16 0.24 ± 0.24 -0.24 ± 0.14 1423113_a_at ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast) Ube2d3 0.43 ± 0.35 0.09 ± 0.11 0.01 ± 0.05 1435712_a_at Mus musculus transcribed sequence with strong similarity to protein ref:NP_072045.1 (H.sa--- 0.43 ± 0.15 0.32 ± 0.21 0.00 ± 0.16 1423281_at stathmin-like 2 Stmn2 0.42 ± 0.14 -0.13 ± 0.27 -0.03 ± 0.27 1448527_at programmed cell death 10 Pdcd10 0.42 ± 0.28 -0.07 ± 0.43 -0.02 ± 0.18 1454627_a_at --- --- 0.42 ± 0.14 0.14 ± 0.19 -0.03 ± 0.12 1455572_x_at Mus musculus transcribed sequence with strong similarity to protein ref:NP_072045.1 (H.sa--- 0.42 ± 0.08 0.08 ± 0.28 -0.01 ± 0.15 1448447_at vacuolar protein sorting 28 (yeast) Vps28 0.41 ± 0.22 0.06 ± 0.11 0.05 ± 0.12 1416938_at RIKEN cDNA 1110001O19 gene 1110001O19Rik 0.40 ± 0.12 -0.20 ± 0.15 -0.02 ± 0.19 1416970_a_at cytochrome c oxidase, subunit VIIa 2 Cox7a2 0.40 ± 0.12 0.08 ± 0.06 -0.03 ± 0.23 1428360_x_at NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7 (B14.5a) Ndufa7 0.40 ± 0.14 0.15 ± 0.24 -0.10 ± 0.23 1442169_at very low density lipoprotein receptor Vldlr 0.40 ± 0.33 0.38 ± 0.13 0.10 ± 0.32 1416219_at ribosomal protein L19 Rpl19 0.39 ± 0.18 0.17 ± 0.29 0.04 ± 0.11 1416603_at ribosomal protein L22 Rpl22 0.39 ± 0.19 0.04 ± 0.05 -0.04 ± 0.33 1421477_at complexin 2 Cplx2 0.39 ± 0.25 0.21 ± 0.65 0.72 ± 1.08 1448427_at NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6 (B14) Ndufa6 0.39 ± 0.29 -0.41 ± 0.24 -0.09 ± 0.33 1416217_a_at ribosomal protein L37a Rpl37a 0.37 ± 0.08 0.07 ± 0.35 -0.25 ± 0.31 1434854_a_at Mus musculus similar to 40S ribosomal protein S10 (LOC385608), mRNA --- 0.37 ± 0.10 -0.15 ± 0.08 -0.11 ± 0.14 1438317_a_at endonuclease G Endog 0.37 ± 0.17 0.06 ± 0.25 0.04 ± 0.18 1460180_at hexosaminidase B Hexb 0.37 ± 0.61 -0.22 ± 0.18 0.02 ± 0.05 1416567_s_at ATP synthase, H+ transporting, mitochondrial F1 complex, epsilon subunit Atp5e 0.36 ± 0.19 -0.02 ± 0.09 -0.16 ± 0.27 1416635_at sphingomyelin phosphodiesterase, acid-like 3A Smpdl3a 0.36 ± 0.35 -0.11 ± 0.18 0.13 ± 0.14 1453729_a_at ribosomal protein L37 Rpl37 0.36 ± 0.20 0.22 ± 0.34 -0.03 ± 0.17 1416616_s_at caseinolytic protease, ATP-dependent, proteolytic subunit homolog (E. coli) Clpp 0.35 ± 0.22 -0.22 ± 0.13 0.08 ± 0.13 1426871_at RIKEN cDNA 5730501N20 gene 5730501N20Rik 0.35 ± 0.40 -0.26 ± 0.13 -0.05 ± 0.23 1422609_at expressed sequence AW559096 AW559096 0.34 ± 0.25 0.13 ± 0.15 -0.09 ± 0.11 1423615_at zinc finger protein 364 Zfp364 0.34 ± 0.20 0.06 ± 0.12 0.06 ± 0.21 1433472_x_at RIKEN cDNA 0610025G13 gene 0610025G13Rik 0.34 ± 0.05 0.07 ± 0.07 -0.04 ± 0.24 1434823_x_at RIKEN cDNA 1110002M09 gene 1110002M09Rik 0.34 ± 0.11 -0.06 ± 0.07 -0.09 ± 0.34 1437706_x_at --- --- 0.34 ± 0.09 0.11 ± 0.10 -0.12 ± 0.17 1438164_x_at flotillin 2 Flot2 0.34 ± 0.12 0.27 ± 0.20 0.27 ± 0.27 1448112_at cytochrome c oxidase, subunit VIIc Cox7c 0.34 ± 0.14 0.22 ± 0.16 -0.16 ± 0.26 1450925_a_at ribosomal protein S27-like Rps27l 0.34 ± 0.28 -0.03 ± 0.24 -0.16 ± 0.22 1460214_at Purkinje cell protein 4 Pcp4 0.34 ± 0.19 -0.06 ± 0.05 -0.18 ± 0.22 1436586_x_at ribosomal protein S14 Rps14 0.33 ± 0.10 0.14 ± 0.09 -0.19 ± 0.23 1437013_x_at ATPase, H+ transporting, V0 subunit B Atp6v0b 0.33 ± 0.15 0.06 ± 0.20 0.14 ± 0.27 1423461_a_at ubiquitin-like 3 Ubl3 0.32 ± 0.27 -0.27 ± 0.30 -0.06 ± 0.14 1433486_at chloride channel 3 Clcn3 0.32 ± 0.35 0.04 ± 0.16 -0.07 ± 0.13 1436803_a_at NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9 Ndufb9 0.31 ± 0.10 0.08 ± 0.19 -0.06 ± 0.13 1448528_at programmed cell death 10 Pdcd10 0.31 ± 0.13 0.08 ± 0.17 0.02 ± 0.14 1439466_s_at RIKEN cDNA 1110069M14 gene 1110069M14Rik 0.30 ± 0.04 0.10 ± 0.11 0.03 ± 0.12 1436995_a_at Mus musculus ribosomal protein L26 (Rpl26), mRNA --- 0.29 ± 0.09 0.13 ± 0.07 -0.12 ± 0.20 1418189_s_at RIKEN cDNA 2210401K01 gene 2210401K01Rik 0.26 ± 0.27 -0.07 ± 0.54 -0.70 ± 0.74 1433474_at EGF-like repeats and discordin I-like domains 3 Edil3 0.24 ± 0.54 0.05 ± 0.39 0.04 ± 0.23 1448307_at Down syndrome critical region homolog 2 (human) Dscr2 0.19 ± 0.56 -0.10 ± 0.48 0.23 ± 0.26 1448245_at laminin receptor 1 (ribosomal protein SA) Lamr1 0.16 ± 0.20 0.11 ± 0.14 -0.09 ± 0.24 1453731_a_at RIKEN cDNA 2610318G18 gene 2610318G18Rik 0.14 ± 0.46 0.27 ± 0.25 0.08 ± 0.24 yellow = Ribosomal function red = Mitochondrial function green gene symbol = in-situ data available at www.brain-map.org Supplementary Table 3 1 Y+SSCx upregulated over Y+MCx (Change call ≥ 66%; average change p-value of all D/MD calls I) Signal / Detection 77 Probe Avg.