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Supplementary Table 2. List of Outlier Genes Identified by Comparing L5

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Supplementary Table 2. List of outlier genes identified by comparing L5 nerve root ligation (LR) and L5 spinal nerve transection (L5tx) lumbar spinal cord gene expression to corresponding sham operated controls at 7 days post-surgery. Color coding corresponds to Fig. 2 1. LR Specific Outlier Genes Ratio Probe Set ID Gene Title LR/Sham 1370810_at Cyclin D2 2.96 1368081_at ATP-binding cassette, sub-family A (ABC1), member 2 2.12 1388541_at EST 1.94 1370209_at basic transcription element binding protein 1 1.89 1398883_at heterogeneous nuclear ribonucleoprotein A2/B1 (predicted) 1.83 1388271_at EST 1.77 1371541_at Similar to Mylk protein 1.71 1373224_at Alpha-2,3-sialyltransferase ST3Gal IV 1.67 1388689_at EST 1.66 CD74 antigen (invariant polpypeptide of major histocompatibility class II 1367679_at 1.63 antigen-associated) 1367846_at S100 calcium-binding protein A4 1.61 1373862_at EST 1.60 1389452_at EST 1.60 1398385_at EST 1.60 1374939_at Similar to p53 inducible protein 1.58 similar to ataxin 2-binding protein 1 isoform 1; hexaribonucleotide binding 1377095_at 1.55 protein 1 1388284_at keratin associated protein 3-1 (predicted) 1.53 1375349_at Similar to sorbin and SH3 domain containing 1 1.53 1389147_at EST 1.52 1372812_at EST 1.50 1398757_at nucleophosmin 1 1.50 1375674_at similar to chromosome 16 open reading frame 5 (predicted) 1.50 1377114_at EST 1.47 1399096_at Adducin 3 (gamma) 1.46 1387909_at abl-interactor 2 1.45 1388983_at EST 1.45 1372947_at EST 1.44 1371890_at Arginine-glutamic acid dipeptide (RE) repeats 1.44 1375144_at Tissue inhibitor of metalloproteinase 2 1.43 1392453_at chloride channel 3 1.43 1394166_at EST 1.43 1375519_at similar to alpha globin 1.42 1388500_at EST 1.42 1373195_at fusion (involved in t(12;16) in malignant liposarcoma) (predicted) 1.42 1386514_at EST 1.42 1367934_at ribosomal protein L39 1.41 1388076_at PAI-1 mRNA-binding protein 1.40 1367637_a_at protein phosphatase 1, catalytic subunit, gamma isoform 1.40 1367497_at phosphatidylserine synthase 1 (predicted) 1.39 1390461_at EST 1.38 1398767_at ubiquitin C 1.38 1370070_at synaptojanin 1 1.38 1367576_at EST 1.38 1369953_a_at CD24 antigen 1.38 1387015_at profilin 2 1.38 1375424_at EST 1.37 1371550_at similar to TSC-22-like (predicted) 1.36 1374635_at EST 1.35 1387856_at calponin 3, acidic 1.34 1367783_at GABA(A) receptor-associated protein like 2 1.33 1399097_at EST 1.33 1375032_at EST 1.33 1367562_at secreted acidic cysteine rich glycoprotein 1.33 1367771_at delta sleep inducing peptide, immunoreactor 1.32 1385868_at EST 1.32 1371434_at EST 1.32 1383162_at EST 1.31 1372002_at gap junction membrane channel protein alpha 1 1.30 Similar to synaptophysin-like protein; pantophysin; Pan I; DNA segment, Chr 1372474_at 1.30 12, ERATO Doi 446, expressed 1368105_at tetraspan 2 1.30 1368511_at basic helix-loop-helix domain containing, class B3 1.29 1398775_at ribosomal protein S15a 1.29 1368504_at lysosomal membrane glycoprotein 1 1.29 1370545_at potassium voltage-gated channel, shaker-related subfamily, member 1 1.29 1367453_at cell division cycle 37 homolog (S. cerevisiae) 1.29 1389221_at Similar to monocyte-to-macrophage differentiation factor 2 1.29 1372080_at inner membrane protein, mitochondrial (predicted) 1.29 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 10 /// NADH 1389334_at 1.28 dehydrogenase 1 alpha subcomplex 10-like protein 1367898_at BCL2/adenovirus E1B 19 kDa-interacting protein 3-like 1.28 1367460_at GDP dissociation inhibitor 2 1.28 myosin, light polypeptide 6, alkali, smooth muscle and non-muscle 1371304_a_at 1.27 (predicted) 1368806_at selenoprotein P, plasma, 1 1.27 1379371_at EST 1.27 1389556_at kinesin-associated protein 3 (predicted) 1.26 1388615_at Ras-related protein RAP-1A 1.26 1372484_at EST 1.26 1371419_at spectrin beta 2 1.26 1368384_at kallikrein 6 1.26 1367476_at signal recognition particle 14 (predicted) 1.26 1398782_at EST 1.25 1371352_at high mobility group protein 17 1.25 1388997_at ADP-ribosylation factor 3 1.25 1370825_a_at cell division cycle 42 homolog (S. cerevisiae) 1.24 1367929_at EST 1.24 1372953_at Similar to neurocalcin delta 1.24 1388159_at EST 1.23 1389586_at EST 1.23 1373133_at EST 1.23 1370866_at ribosomal protein L41 1.23 1375295_at Citrate synthase 1.22 1370243_a_at prothymosin alpha 1.22 1368402_at dynein, cytoplasmic, light intermediate polypeptide 2 1.22 1371694_at dihydropyrimidinase-like 2 1.22 1375108_at EST 1.21 sirtuin 2 (silent mating type information regulation 2, homolog) 2 (S. 1375413_at 1.21 cerevisiae) 1398333_at Endothelial PAS domain protein 1 1.21 1371618_s_at tubulin, beta 3 1.21 1384178_at EST 1.20 1387890_at ribosomal protein S29 1.20 1387040_at myelin and lymphocyte protein 1.20 1370334_at evectin-1 1.19 1376577_at EST 1.19 1371334_at integral membrane protein 2C (predicted) 1.19 1386874_at ribosomal protein S15 1.18 1399012_at EST 1.18 1371798_at Guanine nucleotide binding protein, alpha 12 1.18 1368701_at ATPase, Na+/K+ transporting, alpha 3 polypeptide 1.18 1398764_at ribosomal protein L21 1.18 1388995_at EST 1.18 1389820_at EST 1.17 1389957_at EST 1.17 1398330_at syntaxin binding protein 1 1.17 1398762_at syndecan binding protein 1.17 1372701_at heat shock protein 1, alpha 1.16 1367617_at aldolase A 1.16 1371319_at integral membrane protein 2B 1.16 1372707_at RAB6, member RAS oncogene family 1.16 1386921_at carboxypeptidase E 1.15 1371507_at Similar to 4921517L17Rik protein 1.15 1387897_at Cyclic nucleotide phosphodiesterase 1 1.15 1371327_a_at similar to gamma actin-like protein /// similar to put. type 5 nonmuscle actin 1.15 1370434_a_at myelin-associated oligodendrocytic basic protein 1.15 1370246_at calmodulin 2 1.14 1372542_at EST 1.13 1369897_s_at GNAS complex locus /// XLas protein 1.13 1388303_at ribosomal protein L26 (predicted) 1.12 1386937_at ATPase, Na+/K+ transporting, beta 1 polypeptide 1.11 1375651_at EST 1.10 1367557_s_at glyceraldehyde-3-phosphate dehydrogenase 1.10 1370803_at ZW10 interactor 1.10 1368810_a_at myelin basic protein 1.08 1367653_a_at malate dehydrogenase 1, NAD (soluble) -1.00 1371301_at ribosomal protein L9 -1.00 1370862_at apolipoprotein E -1.00 1375336_at heat shock 90kDa protein 1, beta -1.00 1367625_at EST -1.01 1370156_at prion protein -1.01 1367799_at statin-like -1.02 1368211_at ribosomal protein S14 /// similar to RIKEN cDNA 1810007P19 (predicted) -1.02 1376711_at Claudin 11 -1.02 1371682_at microtubule-associated protein 1 light chain 3 alpha -1.03 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, 1398851_at -1.03 epsilon polypeptide 1386852_x_at polyubiquitin -1.03 1398917_at ribosomal protein L7 -1.03 1388039_a_at gamma-aminobutyric acid (GABA) B receptor 1 -1.03 1375861_at EST -1.03 1367560_at acidic ribosomal phosphoprotein P0 -1.04 solute carrier family 25 (mitochondrial carrier; adenine nucleotide 1388163_at -1.04 translocator), member 5 1367634_at ribosomal protein L31 -1.05 1371761_at ribosomal protein L34 (predicted) -1.05 1371956_at EST -1.06 1371607_at Microtubule-associated protein 4 -1.06 1398761_at ribosomal protein L5 -1.06 glutamate receptor, ionotropic, N-methyl D-asparate-associated protein 1 1372724_at -1.06 (glutamate binding) 1398326_at similar to Nur77 downstream protein 2 -1.06 1387291_at inter-alpha trypsin inhibitor, heavy chain 3 -1.06 1369933_at voltage-dependent anion channel 2 -1.06 1369930_at proteasome (prosome, macropain) subunit, alpha type 6 -1.06 1367645_at ribosomal protein S17 -1.07 1367882_at microtubule-associated protein 1 A -1.07 1371415_at ubiquinol-cytochrome c reductase hinge protein (predicted) -1.07 1372249_at Ac1254 -1.07 1368098_a_at small nuclear ribonucleoprotein N -1.07 1398749_at ribosomal protein L4 -1.08 1370179_at dynein, cytoplasmic, light chain 2A -1.08 1370184_at cofilin 1 -1.08 1386858_at ribosomal protein L13 -1.08 1367721_at syndecan 4 -1.08 1367845_at neurofilament 3, medium -1.08 1370888_at cytochrome c oxidase, subunit Va -1.09 1371702_at Transmembrane 4 superfamily member 2 -1.09 1373255_at EST -1.09 gamma-aminobutyric acid (GABA(A)) receptor-associated protein-like 1 1371680_at -1.10 (predicted) 1369065_a_at ATPase, Ca++ transporting, cardiac muscle, slow twitch 2 -1.10 1372193_at EST -1.10 1388586_at synaptojanin 1 -1.10 1367773_at solute carrier family 25, member 1 -1.11 1370230_at ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F6 -1.11 1388795_at EST -1.11 1387861_at amino-terminal enhancer of split -1.11 1367708_a_at fatty acid synthase -1.11 1375245_at EST -1.11 1387910_at erythrocyte protein band 4.1-like 1 -1.12 1371671_at Similar to orphan G protein-coupled receptor -1.13 1387887_at ribosomal protein L14 -1.13 1389120_at potassium voltage gated channel, Shaw-related subfamily, member 3 -1.13 1369609_at claudin 11 -1.13 1369085_s_at small nuclear ribonucleoprotein N /// SNRPN upstream reading frame -1.14 1388196_at NCK-associated protein 1 -1.14 1368101_at calmodulin 3 -1.14 1398863_at guanine nucleotide binding protein, beta polypeptide 2 -1.15 1375305_at LOC362256 -1.15 1386859_at transketolase -1.15 1387653_at translin-associated factor X -1.15 1370693_a_at cyclic nucleotide phosphodiesterase 1 -1.16 1388300_at microsomal glutathione S-transferase 3 (predicted) -1.16 Similar to UNR-interacting protein (Serine-threonine kinase receptor- 1372077_at -1.17 associated protein) 1367669_a_at microtubule-associated proteins 1A/1B light chain 3 -1.17 1367589_at aconitase 2, mitochondrial -1.18 1368853_at visinin-like 1 -1.19 1388851_at heat shock protein, A (predicted) -1.19 1390714_at Eukaryotic translation initiation
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    Product description version C1-01; Issued 19 March 2021 Product Description SALSA® MS-MLPA® Probemix ME031-C1 GNAS To be used with the MS-MLPA General Protocol. Version C1 As compared to version B2, probemix completely revised, details are shown in complete product history see page 11. Catalogue numbers: ME031-025R: SALSA MS-MLPA Probemix ME031 GNAS, 25 reactions. ME031-050R: SALSA MS-MLPA Probemix ME031 GNAS, 50 reactions. ME031-100R: SALSA MS-MLPA Probemix ME031 GNAS, 100 reactions. To be used in combination with a SALSA MLPA reagent kit, SALSA HhaI (SMR50) and Coffalyser.Net data analysis software. MLPA reagent kits are either provided with FAM or Cy5.0 dye-labelled PCR primer, suitable for Applied Biosystems and Beckman/SCIEX capillary sequencers, respectively (see www.mrcholland.com). Certificate of Analysis Information regarding storage conditions, quality tests, and a sample electropherogram from the current sales lot is available at www.mrcholland.com. Precautions and warnings For professional use only. Always consult the most recent product description AND the MS-MLPA General Protocol before use: www.mrcholland.com. It is the responsibility of the user to be aware of the latest scientific knowledge of the application before drawing any conclusions from findings generated with this product. This SALSA MS-MLPA probemix is intended for experienced MLPA users only! The exact link between the GNAS complex locus genotype and phenotype is still being investigated. Use of this ME031 GNAS probemix will not always provide you with clear-cut answers and interpretation of results can therefore be complicated. MRC Holland can only provide limited support with interpretation of results obtained with this product, and recommends thoroughly screening any available literature.
  • Functional Characterisation of Human Synaptic Genes Expressed in the Drosophila Brain Lysimachos Zografos1,2, Joanne Tang1, Franziska Hesse3, Erich E

    Functional Characterisation of Human Synaptic Genes Expressed in the Drosophila Brain Lysimachos Zografos1,2, Joanne Tang1, Franziska Hesse3, Erich E

    © 2016. Published by The Company of Biologists Ltd | Biology Open (2016) 5, 662-667 doi:10.1242/bio.016261 METHODS & TECHNIQUES Functional characterisation of human synaptic genes expressed in the Drosophila brain Lysimachos Zografos1,2, Joanne Tang1, Franziska Hesse3, Erich E. Wanker3, Ka Wan Li4, August B. Smit4, R. Wayne Davies1,5 and J. Douglas Armstrong1,5,* ABSTRACT systems biology approaches are likely to be the best route to unlock a Drosophila melanogaster is an established and versatile model new generation of neuroscience research and CNS drug organism. Here we describe and make available a collection of development that society so urgently demands (Catalá-López transgenic Drosophila strains expressing human synaptic genes. The et al., 2013). Yet these modelling type approaches also need fast, collection can be used to study and characterise human synaptic tractable in vivo models for validation. genes and their interactions and as controls for mutant studies. It was More than 100 years after the discovery of the white gene in generated in a way that allows the easy addition of new strains, as well Drosophila melanogaster, the common fruit fly remains a key tool as their combination. In order to highlight the potential value of the for the study of neuroscience and neurobiology. The fruit fly collection for the characterisation of human synaptic genes we also genome is well annotated and there is a vast genetic manipulation use two assays, investigating any gain-of-function motor and/or toolkit available. This allows interventions such as high throughput cognitive phenotypes in the strains in this collection. Using these cloning (Bischof et al., 2013; Wang et al., 2012) and the precise assays we show that among the strains made there are both types of insertion of transgenes in the genome (Groth et al., 2004; Venken gain-of-function phenotypes investigated.