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Supporting Information for Proteomics DOI 10.1002/Pmic.200500243

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Supporting Information for Proteomics DOI 10.1002/pmic.200500243 Gustavo A. de Souza, Lyris M. F. Godoy, Veronica R. Teixeira, Andreia H. Otake, Ado Sabino, Jos C. Rosa, Anemari R. Dinarte, Daniel G. Pinheiro, Wilson A. Silva, Jr., Marcos N. Eberlin, Roger Chammas and Lewis J. Greene Proteomic and SAGE profiling of murine melanoma progression indicates the reduction of proteins responsible for ROS degradation ª 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com Genes Up-regulated in Tm1 Difference of Name Simbol Tag Frequence Expression Synaptotagmin 4 syt4 60.55 AATAAACTGC 65 S100 calcium binding protein A11 (calizzarin) s100a11 37.61 TATCCCACGC 41 Channel-interacting PDZ domain protein cipp 33.94 TGCCAAGGGT 444 Solute carrier family 25 (mitochondrial carrier, adenine nucleotide slc25a13 29.36 GTCAGAGGCT 32 translocator), member 13 Gamma-aminobutyric acid (GABA-A) receptor, subunit delta gabrd 28.44 ACACCAAAAA 31 apoliprotein E apoe 20.18 CATCGCCAGT 44 cytochrome b5 cyb5 12.75 GTGATGTTTC 139 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4 ndufa4 12.08 TTGATTTTTT 79 tubulin, beta 5 tubb5 8.65 GCAGGCACTC 462 LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) lsm4 8.39 GTGGCTCACC 64 Tubulin, alpha 1 tuba1 8.26 GCTGCCCTAG 63 Nur77 downstream gene 2 ndg2 7.8 TGACTGGGAG 32 calcyclin binding protein cacybp 6.97 ACGCGAAAAC 38 Nucleophosmin 1 npm1 6.73 TGAAATAAAC 132 Similar to hypothetical protein MGC955 BC035522 5.96 GTGGCTAACA 52 secreted acidic cysteine rich glycoprotein sparc 5.5 CAAACTCTCA 375 Small nuclear ribonucleoprotein polypeptide G snrpg 5.43 TACATTTTCA 77 mitochondrial ribosomal protein L33 mrpl33 5.35 GCCTCGGGGG 35 peptidylprolyl isomerase A ppia 5.12 GAGCGTTTTG 162 thymosin beta 10 tmsb10 4.97 GGGGAAATCG 103 Eukaryotic translation initiation factor 5 eif5 4.59 GAGGTTAACC 30 Leprecan-like 2 leprel2 4.46 GTGGCTCACA 2520 SEC61, gamma subunit sec61 4.38 AAGTAAAGCG 43 proteasome subunit, alpha type 7 psma7 4.19 AGGCGGGATC 32 Retinal S-antigen sag 4.13 ATGGCTCACA 36 Quininoid dihydropteridine reductase qdpr 4.02 TAAAAAAAAA 92 Creatine kinase, brain ckb 3.98 CATCCTTGAT 52 prolyl 4-hydroxylase, beta polypeptide p4hb 3.92 GCCTGTGGCC 47 minichromosome maintenance deficient 7 (Saccharomices cerevisae) mcm7 3.87 CTGCACTTTT 38 Ribosomal protein S3a rps3a 3.81 GGGAAGGCGG 158 lectin, galactose binding, soluble 1 lgals1 3.8 GCGGCGGATG 862 Xylosylprotein beta1,4-galactosyltransferase, polypeptide 7 b4galt7 3.79 TGGTTGCTGG 306 (galactosyltransferase I) ribosomal protein L35 rpl35 3,71 CGCCGCCGGC 296 cystatin E/M cst6 3.67 GTGGAGGCGC 36 enolase 1, alpha non-neuron eno1 3.58 CAAAAATAAA 351 Etoposide induced 2.4 mRNA ei24 3.56 GGTGGGGGGG 31 Poly(rC) binding protein 1 pcbp1 3.49 GATTTTATTT 38 expressed in non-metastatic cells 2, protein nme2 3.48 AAGAAACCAG 72 Eukaryotic translation initiation factor 4A1 eif4a1 3.44 GTGACCGAAG 30 LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) lsm5 3.44 GTTATTTTGG 30 Malic enzyme, supernatant mod1 3.44 TTGTCAGGTA 45 cytochrome c oxidase subunit VIIb cox7b 3.34 TACTCATTAT 80 diazepam binding inhibitor dbi 3.34 AAGACCTATG 40 Baculoviral IAP repeat-containing 1b birc1b 3.16 GTGGTTCACA 31 Transcribed locus, moderately similar to XP_342194.1 similar to GCAATCTGAT 275 Phosphoglycerate kinase, testis specific [Rattus norvegicus] pgk1 3.15 hypoxia induced gene 1 hig1 3.11 TGGGTTTAGA 44 RIO kinase 2 (yeast) riok2 3.04 TAATAAATAA 72 glucose phosphate isomerase 1 gpi1 3.01 GGGGCTCAGC 69 fatty acid binding protein 5, epidermal fabp5 2.96 TCAAACTTGG 213 Ectonucleoside triphosphate diphosphohydrolase 8 entpd8 2.95 GTAAAAAAA 122 Profilin 1 pfn1 2.94 GGCTGGGGGC 112 Matrilin 3 matn3 2.94 GCTGCCAGCA 32 Ribosomal protein S27a rps27a 2.93 GGAAGCCACT 354 heat shock protein 8 hspa8 2.92 GAATAATAAA 267 prothymosin alpha ptma 2.91 TTCATTATAA 54 D18Wsu98e 2.75 GCGAGGGAGC 75 DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 ddx5 2.75 GCCTTCCAAT 117 Cont. Genes Up-regulated in Tm1 Difference of Name Simbol Tag Frequence Expression Glyoxalase 1 glo1 2.67 TCATCTTCAG 32 ribosomal protein S4, X-linked rps4x 2.61 GTGAAACTAA 884 Tropomyosin 1, alpha tpm1 2.59 CCCGTAGCCC 31 ribosomal protein L36 rpl36 2.55 AGGAAGGCGG 453 nucleolar protein family A, member 3 nola3 2.54 CCAGGTTATT 61 carbonic anhydrase 6 car6 2.54 GTAGAGAGCT 105 ribosomal protein L17 rpl17 2.53 GCCCGGGAAT 375 Heat shock protein 1 (chaperonin 10) hspe1 2.5 CCTCCCTTTT 68 split hand/foot deleted gene 1 shfdg1 2.47 TTTATTTCAT 35 cytochrome c, somatic cycs 2.45 AATGGCTAGC 40 ribosomal protein, large, P1 rplp1 2.42 GGCTTCGGTC 1901 RNA polymerase 1-4 rpo1-4 2.38 GCTGGAACTG 57 heterogeneous nuclear ribonucleoprotein A1 hnrpa1 2.37 TGTACTCAAT 62 expressed in non-metastatic cells 1, protein nme1 2.36 GCAGCGATTC 36 ribosomal protein L31 rlp31 2.32 AAGGAAATGG 48 calnexin canx 2.29 TAACAGTTGT 70 Ribosomal protein 10 rpl10 2.27 GTTGCTGAGA 84 beta-glucuronidase gusb 2.26 CAAAATAAAA 59 Ribosomal protein L38 rpl38 2.24 CCTCGGAAAA 39 actin, gamma, cytoplasmic actg1 2.23 TGGCTCGGTC 51 ribosomal protein L11 rpl11 2.23 CGCTGGTTCC 187 eukaryotic translation elongation factor 1 beta 2 eef1b2 2.21 GATGTGGCTG 325 Cyclin D3 ccnd3 2.21 CTGCCTTAAT 82 NADH dehydrogenase (ubiquinone) Fe-S protein 1 ndufs1 2.2 TTAAAAAAAA 36 heat shock 70kD protein 5 (glucose-regulated protein) hspa5 2.18 TGGTGTAGGA 121 Tumor rejection antigen gp96 tra1 2.14 TGTATAAAAA 42 cyclin D1 ccnd1 2.12 GTCCAGGAAA 37 Esterase D/formylglutathione hydrolase esd 2.09 CTCCTGCAGC 50 Similar to 60S ribosomal protein L32 rpl32 2.07 GCTGCCCTCC 657 ATP synthase, H+ transporting, mitochondrial F0 complex, subunit f, atp5j2 2.07 GCCGAGCATA 52 isoform 2 ubiquitin-activating enzyme E1, Chr X ube1x 2.06 TAGCCAAGCC 45 ribosomal protein L4 rpl4 2.02 TGGTGACAAA 407 ribosomal protein L26 rpl26 2.02 TGGGCATCCA 128 Genes Down-regulated in Tm1 Difference of Name Simbol Tag Frequence Expression lectin, galactose binding, soluble 3 lgals3 300.84 CTGAGAGATA 300.84 metallothionein 2 mt2 14.06 TAACTGACAA 140.61 glutamate receptor, ionotropic, N-methyl D-asparate-associated grina 12.17 TTTCAAGGGA 146.06 protein 1 (glutamate binding) amyloid beta (A4) precursor protein app 9.34 ATAGCTTTCT 130.8 Phosphofructokinase, platelet pfkp 9.16 TGTATGTCTT 45.78 histone cell cycle regulation defective homolog A (S. cerevisiae) hira 8.99 CATTGGATAC 35.97 DNA-damage inducible transcript 3 ddit3 8.81 TCCAGTAAAG 105.73 Glycogenin 1 gyg1 8.28 CAGACTTGTT 41.42 Procollagen, type III, alpha 1 col3a1 7.32 TCTTCATTTA 102.46 Tetratricopeptide repeat domain 3 ttc3 7.19 CCTTACACTT 35.97 Eukaryotic translation initiation factor 1A, Y-linked eif1ay 6.54 TAGATAGCAT 32.70 Selenoprotein W, muscle 1 sepw1 5.81 TTTCCAGGTG 34.88 protease, serine, 15 prss15 5.67 AATAAAGAAA 56.68 Mitochondrial ribosomal protein L38 mrpl38 5.27 CTGGCCTCTC 31.61 arginine vasopressin-induced 1 avpi1 4.81 GCGTTCCTCT 81.75 LPS-induced TN factor litaf 4.67 ACTTTGATAT 32.70 cathepsin B ctsb 4.63 GTTTGCTGTG 37.06 zinc finger, DHHC domain containing 14 zdhhc14 4.47 TAGTTACTTA 44.69 Stress-70 protein, mitochondrial precursor hspa9a 4.32 GGCCTGAGGC 120.99 lectin, galactoside-binding, soluble, 3 binding protein lgals3bp 4.27 AGGTCCTGTG 51.23 deleted in polyposis 1 dp1 4.19 CTAGGGACAG 54.50 Fgfr1 oncogene partner fgfr1op 4.09 GCTCCAAGGA 32.70 Phosphoserine aminotransferase 1 psat1 3.89 GAAAACATTA 81.75 mitochondrial ribosomal protein S6 mrps6 3.82 ACTTTATCAA 38.15 Zinc finger protein 180 zfp180 3.82 GTACAAGGAA 30.52 MAF1 homolog (yeast) maf1 3.77 CACTGAGTGT 49.05 Activating transcription factor 4 atf4 3.72 TGTAAAGGAG 44.69 Rho/rac guanine nucleotide exchange factor (GEF) 2 arhgef2 3.63 AATGGATGCA 43.60 acetyl-Coenzyme A acyltransferase 1 acaa1 3.6 GGACACCCTG 35.97 protein phosphatase 1F (PP2C domain containing) ppm1f 3.54 GGGCCCTGTA 36.68 Macrophage erythroblast attacher maea 3.51 TTGATGTTGA 31.61 ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit atp5o 3.38 CGGGAGATGC 236.53 brevican bcan 3.33 TCAGCTGCCT 63.22 NADH dehydrogenase (ubiquinone) Fe-S protein 2 ndufs2 3.27 AACTAGAAAA 42.51 mitochondrial ribosomal protein L44 mrpl44 3.07 CCATATGTGA 33.79 lysyl-tRNA synthetase kars 3 CAACTATGGT 47.96 Alanyl-tRNA synthetase aars 3 TGCAATAAAA 107.91 calumenin calu 2.93 TCTATAGAGT 38.15 Lysosomal-associated protein transmembrane 4B laptm4b 2.88 TCTCTGAATG 40.33 basigin bsg 2.83 CTCTGACTTA 127.53 Tyrosinase-related protein 1 tyrp1 2.77 AAACTGCCTG 260.51 Adaptor-related protein complex 3, delta 1 subunit ap3d1 2.77 TGAAGAGAGA 30.52 protease 26S subunit, ATPase 5 psmc5 2.76 TCCATCAAGA 41.42 polymerase (RNA) II (DNA directed) polypeptide G polr2g 2.73 GAAATGTTGT 49.05 ATPase, H+ transporting, V1 subunit G isoform 1 atp6v1g1 2.73 TTTTTGGTGT 43.60 seryl-aminoacyl-tRNA synthetase 1 sars1 2.66 GAGGTCACTG 42.51 Dr1 associated protein 1 (negative cofactor 2 alpha) drap1 2.63 CTCTCTTCTA 44.69 DNA segment, Chr 8, ERATO Doi 325, expressed D8Ertd325e 2.6 TAGTCAGGGA 54.50 eukaryotic translation termination factor 1 etf1 2.57 CAACTTAAGT 35.97 Asparagine synthetase asns 2.56 AAAAGAAATA 74.12 Storage granule protein 23 gars 2.47 TCCACTACAC 37.06 psmd7 2.35 TATTGTTTAC 30.52 Golgi associated, gamma adaptin ear containing, ARF binding protein gga2 2.33 TGGTGACTAA 51.23 2 DNA segment, Chr 10, Wayne State University 52, expressed D10Wsu52e 2.32 CTATTAAATA 37.06 nischarin nisch 2.31 GGTCCAAGAG 39.24 Proteasome (prosome, macropain) 26S subunit, ATPase 3 psmc3 2.29 GAGGGCATCC 66.49 Superoxide dismutase 1, soluble sod1 2.26 AGAAACAAGA 31.61 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex,
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    Plant Pathology and Microbiology Publications Plant Pathology and Microbiology 5-2017 Differential Requirement of the Ribosomal Protein S6 and Ribosomal Protein S6 Kinase for Plant- Virus Accumulation and Interaction of S6 Kinase with Potyviral VPg Minna-Liisa Rajamäki University of Helsinki Dehui Xi Sichuan University Sidona Sikorskaite-Gudziuniene University of Helsinki Jari P. T. Valkonen University of Helsinki Follow this and additional works at: http://lib.dr.iastate.edu/plantpath_pubs StevePanr tA of. W thehithAgramicultural Science Commons, Agriculture Commons, Plant Breeding and Genetics CIowommona State Usn, iaverndsit they, swPhithlanatm@i Pathoastalote.geduy Commons The ompc lete bibliographic information for this item can be found at http://lib.dr.iastate.edu/ plantpath_pubs/211. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Plant Pathology and Microbiology at Iowa State University Digital Repository. It has been accepted for inclusion in Plant Pathology and Microbiology Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Differential Requirement of the Ribosomal Protein S6 and Ribosomal Protein S6 Kinase for Plant-Virus Accumulation and Interaction of S6 Kinase with Potyviral VPg Abstract Ribosomal protein S6 (RPS6) is an indispensable plant protein regulated, in part, by ribosomal protein S6 kinase (S6K) which, in turn, is a key regulator of plant responses to stresses and developmental cues. Increased expression of RPS6 was detected in Nicotiana benthamiana during infection by diverse plant viruses. Silencing of the RPS6and S6K genes in N.
  • Characterization of Gene Expression Phenotype in Amyotrophic Lateral Sclerosis Monocytes

    Characterization of Gene Expression Phenotype in Amyotrophic Lateral Sclerosis Monocytes

    Supplementary Online Content Zhao W, Beers DR, Hooten KG, et al. Characterization of Gene Expression Phenotype in Amyotrophic Lateral Sclerosis Monocytes. JAMA Neurol. Published online April 24, 2017. doi:10.1001/jamaneurol.2017.0357. eFigure 1. Principle Component Analysis (PAC) Indicates That Positive Selection Failed to Distinguish ALS and Control Monocyte Samples While Negative Selected ALS Monocytes Were Distinguishable From Control Monocytes. eFigure 2. Venn Diagram of Differentially Expressed Genes (DEGs) in Monocytes From ALS Slow and Fast Patients eFigure 3. IL-8 Protein Levels in Sera of ALS Patients and Healthy Controls. eTable 1. DEGs of Monocytes Isolated From Total ALS Patients (vs Control) eTable 2. Disease Progression of ALS Patients for RNA-seq Study Based on a Cutoff of 1.5 AALS Points/Month or a Cutoff of 1.0 ALS FRS Points/Month eTable 3. 65 DEGs Solely Found in Monocytes From Slowly Progressing ALS Patients (vs Control) eTable 4. 237 DEGs Solely Found in Monocytes From Rapidly Progressing ALS Patients (vs Control) eTable 5. 43 DEGs Expressed in Monocytes of Both Slow and Fast Groups (vs Control) This supplementary material has been provided by the authors to give readers additional information about their work. © 2017 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/27/2021 eFigure 1. Principle component analysis (PAC) indicates that positive selection failed to distinguish ALS and control monocyte samples while negative selected ALS monocytes were distinguishable from control monocytes. Monocytes by CD14+ monocytes by negative selection positive selection ALS monocytes by negative selection Control monocytes by negative selection ALS CD14+ monocytes by positive selection Control CD14+ monocytes by positive selection PAC represents the distribution of RNA expression data (FPKM) from positively selected CD14+ monocytes and Pan monocytes by negative selection.
  • Translation Initiation Factor Modifications and the Regulation of Protein Synthesis in Apoptotic Cells

    Translation Initiation Factor Modifications and the Regulation of Protein Synthesis in Apoptotic Cells

    Cell Death and Differentiation (2000) 7, 603 ± 615 ã 2000 Macmillan Publishers Ltd All rights reserved 1350-9047/00 $15.00 www.nature.com/cdd Translation initiation factor modifications and the regulation of protein synthesis in apoptotic cells ,1 1 1 2 MJ Clemens* , M Bushell , IW Jeffrey , VM Pain and Introduction SJ Morley2 Apoptosis is now recognized to be an important physiological 1 Department of Biochemistry and Immunology, Cellular and Molecular process by which cell and tissue growth, differentiation and Sciences Group, St George's Hospital Medical School, Cranmer Terrace, programmes of development are regulated. The molecular London SW17 ORE, UK mechanisms of apoptosis have been the subject of intense 2 Biochemistry Group, School of Biological Sciences, University of Sussex, research in recent years (for reviews see1±5). Cell death is Brighton BN1 9QG, UK induced following the stimulation of specific cell surface * Corresponding author: MJ Clemens, Department of Biochemistry and Immunology, Cellular and Molecular Sciences Group, St George's Hospital receptors such as the CD95 (Apo-1/Fas) antigen or the 6 Medical School, Cranmer Terrace, London SW17 ORE, UK. Tel: +44 20 8725 tumour necrosis factor-a (TNFa) receptor-1 (TNFR-1). It can 5770; Fax: +44 20 8725 2992; E-mail: [email protected] also result from intracellular events such as DNA damage or from a lack of specific growth factors. The relative importance Received 6.12.99; revised 25.1.00; accepted 20.3.00 of these different influences varies between cell types. The Edited by M Piacentini apoptotic process can be divided into a commitment phase and an execution phase.