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Supplementary Table S4 - Genes downregulated by anti-MYCN PNA ProbeID Symbol Description RH30ctrl_SignalRH30mut__SignalRH30pna_Signalpna vs mut pna vs ctrl 210842_at NRP2 neuropilin 2 109.8 83.2 3.4 -4.613 -5.013 219239_s_at ZNF654 zinc finger protein 654 155.9 140.8 6.8 -4.372 -4.519 220786_s_at SLC38A4 solute carrier family 38, member 4 91.8 135.1 17.7 -2.932 -2.375 206205_at MPHOSPH9 M-phase phosphoprotein 9 208.2 235.7 39.2 -2.588 -2.409 201171_at ATP6V0E ATPase, H+ transporting, lysosomal 9kDa, V0 subunit e 93.5 105 19.1 -2.459 -2.291 204732_s_at TRIM23 tripartite motif-containing 23 132.9 126.3 31 -2.027 -2.100 221079_s_at METTL2B methyltransferase like 2B 141.8 236.9 58.8 -2.010 -1.270 216971_s_at PLEC1 plectin 1, intermediate filament binding protein 500kDa 170 176.3 44.7 -1.980 -1.927 221703_at BRIP1 BRCA1 interacting protein C-terminal helicase 1 137 200.4 52.6 -1.930 -1.381 213647_at DNA2L DNA2 DNA replication helicase 2-like (yeast) 180.5 226.1 61.4 -1.881 -1.556 217547_x_at ZNF675 zinc finger protein 675 89.6 93.3 26 -1.843 -1.785 209865_at SLC35A3 solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3 191.6 171.3 50.4 -1.765 -1.927 AFFX-M27830_5_atSOX18 SRY (sex determining region Y)-box 18 755.4 982.7 295.8 -1.732 -1.353 212177_at C6orf111 chromosome 6 open reading frame 111 453.6 484.7 147.8 -1.713 -1.618 211088_s_at PLK4 polo-like kinase 4 (Drosophila) 174.6 122.1 37.4 -1.707 -2.223 213880_at LGR5 leucine-rich repeat-containing G protein-coupled receptor 5 172 178 56.2 -1.663 -1.614 201534_s_at UBL3 ubiquitin-like 3 948 900.4 287.1 -1.649 -1.723 219787_s_at ECT2 epithelial cell transforming sequence 2 oncogene 590.7 640.6 205.5 -1.640 -1.523 206852_at EPHA7 EPH receptor A7 287.7 292.6 97 -1.593 -1.569 201083_s_at BCLAF1 BCL2-associated transcription factor 1 338.7 405.8 135.5 -1.582 -1.322 204873_at PEX1 peroxisome biogenesis factor 1 349.9 487.7 164.2 -1.571 -1.091 214429_at MTMR6 myotubularin related protein 6 1213.5 830.9 291.5 -1.511 -2.058 200733_s_at PTP4A1 protein tyrosine phosphatase type IVA, member 1 1139.7 1289.3 457.9 -1.493 -1.316 201437_s_at EIF4E eukaryotic translation initiation factor 4E 1195.8 1312 466.3 -1.492 -1.359 40612_at DOPEY1 dopey family member 1 77.1 107.5 38.6 -1.478 -0.998 218772_x_at TMEM38B transmembrane protein 38B 489.4 505.1 181.4 -1.477 -1.432 221568_s_at LIN7C lin-7 homolog C (C. elegans) 1105.3 1300.6 468.9 -1.472 -1.237 204525_at PHF14 PHD finger protein 14 189.1 241 86.9 -1.472 -1.122 212930_at ATP2B1 ATPase, Ca++ transporting, plasma membrane 1 777.7 868.4 313.3 -1.471 -1.312 203078_at CUL2 cullin 2 166.1 155.6 56.2 -1.469 -1.563 213118_at KIAA0701 271 231.6 83.7 -1.468 -1.695 222250_s_at C1orf73 chromosome 1 open reading frame 73 355.3 397.8 144.4 -1.462 -1.299 215385_at FTO 175.8 214.3 78 -1.458 -1.172 205964_at ZNF426 zinc finger protein 426 267.5 242.9 88.7 -1.453 -1.593 214155_s_at LARP4 La ribonucleoprotein domain family, member 4 404 494 182.5 -1.437 -1.146 218649_x_at SDCCAG1 serologically defined colon cancer antigen 1 605.4 575.4 213 -1.434 -1.507 203791_at DMXL1 Dmx-like 1 188.6 145.4 53.9 -1.432 -1.807 32723_at CSTF1 cleavage stimulation factor, 3' pre-RNA, subunit 1, 50kDa 657.5 805.5 298.7 -1.431 -1.138 206770_s_at SLC35A3 solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3 280.9 282.6 104.9 -1.430 -1.421 215143_at FLJ36166 119.9 104.1 38.7 -1.428 -1.631 212927_at SMC5L1 SMC5 structural maintenance of chromosomes 5-like 1 (yeast) 475.4 534.7 199.8 -1.420 -1.251 203049_s_at KIAA0372 KIAA0372 711.6 769.9 288 -1.419 -1.305 215936_s_at KIAA1033 KIAA1033 433.1 333.5 125 -1.416 -1.793 212388_at USP24 ubiquitin specific peptidase 24 733.9 770.1 292.4 -1.397 -1.328 213049_at GARNL1 GTPase activating Rap/RanGAP domain-like 1 372.5 377 143.5 -1.394 -1.376 214306_at OPA1 optic atrophy 1 (autosomal dominant) 433.2 419.2 159.7 -1.392 -1.440 213225_at PPM1B protein phosphatase 1B (formerly 2C), magnesium-dependent, beta isoform 663.3 940.4 359.8 -1.386 -0.882 209314_s_at HBS1L HBS1-like (S. cerevisiae) 328.2 298.4 114.5 -1.382 -1.519 213372_at PAQR3 progestin and adipoQ receptor family member III 842.2 1211.4 466.3 -1.377 -0.853 212984_at ATF2 activating transcription factor 2 302.8 266.2 102.9 -1.371 -1.557 209551_at YIPF4 Yip1 domain family, member 4 383.1 367.1 142.7 -1.363 -1.425 218196_at OSTM1 osteopetrosis associated transmembrane protein 1 618 612.2 238.9 -1.358 -1.371 212060_at SR140 731.8 696.7 272.7 -1.353 -1.424 206555_s_at THUMPD1 THUMP domain containing 1 981.4 967.3 379.2 -1.351 -1.372 216609_at TXN thioredoxin 466.4 521.4 204.5 -1.350 -1.189 219439_at C1GALT1 core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1 389.1 501.4 197.4 -1.345 -0.979 205430_at BMP5 bone morphogenetic protein 5 567.9 552.6 217.7 -1.344 -1.383 209657_s_at HSF2 heat shock transcription factor 2 684.2 780.2 309.2 -1.335 -1.146 208653_s_at CD164 CD164 antigen, sialomucin 725.1 737.2 292.5 -1.334 -1.310 201151_s_at MBNL1 muscleblind-like (Drosophila) 343.1 385.9 153.3 -1.332 -1.162 210281_s_at ZNF198 zinc finger protein 198 220.9 200.5 80.2 -1.322 -1.462 215629_s_at KIAA1799 1369.5 1290.3 522 -1.306 -1.392 208883_at EDD1 E3 ubiquitin protein ligase, HECT domain containing, 1 316.1 338.6 137.2 -1.303 -1.204 218352_at RCBTB1 regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1 528.6 586.9 239.1 -1.296 -1.145 212569_at SMCHD1 structural maintenance of chromosomes flexible hinge domain containing 1 468.8 430.9 176.6 -1.287 -1.408 219625_s_at COL4A3BP collagen, type IV, alpha 3 (Goodpasture antigen) binding protein 391.7 334.4 137.4 -1.283 -1.511 210293_s_at SEC23B Sec23 homolog B (S. cerevisiae) 1138.4 878.3 362.2 -1.278 -1.652 220295_x_at DEPDC1 DEP domain containing 1 360.3 464.3 191.8 -1.275 -0.910 218578_at CDC73 cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae) 322.9 307.7 127.2 -1.274 -1.344 204342_at SLC25A24 solute carrier family 25 (mitochondrial carrier, phosphate carrier), member 24 1658.1 2225.4 924.6 -1.267 -0.843 212917_x_at FLJ22028 648.7 714.3 297.2 -1.265 -1.126 200841_s_at EPRS glutamyl-prolyl-tRNA synthetase 343.6 347.5 144.6 -1.265 -1.249 202259_s_at PFAAP5 778.2 821.2 343.3 -1.258 -1.181 203510_at MET met proto-oncogene (hepatocyte growth factor receptor) 2448.9 2994.1 1253.9 -1.256 -0.966 202034_x_at RB1CC1 RB1-inducible coiled-coil 1 357.2 391.2 164.1 -1.253 -1.122 59644_at BMP2K BMP2 inducible kinase 307.2 302.3 127.1 -1.250 -1.273 221749_at YTHDF3 YTH domain family, member 3 1406.8 1386 588.4 -1.236 -1.258 205122_at TMEFF1 transmembrane protein with EGF-like and two follistatin-like domains 1 739.3 1184.6 503.2 -1.235 -0.555 200685_at SFRS11 splicing factor, arginine/serine-rich 11 359.1 386.4 164.2 -1.235 -1.129 205091_x_at RECQL RecQ protein-like (DNA helicase Q1-like) 367.4 430.5 184.2 -1.225 -0.996 212417_at SCAMP1 secretory carrier membrane protein 1 311.2 292.9 125.8 -1.219 -1.307 203525_s_at APC adenomatosis polyposis coli 263.6 286.1 122.9 -1.219 -1.101 218311_at MAP4K3 mitogen-activated protein kinase kinase kinase kinase 3 700.3 892 383.9 -1.216 -0.867 214658_at TMED7 transmembrane emp24 protein transport domain containing 7 601 566.3 244.6 -1.211 -1.297 218875_s_at FBXO5 F-box protein 5 849.8 1005.6 435.9 -1.206 -0.963 202933_s_at YES1 v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1 3271.6 3247.5 1412 -1.202 -1.212 208296_x_at TNFAIP8 tumor necrosis factor, alpha-induced protein 8 509.4 559.1 243.4 -1.200 -1.065 215245_x_at FMR1 fragile X mental retardation 1 3125.6 4346.9 1901.8 -1.193 -0.717 203651_at ZFYVE16 zinc finger, FYVE domain containing 16 575.9 824.4 361.1 -1.191 -0.673 212179_at C6orf111 chromosome 6 open reading frame 111 1048.5 874.6 383.9 -1.188 -1.450 203970_s_at PEX3 peroxisomal biogenesis factor 3 335.8 347.5 152.6 -1.187 -1.138 214804_at FSHPRH1 FSH primary response (LRPR1 homolog, rat) 1 393.7 439.7 193.6 -1.183 -1.024 203276_at LMNB1 lamin B1 1675.9 2259.4 998.1 -1.179 -0.748 204832_s_at BMPR1A bone morphogenetic protein receptor, type IA 368.2 378.5 167.4 -1.177 -1.137 209681_at SLC19A2 solute carrier family 19 (thiamine transporter), member 2 763.5 901.4 398.9 -1.176 -0.937 221596_s_at DKFZP564O0523 257.2 249.7 110.6 -1.175 -1.218 209004_s_at FBXL5 F-box and leucine-rich repeat protein 5 1104.2 1251.6 557.3 -1.167 -0.986 212636_at QKI quaking homolog, KH domain RNA binding (mouse) 909.1 1235.2 550.1 -1.167 -0.725 213817_at 520.5 534 238.6 -1.162 -1.125 219631_at LRP12 low density lipoprotein-related protein 12 353.5 399.8 179.1 -1.159 -0.981 207719_x_at CEP170 centrosomal protein 170kDa 849.6 1085.7 487 -1.157 -0.803 203830_at C17orf75 chromosome 17 open reading frame 75 410.4 500.4 226.2 -1.145 -0.859 212138_at SCC-112 1312.7 1107.1 500.9 -1.144 -1.390 212526_at SPG20 spastic paraplegia 20, spartin (Troyer syndrome) 1076.8 1338.9 606.5 -1.142 -0.828 218490_s_at ZNF302 zinc finger protein 302 576.3 582.8 264.9 -1.138 -1.121 220327_at VGLL3 vestigial like 3 (Drosophila) 345.4 343 156.1 -1.136 -1.146 212420_at ELF1 E74-like factor 1 (ets domain transcription factor) 271.8 272.5 124.2 -1.134 -1.130 221931_s_at SEH1L SEH1-like (S.
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  • A Systematic Review on the Implications of O-Linked Glycan Branching and Truncating Enzymes on Cancer Progression and Metastasis

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    cells Review A Systematic Review on the Implications of O-linked Glycan Branching and Truncating Enzymes on Cancer Progression and Metastasis 1, 1, 1 1,2,3, Rohitesh Gupta y, Frank Leon y, Sanchita Rauth , Surinder K. Batra * and Moorthy P. Ponnusamy 1,2,* 1 Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68105, USA; [email protected] (R.G.); [email protected] (F.L.); [email protected] (S.R.) 2 Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 681980-5900, USA 3 Department of Pathology and Microbiology, UNMC, Omaha, NE 68198-5900, USA * Correspondence: [email protected] (S.K.B.); [email protected] (M.P.P.); Tel.: +402-559-5455 (S.K.B.); +402-559-1170 (M.P.P.); Fax: +402-559-6650 (S.K.B. & M.P.P.) Equal contribution. y Received: 21 January 2020; Accepted: 12 February 2020; Published: 14 February 2020 Abstract: Glycosylation is the most commonly occurring post-translational modifications, and is believed to modify over 50% of all proteins. The process of glycan modification is directed by different glycosyltransferases, depending on the cell in which it is expressed. These small carbohydrate molecules consist of multiple glycan families that facilitate cell–cell interactions, protein interactions, and downstream signaling. An alteration of several types of O-glycan core structures have been implicated in multiple cancers, largely due to differential glycosyltransferase expression or activity. Consequently, aberrant O-linked glycosylation has been extensively demonstrated to affect biological function and protein integrity that directly result in cancer growth and progression of several diseases.
  • FUSIP1 (SRSF10) (NM 006625) Human Tagged ORF Clone Product Data

    FUSIP1 (SRSF10) (NM 006625) Human Tagged ORF Clone Product Data

    OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RC221759 FUSIP1 (SRSF10) (NM_006625) Human Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: FUSIP1 (SRSF10) (NM_006625) Human Tagged ORF Clone Tag: Myc-DDK Symbol: SRSF10 Synonyms: FUSIP1; FUSIP2; NSSR; PPP1R149; SFRS13; SFRS13A; SRp38; SRrp40; TASR; TASR1; TASR2 Vector: pCMV6-Entry (PS100001) E. coli Selection: Kanamycin (25 ug/mL) Cell Selection: Neomycin ORF Nucleotide >RC221759 ORF sequence Sequence: Red=Cloning site Blue=ORF Green=Tags(s) TTTTGTAATACGACTCACTATAGGGCGGCCGGGAATTCGTCGACTGGATCCGGTACCGAGGAGATCTGCC GCCGCGATCGCC ATGTCCCGCTACCTGCGTCCCCCCAACACGTCTCTGTTCGTCAGGAACGTGGCCGACGACACCAGGTCTG AAGACTTGCGGCGTGAATTTGGTCGTTATGGTCCTATAGTTGATGTGTATGTTCCACTTGATTTCTACAC TCGCCGTCCAAGAGGATTTGCTTATGTTCAATTTGAGGATGTTCGTGATGCTGAAGACGCTTTACATAAT TTGGACAGAAAGTGGATTTGTGGACGGCAGATTGAAATACAGTTTGCCCAGGGGGATCGAAAGACACCAA ATCAGATGAAAGCCAAGGAAGGGAGGAATGTGTACAGTTCTTCACGCTATGATGATTATGACAGATACAG ACGTTCTAGAAGCCGAAGTTATGAAAGGAGGAGATCAAGAAGTCGGTCTTTTGATTACAACTATAGAAGA TCGTATAGTCCTAGAAACAGTAGACCGACTGGAAGACCACGGCGTAGCAGAAGCCATTCCGACAATGATA GACCAAACTGCAGCTGGAATACCCAGTACAGTTCTGCTTACTACACTTCAAGAAAGATC ACGCGTACGCGGCCGCTCGAGCAGAAACTCATCTCAGAAGAGGATCTGGCAGCAAATGATATCCTGGATT ACAAGGATGACGACGATAAGGTTTAA Protein Sequence: >RC221759 protein sequence Red=Cloning site Green=Tags(s) MSRYLRPPNTSLFVRNVADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHN
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
  • Ubiquitylome Profiling of Parkin-Null Brain Reveals Dysregulation Of

    Ubiquitylome Profiling of Parkin-Null Brain Reveals Dysregulation Of

    Neurobiology of Disease 127 (2019) 114–130 Contents lists available at ScienceDirect Neurobiology of Disease journal homepage: www.elsevier.com/locate/ynbdi Ubiquitylome profiling of Parkin-null brain reveals dysregulation of calcium T homeostasis factors ATP1A2, Hippocalcin and GNA11, reflected by altered firing of noradrenergic neurons Key J.a,1, Mueller A.K.b,1, Gispert S.a, Matschke L.b, Wittig I.c, Corti O.d,e,f,g, Münch C.h, ⁎ ⁎ Decher N.b, , Auburger G.a, a Exp. Neurology, Goethe University Medical School, 60590 Frankfurt am Main, Germany b Institute for Physiology and Pathophysiology, Vegetative Physiology and Marburg Center for Mind, Brain and Behavior - MCMBB; Clinic for Neurology, Philipps-University Marburg, 35037 Marburg, Germany c Functional Proteomics, SFB 815 Core Unit, Goethe University Medical School, 60590 Frankfurt am Main, Germany d Institut du Cerveau et de la Moelle épinière, ICM, Paris, F-75013, France e Inserm, U1127, Paris, F-75013, France f CNRS, UMR 7225, Paris, F-75013, France g Sorbonne Universités, Paris, F-75013, France h Institute of Biochemistry II, Goethe University Medical School, 60590 Frankfurt am Main, Germany ARTICLE INFO ABSTRACT Keywords: Parkinson's disease (PD) is the second most frequent neurodegenerative disorder in the old population. Among Parkinson's disease its monogenic variants, a frequent cause is a mutation in the Parkin gene (Prkn). Deficient function of Parkin Mitochondria triggers ubiquitous mitochondrial dysfunction and inflammation in the brain, but it remains unclear howse- Parkin lective neural circuits become vulnerable and finally undergo atrophy. Ubiquitin We attempted to go beyond previous work, mostly done in peripheral tumor cells, which identified protein Calcium targets of Parkin activity, an ubiquitin E3 ligase.