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Table I: Top 100 ranked up‐ and down‐regulated differentially expressed genes at 24h and 48h GENE SYMBOL GENE NAME FOLD‐CHANGE Up‐regulated at 24h HEY2 Hairy/enhancer‐of‐split related with YRPW motif 2 6.87 TM4SF5 Transmembrane 4L six family member 5 5.77 GJD3 Gap junction protein delta 3 5.29 HSD11B1 Hydroxysteroid (11‐beta) dehydrogenase 1, transcript variant 2 4.73 FGFR2 Fibroblast growth factor receptor 2, transcript variant 2 4.54 SERHL2 Serine hydrolase‐like 2 4.48 CDH13 Cadherin 13 H‐cadherin (heart) 4.33 ID4 Inhibitor of DNA binding 4 dominant negative helix‐loop‐helix protein 4.29 BRDT Bromodomain testis‐specific, transcript variant 2 3.92 SSX8 Synovial sarcoma X breakpoint 8 3.85 PDLIM4 PDZ and LIM domain 4 3.83 NPAS1 Neuronal PAS domain protein 1 3.83 SNORD126 Small nucleolar RNA C/D box 126, small nucleolar RNA 3.67 AWAT2 Acyl‐CoA wax alcohol acyltransferase 2 3.60 ARHGEF15 Rho guanine nucleotide exchange factor (GEF) 15 3.58 MTBP Mdm2 transformed 3T3 cell double minute 2 p53 binding protein (mouse) binding protein 3.51 PSG8 Pregnancy specific beta‐1‐glycoprotein 8 3.45 VANGL1 Vang‐like 1 (van gogh Drosophila) 3.44 TAS2R31 Taste receptor type 2 member 31 3.42 FAM231A Family with sequence similarity 231 member A 3.31 PBK PDZ binding kinase 3.30 MMD2 Monocyte to macrophage differentiation‐associated 2 3.26 UNC5A Unc‐5 homolog A (C. elegans) 3.25 PDGF1 Platelet‐derived growth factor alpha polypeptide 3.21 ZP2 Zona pellucida glycoprotein 2 (sperm receptor) 3.17 FUT1 Fucosyltransferase 1 (galactoside 2‐alpha‐L‐fucosyltransferase H blood group) 3.16 GUSBP7 Glucuronidase beta pseudogene 7 3.10 BTNL9 Butyrophilin‐like 9 3.04 WNK4 WNK lysine deficient protein kinase 4 3.03 HHAT Hedgehog acyltransferase 2.99 RPS3AP14 Ribosomal protein S3a pseudogene 14 2.99 HOXB8 Homeobox B8 2.98 RAP1GAP RAP1 GTPase activating protein 2.97 ARHGEF4 Rho guanine nucleotide exchange factor (GEF) 4, transcript variant 1 2.96 GJB5 Gap junction protein beta 5 2.95 ANTXRL Anthrax toxin receptor‐like, non‐coding RNA 2.93 OR8B2 Olfactory receptor family 8 subfamily B member 2 2.90 KRT222 Keratin 222 2.90 CABP5 Calcium binding protein 5 2.89 PDILT Protein disulfide isomerase‐like testis expressed 2.89 TP73 Tumor protein p73 2.87 KRTHA5 Keratin hair acidic 5 2.86 NME1 Non‐metastatic cells 1 protein (NM23A) expressed in, transcript variant 1 2.86 DAPL1 Death associated protein‐like 1 2.85 OR13C8 Olfactory receptor family 13 subfamily C member 8 2.83 XKRY2 XK Kell blood group complex subunit‐related Y‐linked 2 2.82 TM7SF4 Transmembrane 7 superfamily member 4 2.79 SKIDA1 SKI/DACH domain containing 1 2.78 FRMPD1 FERM and PDZ domain containing 1 2.77 CYP24A1 Cytochrome P450 family 24 subfamily A polypeptide 1 nuclear gene encoding mitochondrial protein 2.76 ATP1A2 ATPase Na+/K+ transporting alpha 2 (+) polypeptide 2.74 SETP20 SET pseudogene 20 2.72 CLEC18B C‐type lectin domain family 18 member B 2.72 PRLHR Prolactin releasing hormone receptor 2.69 POLN Polymerase (DNA directed) nu 2.69 MAGEA2B Melanoma antigen family A 2B 2.67 FOXA1 Forkhead box A1 2.67 KRTAP1‐3 Keratin associated protein 1‐3 2.67 PKD1L3 Polycystic kidney disease 1‐like 3 2.63 SLC28A3 Solute carrier family 28 (sodium‐coupled nucleoside transporter) member 3 2.63 IL17REL Interleukin 17 receptor E‐like 2.62 SLC5A7 Solute carrier family 5 (choline transporter) member 7 2.61 EPO Erythropoietin 2.61 SERPINA7P1 Serpin peptidase inhibitor clade A (alpha‐1 antiproteinase, antitrypsin) member 7 pseudogene 1 2.60 MAT1A Methionine adenosyltransferase I alpha 2.60 SFTPA1B Surfactant protein A1B 2.60 TACSTD2 Tumor‐associated calcium signal transducer 2 2.59 RPRD1B Regulation of nuclear pre‐mRNA domain containing 1B 2.58 HOXD12 Homeobox D12 2.58 HYPB Huntingtin interacting protein B, transcript variant 2 2.58 TTBK1 Tau tubulin kinase 1 2.58 AMTN Amelotin 2.57 MAGEB4 Melanoma antigen family B4 2.56 GDF6 Growth differentiation factor 6 2.56 GSX2 GS homeobox 2 2.55 GADL1 Glutamate decarboxylase‐like 1 2.54 CNTF Ciliary neurotrophic factor 2.53 OTOS Otospiralin 2.52 SCGB2A1 Secretoglobin family 2A member 1 2.52 CENPVP3 Centromere protein V pseudogene 3 2.50 MIR942 MicroRNA 942 2.47 CPA1 Carboxypeptidase A1 (pancreatic) 2.45 ELSPBP1 Epididymal sperm binding protein 1 2.44 OR5AY1 Olfactory receptor family 5 subfamily AY member 1 2.42 PRSS16 Protease serine 16 (thymus) 2.42 OR6Q1 Olfactory receptor family 6 subfamily Q member 1 2.41 TFAP2C Transcription factor AP‐2 gamma (activating enhancer binding protein 2 gamma) 2.40 METTL1 Methyltransferase like 1, transcript variant 2 2.40 SLC10A4 Solute carrier family 10 (sodium/bile acid cotransporter family) member 4 2.40 VIL1 Villin 1 2.39 ZNF366 Zinc finger protein 366 2.39 GOLSYN Golgi‐localized protein, transcript variant 7 2.39 C9 Complement component 9 2.38 ELFN2 Extracellular leucine‐rich repeat and fibronectin type III domain containing 2 2.37 CDCA3 Cell division cycle associated 3 2.36 HMGB4 High‐mobility group box 4, transcript variant 1 2.36 KLF14 Kruppel‐like factor 14 2.36 HIST1H2AJ Histone cluster 1 H2aj 2.36 QPRT Quinolinate phosphoribosyltransferase 2.35 SLURP1 Secreted LY6/PLAUR domain containing 1 2.35 Down‐regulated at 24h SLC16A10 Solute carrier family 16 member 10 (aromatic amino acid transporter) ‐4.98 GJB2 Gap junction protein beta 2 ‐4.96 IL24 Interleukin 24, transcript variant 1 ‐4.74 OSM Oncostatin M ‐4.71 DLL1 Delta‐like 1 (Drosophila) ‐4.19 LRRC31 Leucine rich repeat containing 31 ‐4.13 SDS Serine dehydratase ‐3.73 VNN2 Vanin 2, transcript variant 1 ‐3.64 CXCL5 Chemokine (C‐X‐C motif) ligand 5 ‐3.63 OLIG1 Oligodendrocyte transcription factor 1 ‐3.60 THBS1 Thrombospondin 1 ‐3.56 CXCL2 Chemokine (C‐X‐C motif) ligand 2 ‐3.43 CXCL1 Chemokine (C‐X‐C motif) ligand 1 (melanoma growth stimulating activity alpha) ‐3.38 TNFAIP6 Tumor necrosis factor alpha‐induced protein 6 ‐3.14 OLIG2 Oligodendrocyte lineage transcription factor 2 ‐3.11 NEU4 Sialidase 4 ‐3.10 PPAP2B Phosphatidic acid phosphatase type 2B, transcript variant 2 ‐3.09 MET Met proto‐oncogene (hepatocyte growth factor receptor), transcript variant 2 ‐2.98 PTGES Prostaglandin E synthase ‐2.97 E2F2 E2F transcription factor 2 ‐2.96 PROK2 Prokineticin 2 ‐2.94 MERTK C‐mer proto‐oncogene tyrosine kinase ‐2.93 ARL4C ADP‐ribosylation factor‐like 4C ‐2.83 SERPINB2 Serpin peptidase inhibitor clade B (ovalbumin) member 2 ‐2.83 ADA Adenosine deaminase ‐2.81 CCL7 Chemokine (C‐C motif) ligand 7 ‐2.81 DHRS3 Dehydrogenase/reductase (SDR family) member 3 ‐2.79 GAGE12H G antigen 12H ‐2.75 GAGE12C G antigen 12C ‐2.75 HPSE Heparanase ‐2.72 DNER Delta/notch‐like EGF repeat containing ‐2.71 PAPLN Papilin proteoglycan‐like sulfated glycoprotein ‐2.71 GPR160 G protein‐coupled receptor 160 ‐2.69 PRDM8 PR domain containing 8, transcript variant 1 ‐2.67 VMO1 Vitelline membrane outer layer 1 homolog (chicken) ‐2.67 ADAM8 ADAM metallopeptidase domain 8 ‐2.62 SLC22A18AS Solute carrier family 22 (organic cation transporter) member 18 antisense ‐2.62 PPIEL Peptidylprolyl isomerase E‐like pseudogene ‐2.58 CD93 CD93 molecule ‐2.57 SMPDL3A Sphingomyelin phosphodiesterase acid‐like 3A ‐2.55 HIF1A Hypoxia‐inducible factor 1 alpha subunit, transcript variant 2 ‐2.55 WIPI1 WD repeat domain phosphoinositide interacting 1 ‐2.53 GAGE2B G antigen 2B ‐2.50 KIR2DL4 Killer cell immunoglobulin‐like receptor two domains long cytoplasmic tail 4, transcript variant 1 ‐2.50 PID1 Phosphotyrosine interaction domain containing 1 ‐2.49 PPBP Pro‐platelet basic protein (chemokine (C‐X‐C motif) ligand 7) ‐2.45 MS4A4A Membrane‐spanning 4‐domains subfamily A member 4, transcript variant 2 ‐2.41 CHST7 Carbohydrate (N‐acetylglucosamine 6‐O) sulfotransferase 7 ‐2.41 RNASE1 Ribonuclease RNase A family 1 (pancreatic), transcript variant 3 ‐2.38 KIR2DL3 Killer cell immunoglobulin‐like receptor two domains long cytoplasmic tail 3, transcript variant 1 ‐2.37 IL19 Interleukin 19, transcript variant 2 ‐2.34 LGMN Legumain, transcript variant 2 ‐2.31 PFKFB3 6‐phosphofructo‐2‐kinase/fructose‐2,6‐biphosphatase 3 ‐2.29 KIFC3 Kinesin family member C3 ‐2.24 CHST15 Carbohydrate (N‐acetylgalactosamine 4‐sulfate 6‐O) sulfotransferase 15 ‐2.23 GAGE2E G antigen 2E ‐2.23 MS4A14 Membrane‐spanning 4‐domains subfamily A member 14, transcript variant 2 ‐2.23 VNN3 Vanin 3, transcript variant 2 ‐2.22 GATSL3 GATS protein‐like 3 ‐2.19 GAGE6 G antigen 6 ‐2.18 BASP1 Brain abundant membrane attached signal protein 1 ‐2.17 EMR3 Egf‐like module containing mucin‐like hormone receptor‐like 3 ‐2.17 CABLES1 Cdk5 and Abl enzyme substrate 1, transcript variant 1 ‐2.15 PDPN Podoplanin, transcript variant 4 ‐2.12 OLFML2B Olfactomedin‐like 2B ‐2.11 HTRA1 HtrA serine peptidase 1 ‐2.11 CTSLP4 Cathepsin L pseudogene 4 ‐2.10 BTG1 B‐cell translocation gene 1 anti‐proliferative ‐2.10 PLD1 Phospholipase D1 phosphatidylcholine‐specific ‐2.10 THBD Thrombomodulin ‐2.09 INDO Indoleamine‐pyrrole 2,3 dioxygenase ‐2.07 ABTB1 Ankyrin repeat and BTB (POZ) domain containing 1, transcript variant 3 ‐2.07 MAP3K7 MAP3K7 C‐terminal like, transcript variant 1 ‐2.06 CTSLP6 Cathepsin L pseudogene 6 ‐2.05 TMEM71 Transmembrane protein 71 ‐2.05 GAGE12B G antigen 12B ‐2.03 DDIT4 DNA‐damage‐inducible transcript 4 ‐2.00 FLT4 Fms‐related tyrosine kinase 4, transcript variant 2 ‐1.99 APBB3 Amyloid beta (A4) precursor protein‐binding family B member 3, transcript variant 3 ‐1.98 RASGRP3 RAS guanyl releasing protein 3 (calcium and DAG‐regulated) ‐1.98 MAP3K8 Mitogen‐activated protein kinase kinase kinase 8 ‐1.97 PMP22 Peripheral myelin protein 22, transcript variant 2 ‐1.96 TFPI Tissue factor pathway inhibitor (lipoprotein‐associated
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  • Supplementary Figure S4

    Supplementary Figure S4

    18DCIS 18IDC Supplementary FigureS4 22DCIS 22IDC C D B A E (0.77) (0.78) 16DCIS 14DCIS 28DCIS 16IDC 28IDC (0.43) (0.49) 0 ADAMTS12 (p.E1469K) 14IDC ERBB2, LASP1,CDK12( CCNE1 ( NUTM2B SDHC,FCGR2B,PBX1,TPR( CD1D, B4GALT3, BCL9, FLG,NUP21OL,TPM3,TDRD10,RIT1,LMNA,PRCC,NTRK1 0 ADAMTS16 (p.E67K) (0.67) (0.89) (0.54) 0 ARHGEF38 (p.P179Hfs*29) 0 ATG9B (p.P823S) (0.68) (1.0) ARID5B, CCDC6 CCNE1, TSHZ3,CEP89 CREB3L2,TRIM24 BRAF, EGFR (7p11); 0 ABRACL (p.R35H) 0 CATSPER1 (p.P152H) 0 ADAMTS18 (p.Y799C) 19q12 0 CCDC88C (p.X1371_splice) (0) 0 ADRA1A (p.P327L) (10q22.3) 0 CCNF (p.D637N) −4 −2 −4 −2 0 AKAP4 (p.G454A) 0 CDYL (p.Y353Lfs*5) −4 −2 Log2 Ratio Log2 Ratio −4 −2 Log2 Ratio Log2 Ratio 0 2 4 0 2 4 0 ARID2 (p.R1068H) 0 COL27A1 (p.G646E) 0 2 4 0 2 4 2 EDRF1 (p.E521K) 0 ARPP21 (p.P791L) ) 0 DDX11 (p.E78K) 2 GPR101, p.A174V 0 ARPP21 (p.P791T) 0 DMGDH (p.W606C) 5 ANP32B, p.G237S 16IDC (Ploidy:2.01) 16DCIS (Ploidy:2.02) 14IDC (Ploidy:2.01) 14DCIS (Ploidy:2.9) -3 -2 -1 -3 -2 -1 -3 -2 -1 -3 -2 -1 -3 -2 -1 -3 -2 -1 Log Ratio Log Ratio Log Ratio Log Ratio 12DCIS 0 ASPM (p.S222T) Log Ratio Log Ratio 0 FMN2 (p.G941A) 20 1 2 3 2 0 1 2 3 2 ERBB3 (p.D297Y) 2 0 1 2 3 20 1 2 3 0 ATRX (p.L1276I) 20 1 2 3 2 0 1 2 3 0 GALNT18 (p.F92L) 2 MAPK4, p.H147Y 0 GALNTL6 (p.E236K) 5 C11orf1, p.Y53C (10q21.2); 0 ATRX (p.R1401W) PIK3CA, p.H1047R 28IDC (Ploidy:2.0) 28DCIS (Ploidy:2.0) 22IDC (Ploidy:3.7) 22DCIS (Ploidy:4.1) 18IDC (Ploidy:3.9) 18DCIS (Ploidy:2.3) 17q12 0 HCFC1 (p.S2025C) 2 LCMT1 (p.S34A) 0 ATXN7L2 (p.X453_splice) SPEN, p.P677Lfs*13 CBFB 1 2 3 4 5 6 7 8 9 10 11
  • DNA Supercoiling with a Twist Edwin Kamau Louisiana State University and Agricultural and Mechanical College, Ekamau1@Lsu.Edu

    DNA Supercoiling with a Twist Edwin Kamau Louisiana State University and Agricultural and Mechanical College, [email protected]

    Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2005 DNA supercoiling with a twist Edwin Kamau Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Recommended Citation Kamau, Edwin, "DNA supercoiling with a twist" (2005). LSU Doctoral Dissertations. 999. https://digitalcommons.lsu.edu/gradschool_dissertations/999 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. DNA SUPERCOILING WITH A TWIST A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Biological Sciences By Edwin Kamau B.S. Horticulture, Egerton University, Kenya, 1996, May, 2005 DEDICATIONS I would like to dedicate this dissertation to my son, Ashford Kimani Kamau. Your age marks the life of my graduate school career. I have been a weekend dad, broke and with enormous financial responsibilities; it kills me to see how sometimes you cry your heart out on Sunday evening when our weekend time together is over. I miss you too every moment, you have encouraged me to be a better person, a better dad so that I can make you proud. At your tender age, I have learned a lot from you. We will soon spend all the time in the world we need together; travel, sports, music, pre-historic discoveries and adventures; the road is wide open.
  • Isolation and Nucleotide Sequence of the Cdna for Rat Liver Serine

    Isolation and Nucleotide Sequence of the Cdna for Rat Liver Serine

    Proc. Natl. Acad. Sci. USA Vol. 85, pp. 5809-5813, August 1988 Biochemistry Isolation and nucleotide sequence of the cDNA for rat liver serine dehydratase mRNA and structures of the 5' and 3' flanking regions of the serine dehydratase gene (threonine dehydratase/hormonal regulation/consensus sequences) HIROFUMI OGAWA*t, DUNCAN A. MILLER*, TRACY DUNN*, YEU SU*, JAMES M. BURCHAMt, CARL PERAINOt, MOTOJI FUJIOKAt, KAY BABCOCK*, AND HENRY C. PITOT*§ *McArdle Laboratory for Cancer Research, The Medical School, University of Wisconsin, Madison, WI 53706; tDepartment of Biochemistry, Toyama Medical and Pharmaceutical University, Faculty of Medicine, Sugitani, Toyama 930-01, Japan; and tDivision of Biological and Medical Research, Argonne National Laboratory, Argonne, IL 60439 Communicated by Van R. Potter, April 15, 1988 (received for review December 29, 1987) ABSTRACT Rat serine dehydratase cDNA clones were determination of the exact size of DNA complementary to isolated from a Agtll cDNA library on the basis of their serine dehydratase mRNA was made by S1 nuclease and reactivity with monospecific immunoglobulin to the purified sequencing of genomic clones of the regions flanking the enzyme. Using the cDNA insert from a clone that encoded the gene. serine dehydratase subunit as a probe, additional clones were isolated from the same library by plaque hybridization. Nucle- otide sequence analysis of the largest clone obtained showed MATERIALS AND METHODS that it has 1444 base pairs with an open reading frame consisting of 1089 base pairs. The deduced amino acid sequence cDNA Cloning. A rat liver cDNA library constructed in contained sequences of several portions of the serine dehydra- Agtll phage (13) was screened for antibody-reactive plaques tase protein, as determined by Edman degradation.
  • Fucosyltransferase Genes on Porcine Chromosome 6Q11 Are Closely Linked to the Blood Group Inhibitor (S) and Escherichia Coli F18 Receptor (ECF18R) Loci

    Fucosyltransferase Genes on Porcine Chromosome 6Q11 Are Closely Linked to the Blood Group Inhibitor (S) and Escherichia Coli F18 Receptor (ECF18R) Loci

    Mammalian Genome 8, 736–741 (1997). © Springer-Verlag New York Inc. 1997 Two a(1,2) fucosyltransferase genes on porcine Chromosome 6q11 are closely linked to the blood group inhibitor (S) and Escherichia coli F18 receptor (ECF18R) loci E. Meijerink,1 R. Fries,1,*P.Vo¨geli,1 J. Masabanda,1 G. Wigger,1 C. Stricker,1 S. Neuenschwander,1 H.U. Bertschinger,2 G. Stranzinger1 1Institute of Animal Science, Swiss Federal Institute of Technology, ETH-Zentrum, CH-8092 Zurich, Switzerland 2Institute of Veterinary Bacteriology, University of Zurich, CH 8057 Zurich, Switzerland Received: 17 February 1997 / Accepted: 30 May 1997 Abstract. The Escherichia coli F18 receptor locus (ECF18R) has fimbriae F107, has been shown to be genetically controlled by the been genetically mapped to the halothane linkage group on porcine host and is inherited as a dominant trait (Bertschinger et al. 1993) Chromosome (Chr) 6. In an attempt to obtain candidate genes for with B being the susceptibility allele and b the resistance allele. this locus, we isolated 5 cosmids containing the a(1,2)fucosyl- The genetic locus for this E. coli F18 receptor (ECF18R) has been transferase genes FUT1, FUT2, and the pseudogene FUT2P from mapped to porcine Chr 6 (SSC6), based on its close linkage to the a porcine genomic library. Mapping by fluorescence in situ hy- S locus and other loci of the halothane (HAL) linkage group (Vo¨- bridization placed all these clones in band q11 of porcine Chr 6 geli et al. 1996). The epistatic S locus suppresses the phenotypic (SSC6q11). Sequence analysis of the cosmids resulted in the char- expression of the A-0 blood group system when being SsSs (Vo¨geli acterization of an open reading frame (ORF), 1098 bp in length, et al.