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Supplementary Table 1: List of the Lung Cancer Cell Lines Used in the Present Study for Determining the Status of PARD3

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Supplementary Table 1: List of the lung cancer cell lines used in the present study for determining the status of PARD3. The histopathological type of each cell line is also indicated. CELL LINE ID HISTOPATHOLOGICAL TYPE A427 ADENOCARCINOMA Calu3 ADENOCARCINOMA DMS-273 SMALL CELL LUNG CANCER EBC1 SQUAMOUS CELL CARCINOMA H1155 NON-SMALL CELL LUNG CANCER H128 SMALL CELL LUNG CANCER H1299 NON-SMALL CELL LUNG CANCER H1395 ADENOCARCINOMA H1437 ADENOCARCINOMA H157 SQUAMOUS CELL CARCINOMA H1573 ADENOCARCINOMA H1650 ADENOCARCINOMA H1703 ADENOCARCINOMA H1770 NEUROENDOCRINE H1975 ADENOCARCINOMA H1993 ADENOCARCINOMA H2029 SMALL CELL LUNG CANCER H2107 SMALL CELL LUNG CANCER H2126 ADENOCARCINOMA H2141 SMALL CELL LUNG CANCER H2170 SQUAMOUS CELL CARCINOMA H2171 SMALL CELL LUNG CANCER H2195 SMALL CELL LUNG CANCER H23 ADENOCARCINOMA H345 SMALL CELL LUNG CANCER H441 ADENOCARCINOMA H446 SMALL CELL LUNG CANCER H460 LARGE CELL CARCINOMA H520 SQUAMOUS CELL CARCINOMA H522 ADENOCARCINOMA H596 SQUAMOUS CELL CARCINOMA H69 SMALL CELL LUNG CANCER H82 SMALL CELL LUNG CANCER H889 SMALL CELL LUNG CANCER HCC15 SQUAMOUS CELL CARCINOMA HCC366 NON-SMALL CELL LUNG CANCER HCC95 SQUAMOUS CELL CARCINOMA HTB58 SQUAMOUS CELL CARCINOMA LC1SQ SQUAMOUS CELL CARCINOMA LK-2 SQUAMOUS CELL CARCINOMA LU-134 SMALL CELL LUNG CANCER LU-135 SMALL CELL LUNG CANCER LU-139 SMALL CELL LUNG CANCER LU-65 LARGE CELL CARCINOMA LUDLU-1 SQUAMOUS CELL CARCINOMA PC10 SQUAMOUS CELL CARCINOMA PC-14 SQUAMOUS CELL CARCINOMA PC9 ADENOCARCINOMA RERF-LCMS ADENOCARCINOMA SKMES1 SQUAMOUS CELL CARCINOMA SQ1 SQUAMOUS CELL CARCINOMA Supplementary Table 2 DNA 5'-3' PARD3_E1F TCCTCGGTCCCGGCC PARD3_E1R CCAGGAAGCGCCATATTGATC PARD3_E2F ATGGGCAGGAAGTTATCACG PARD3_E2R CCTAGTGTTAAGTCCCAGGTATCAAG PARD3_E3F TTTGAATGTGAAATGTACGACTTAG PARD3_E3R TTCCATTTACAGGGTCATGG PARD3_E4F TTTAGGATTTCCCTACGTTCTCC PARD3_E4R CAATGGTTTACCCAAGACACG PARD3_E5F TCGGCACATGGTTATAATTCC PARD3_E5R CCAGAAATATCCTGCATTTATGTTAG PARD3_E6F CAAGATCATAATGCCTATTAGACTTCC PARD3_E6R TCCTCATGCCATATGCTTTC PARD3_E7F TGTGTGTCTGTGTTGTTGCAG PARD3_E7R TCAACACCACTCTCTATCTGAGC PARD3_E8F TCATTTTAACATGCTCCTTTGTAAG PARD3_E8R GGCAGAAAATATTCCTCTCCAG PARD3_E9F AACAGCCTGTCAGTTCTTATTGC PARD3_E9R AGGGTGCTTTGGGTTAGTAGG PARD3_E10F GAAATGTGGACCATTGTGAAAG PARD3_E10R CGCATACTTCCGCTAAAATG PARD3_E11F GGCTAGTCCTAGAGTGTGTGTGTG PARD3_E11R CTCAATAAACATTTGCCATCAGG PARD3_E12F ACAGAGCATTATGTCAGCCATC PARD3_E12R GACCACTTTGGCATTTAATAAACC PARD3_E13F TTTCATGGATCTTGCTGTGG PARD3_E13R CGTGACACATCACTGATACACC PARD3_E14F CGTTCAATTGGGCATAATCC PARD3_E14R AAGGTCCTGGAACCTAATACCC PARD3_E15F TCGGGCAAGTTGTTATAATTCTC PARD3_E15R TTTGGTTGCTTCGTCATGTTAC PARD3_E16F AGACTCGAGGTCTCTGTTTGAC PARD3_E16R TTAAATTTACAGAGTTCGGGTATAATC PARD3_E17F CACTTGCAGGTATGTATGAACCTC PARD3_E17R GACATCTGCTTGGGACCATC PARD3_E18F ATGACTGGCATATTGCATGG PARD3_E18R GGCATATGATTGGCAGCTC PARD3_E19F TGAGCAAATAATTGTTATGTACCTG PARD3_E19R GAGTAAAGGGCAAATAATATCGTC PARD3_E20F GCATTGCAGTCCATGTTGC PARD3_E20R TTCAGCCTCCCAAGTAGCTG PARD3_E21F ACTGCAGAAGACACCTGATCC PARD3_E21R CCATCAATATTTGGGTTGATACAG PARD3_E22F CCACTGATCTTCTATAGCTGCAAG PARD3_E22R AAGGCAATTCTGGTTTGAGG PARD3_E23F CAGCAAGTTGCCATGTTTTG PARD3_E23R TCGTTTCATAGAGCATTGAGGTC PARD3_E24F CATGCCAAAGCCAAAATCAC PARD3_E24R CGGGACATTTATTGGTTCCTC PARD3_E25F GCATATTCCATCCCATCCTG PARD3_E25R GAAACAGACACTTGAGACATAGTGG cloning 5'-3' PARD3_F ATAAGCTTAGCATGAAAGTGACCGTGTGCTTCGGACGGAC PARD3_R ATGCGGCCGCGGAATAGAAGGGCCTCCCTTTCTCAGGAG cDNA 5'-3' PARD3_E4F TTGGCCTCTCCACTTCTGTC PARD3_E7R TCGTTGGGGACTTCTACGAG PARD3_E11F GTGGGCAAATCCCAAGAGG PARD3_E13R GACAAAGATTCCCAAATCTGC PARD3_E15F AGCGTTGGATGATAGAGAACG PARD3_E19R TCTTCAGACCCAGGGAAGG PARD3_E20F TGAATGGAAACCAAGAGAAAGG PARD3_E22R GGAACCTTCATAAGAAGAAACTCC Supplementary Table 3: List of the different single nucleotide polymorphisms (SNPs) and variants of unknown biological significance identified in the lung cancer cell lines and in the lung primary tumors tested in the present study. protein Frequency cDNA nucleotide change change SNP (%) c.258C>T p.H86H rs112281243 0.69 c.321G>C p.E107D rs1436731 1.38 c.339C>G p.V113V rs41276096 0.69 c.581A>G p.K194R no reference 0.69 c.582+36C>G NO CHANGE rs150161748 0.69 c.714+26C>T NO CHANGE rs1370084 0.69 c.714+79A>G NO CHANGE rs982687 6.21 c.714+117C>T NO CHANGE rs74134137 0.69 c.861T>C NO CHANGE rs2796011 0.69 c.891-95C>T NO CHANGE rs117300707 2.76 c.1045C>T p.R349C rs201536019 0,69 c.1539+31G>A NO CHANGE rs10740890 72.41 c.1669-91C>G NO CHANGE rs10763987 35.86 c.1749C>G p.T583T rs61735565 6.90 c.1896+116C>T NO CHANGE rs78468914 0.69 c.2227+64G>A NO CHANGE rs7077783 28.97 c.2228-40G>T NO CHANGE no reference 0.69 c.2402G>A p.S801N rs118153230 0.69 c.2569+10A>G NO CHANGE rs58731858 0.69 c.2604C>G N868E no reference 0,69 2614+26 C>T NO CHANGE TMP_ESP_10_34625101 0.69 c.2667G>A p.S889S rs.3781128 71.72 c.2843+99T>G NO CHANGE rs10740885 58.62 c.2810C>T p.A937V rs16935326 2.07 c.2615-62A>G NO CHANGE rs11009737 1.38 c.3185+12T>A NO CHANGE no reference 1.38 3186-12C>T NO CHANGE rs41276094 4.14 c.3549+23C>T NO CHANGE rs116214419 0.69 c.3550-77T>G NO CHANGE rs3004928 71.72 c.3582A>G p.R1191R rs11009651 26.21 c.3550-133G>A NO CHANGE rs143734834 0.69 c.3569C>T p.T1190M rs61735568 0.69 c.3678-28A>G NO CHANGE no reference 0.69 c.3765G>A p.E1255E rs144844232 0.69 c.4019C>T p.A1340V rs144433754 0.69 c.*29C>T UNKNOWN rs150058603 0.69 SUPPLEMENTARY TABLE 4 Tumor ID TYPE AGE GENDER DIFFERENTIATION TNM STAGE METASTASIS SURVIVAL PARD3 GENE STATUS PAR3 IHC pY-STAT3 IHC NI_NO INFORMATION AVAILABLE 100 SCC 77 M MODERATE NI NI NI NI wt 11 104 SCC 58 M POOR T3N0 IIB NO 48+ wt 01 108 SCC 73 M MODERATE T1NX ? NO 48+ wt 10 110 SCC 43 M MODERATE T2NX IV YES 10 wt 11 114 SCC 70 M MODERATE T3NX IV YES 51 c.121-?_2067+?del; p.D41_E689del 0NI 116 SCC 52 M POOR T2N0 IB NO 55 wt 0NI 120 SCC 69 M POOR T2N0 IB NO 13+ wt 21 139 SCC 60 M MODERATE T2N2 IIIA NO 47+ wt 11 141 SCC 77 M MODERATE T2N0MX IB NI NI c.121-2A>G; p.D41_R74del 1NI 143 SCC 80 M MODERATE T2N1 IIB YES 13 wt 11 149 SCC 80 M POOR T3N0MX IIB NO 48+ wt 21 156 SCC 67 M POOR T2N0 IB NO 59+ wt 11 159 SCC 70 M WELL T1N2 IIIA NO 47+ wt 00 160 SCC 73 M WELL T2N0 IB NI 42 wt 0NI 162 SCC 46 M WELL T1N1 IIA NO 37+ wt 01 164 SCC 61 M POOR T2N1 IIB NI wt 1NI 167 SCC 75 M WELL T4N0 IIIB NO 53+ wt 01 168 SCC 69 M WELL T2N0 IB NO 13+ wt 10 170 SCC 71 M WELL T2N0 IB NO 48+ wt 11 172 SCC 66 M NI T3 IIB NI NI wt 10 181 SCC 71 M POOR T2N1 IIB NI NI c.404-?_582+?del; No protein 10 184 SCC 76 M NI T2 IB NI NI wt 11 186 SCC NI NI NI T1 IA NI NI wt 00 189 SCC 66 M WELL T1 IA NI NI wt NI 0 190 SCC 71 M WELL T2 IB NI NI wt 10 192 SCC 57 M POOR T1 IA NI NI wt 00 193 SCC 64 M POOR T1 IA NI NI wt NI NI 194 SCC 78 M POOR T1 IA NI NI wt NI NI 196 SCC 65 M POOR T1 IA NI NI wt 01 197 SCC 68 M WELL T2 IB NI NI wt NI NI 199 SCC 72 M POOR T2 IB NI NI wt 10 200 SCC 77 M MODERATE T2 IB NI NI c.1492insG; p.A498Gfs*9 00 202 SCC 69 M NI T2 IB NI NI wt 11 203 SCC 63 M NI T3 IIB NI NI wt 21 205 SCC 72 M WELL T2 IB NI NI wt 10 207 SCC 65 M NI T2 IB NI NI wt 31 210 SCC 69 M POOR T3 IIB NI NI wt 20 212 SCC 61 M POOR T2 IB NI NI wt 10 213 SCC 60 M WELL T2 IB NI NI wt 10 217 SCC 66 M POOR T3N1 IIIA NI NI wt 10 218 SCC 68 M WELL T1 IA NI NI wt 11 224 SCC 56 M WELL T2N0 IB NO 48+ wt 30 229 SCC 67 M NI T1NX NI NI NI wt 20 237 SCC 61 M WELL T2N0 IB NO 52+ wt NI NI 238 SCC 69 M WELL T2 IB NI NI wt 10 239 SCC 69 M WELL T2 IB NI NI wt 20 240 SCC 59 M WELL T1N0 IA NI 47 wt NI NI 251 SCC NI NI NI NI NI NI NI wt 31 252 SCC 64 M WELL T1N0 IA NO 48+ wt 20 254 SCC 74 M WELL T2 IB NI NI wt 11 256 SCC 47 M MODERATE T2N0 IB NO 47+ wt 11 264 SCC 66 M POOR T2N0 IB NI 19 wt 20 267 SCC 61 M MODERATE T1N0 IA NO 48+ wt 10 269 SCC 79 M MODERATE T2N0 IB NI 28 c.1034G>A; p.R345H 10 273 SCC 74 M POOR T3 IIB NI NI c.3129A>G; p.I1043M NI NI 276 SCC 73 M WELL T3N0 IIB NO 42+ wt 30 360 SCC 66 M POOR T1N0 IA NO 62+ wt 20 362 SCC 69 M POOR T2N1 IIB NI 1 wt 20 368 SCC 63 M WELL T1N0 IA NI 1 wt 2NI 370 SCC 65 M POOR T2 NI NI NI wt 2NI 374 SCC 54 M WELL T1N2 IIIA NO 39+ wt 2NI 388 SCC 76 M WELL T2N0 IB NI 34 wt 1NI 471 SCC 74 M WELL T2N2MX NI NI NI wt NI NI 474 SCC 59 M WELL NI NI NI NI wt NI NI 478 SCC 64 M WELL T1N0MX NI NI NI wt NI NI 482 SCC 71 M WELL NI NI NI NI wt NI NI 490 SCC 55 M WELL T2NOMX NI NI NI wt NI NI 495 SCC 62 M WELL NI NI NI NI wt NI NI 617 SCC 63 M POOR T3N0 IIB NI NI wt NI NI 619 SCC NI NI MODERATE T2N0 IB NI NI wt NI NI 847 SCC 72 M MODERATE T3N0 IIB NI 2 wt NI NI 857 SCC 79 F MODERATE T1N2 IIIA NI 15 wt NI NI 901 SCC 70 M MODERATE T1N0 IA NO 17+ wt NI NI 915 SCC 82 M MODERATE T2N0 1B NO 20+ wt NI NI 943 SCC 74 F MODERATE T2N0 IB NI 8 wt NI NI 958 SCC 72 M MODERATE T1N0 IA NO 11+ wt NI NI 961 SCC 72 F MODERATE T1N0 IA NO 19+ wt NI NI 975 SCC 65 F POOR T2N2 IIIA NI 11 wt NI NI 978 SCC 72 M MODERATE T2N2 IIIA NO 15+ wt NI NI 1101 SCC 63 M MODERATE T1N0 IA NO 12+ wt NI NI 1375 SCC 75 F POOR T2N0 IB NO 6+ wt NI NI 1529 SCC 69 M MODERATE T2N0 IB NI NI c.404-?_3549+?del; No protein NI NI 1631 SCC 76 M MODERATE T1N0 IA NI NI wt NI NI 1642 SCC 54 M MODERATE T1N0 IA NI NI wt NI NI 1681 SCC NI NI NI NI NI NI NI c.223-?_3549+?del; No protein NI NI 1928 SCC NI NI NI NI NI NI NI wt NI NI 1953 SCC NI NI NI NI NI NI NI wt NI NI 2022 SCC NI NI NI NI NI NI NI wt NI NI T1 SCC 68 F NI T2N1M0 IIb NO 23 wt NI NI T10 SCC 73 M MODERATE T1N0M0 Ia YES 11 wt NI NI T11 SCC 72 M MODERATE T3N0M0 IIb YES 18 wt NI NI T12 SCC 56 M MODERATE T2N2M0 IIIa NO 19+ wt NI NI T13 SCC 75 M MODERATE T2N0M0 Ib NO 11 wt NI NI T14 SCC 76 M MODERATE T2N2M0 IIIa NO 19+ wt NI NI T15 SCC 80 M MODERATE T3N0M0 IIb NO 19 wt NI NI T16 SCC 67 M NI T2N0M0 Ib NO 18+ wt NI NI T17 SCC 66 M MODERATE T2N0M0 Ib
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    University of Kentucky UKnowledge Theses and Dissertations--Animal and Food Sciences Animal and Food Sciences 2019 FORMS OF SUPPLEMENTAL SELENIUM IN VITAMIN-MINERAL MIXES DIFFERENTIALLY AFFECT SEROLOGICAL AND HEPATIC PARAMETERS OF GROWING BEEF STEERS GRAZING ENDOPHYTE-INFECTED TALL FESCUE Yang Jia University of Kentucky, [email protected] Digital Object Identifier: https://doi.org/10.13023/etd.2019.028 Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Jia, Yang, "FORMS OF SUPPLEMENTAL SELENIUM IN VITAMIN-MINERAL MIXES DIFFERENTIALLY AFFECT SEROLOGICAL AND HEPATIC PARAMETERS OF GROWING BEEF STEERS GRAZING ENDOPHYTE- INFECTED TALL FESCUE" (2019). Theses and Dissertations--Animal and Food Sciences. 97. https://uknowledge.uky.edu/animalsci_etds/97 This Doctoral Dissertation is brought to you for free and open access by the Animal and Food Sciences at UKnowledge. It has been accepted for inclusion in Theses and Dissertations--Animal and Food Sciences by an authorized administrator of UKnowledge. For more information, please contact [email protected]. STUDENT AGREEMENT: I represent that my thesis or dissertation and abstract are my original work. Proper attribution has been given to all outside sources. I understand that I am solely responsible for obtaining any needed copyright permissions. I have obtained needed written permission statement(s) from the owner(s) of each third-party copyrighted matter to be included in my work, allowing electronic distribution (if such use is not permitted by the fair use doctrine) which will be submitted to UKnowledge as Additional File. I hereby grant to The University of Kentucky and its agents the irrevocable, non-exclusive, and royalty-free license to archive and make accessible my work in whole or in part in all forms of media, now or hereafter known.
  • The Histone Variant Macroh2a1 Regulates Key Genes for Myogenic Cell Fusion in a Splice-Isoform Dependent Manner

    The Histone Variant Macroh2a1 Regulates Key Genes for Myogenic Cell Fusion in a Splice-Isoform Dependent Manner

    cells Article The Histone Variant MacroH2A1 Regulates Key Genes for Myogenic Cell Fusion in a Splice-Isoform Dependent Manner Sarah Hurtado-Bagès 1, Melanija Posavec Marjanovic 2, Vanesa Valero 1, Roberto Malinverni 1, David Corujo 1 , Philippe Bouvet 3 , Anne-Claire Lavigne 4 , Kerstin Bystricky 4 and Marcus Buschbeck 1,2,* 1 Cancer and Leukemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, 08916 Badalona, Spain; shb.scientifi[email protected] (S.H.-B.); [email protected] (V.V.); [email protected] (R.M.); [email protected] (D.C.) 2 Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), 08916 Badalona, Spain; [email protected] 3 Université de Lyon, Ecole Normale Supérieure de Lyon, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, INSERM 1052, CNRS 5286, F-69008 Lyon, France; [email protected] 4 Center for Integrative Biology (CBI), LBME, University of Toulouse, UPS, CNRS, F-31062 Toulouse, France; [email protected] (A.-C.L.); [email protected] (K.B.) * Correspondence: [email protected]; Tel.: +34-93-557-2800 Received: 31 March 2020; Accepted: 23 April 2020; Published: 30 April 2020 Abstract: MacroH2A histone variants have functions in differentiation, somatic cell reprogramming and cancer. However, at present, it is not clear how macroH2As affect gene regulation to exert these functions. We have parted from the initial observation that loss of total macroH2A1 led to a change in the morphology of murine myotubes differentiated ex vivo. The fusion of myoblasts to myotubes is a key process in embryonic myogenesis and highly relevant for muscle regeneration after acute or chronic injury.
  • Supplemental Materials

    Supplemental Materials

    The infection-tolerant mammalian reservoir of Lyme disease and other zoonoses broadly counters the inflammatory effects of endotoxin Supplemental Materials Figures S1-S5 Tables S1-S20 Figure S1. Digital photograph of two adult Peromyscus leucopus with exudative conjunctivitis and huddled together. The animals had received 10 mg/gm body of Escherichia coli lipopolysaccharide intraperitoneally the day before. Figure S2. Species- and tissue-specific responses to LPS. Independent differential gene expression analysis of RNA-seq data were performed for blood, spleen, and liver tissues of P. leucopus and M. musculus collected 4 h after injection with LPS or buffer alsone as control. These are represented as volcano plots with range- adjusted scales for the log2-transformed fold-changes on x-axes and log10-transformed FDR p values on y- axes. Colors of symbols denote the following: red, up-regulated gene with absolute fold-change > 4.0 and p value < 0.05; purple, down-regulated gene with absolute fold-change > 4.0 and p value < 0.05; and gray, all others. Numbers at the top left and right corners in each plot respresent numbers of down- and up-regulated genes, respectively. Figure 3 is same data with constant scales for x- and y-axes across the plots. Numerical values for each gene in the 6 datasets are provided in Tables S4-S9. Figure S3. Correlation of IL-10 and IL-10 P. leucopus and M. musculus from RNA-seq of spleen and of Figure 6B and TaBle S14. The scatter plot is log10 values of normalized unique reads of one coding sequence against another for each of the four groups, as defined in the legend for Figure 6 and indicated By different symBols.
  • Normalized Expression Values *

    Normalized Expression Values *

    Normalized expression values 0.0 0.2 0.4 0.6 0.8 1.0 1.2 PLCG1 * T CD5 MP T B TCF7 cDC UBASH3A BCL11B C5AR1 * MP TLR4 CXCR5 B CD79B VPREB3 XCR1 CADM1 BEND5 * ARGHAP22 * cDC CIITA ZBTB46 FLT3 PLEKHA5 Figure S1. qPCR analysis of the core gene expression signature of cDC, MP, B and T cells in the chicken cell suBsets. RNA from cDC, MP, T and B cells of 2 disUnct pools of 4 chicken spleen was subjected to qPCR detecUon of the core gene expression signatures of immune cell subsets established in Fig. 3 and of transcripts from the mouse and human gene subset selected compendia that could not be detected on the array due to defecUve probes, i.e. ARGHAP22, BEND5, C5AR1, and PLCG1 (labeled by a star on the figure). Data are represented as the mean and SD of relave gene expression levels normalized to GAPDH expression and the maximal expression across the cell types was set to 1 (independent experimental duplicates). B cell T cell cDC Monocyte/MP Chicken Human Mouse Figure S2. Unsupervised hierarchical clustering of orthologous immune response genes across chicken, human and mouse reveals globally conserved clusters of lymphoïd- specific and myeloïd- specific genes. Heatmap of cross-normalized expression profiles for immune response genes present on all three species arrays and regulated at least 2 folds across all cell suBsets, including chicken B cells (c_B), T cells (c_CD3), MP (c_MP) and cDC (c_cDC), human B cells (h_B), T cells (h_CD4_T and h_CD8_T), monocyte-derived MP (h_MoMP), peripheral blood mononucleated cell-derived MP (h_PBMC_MP), non-classical monocytes (h_non- classical_MO), classical monocytes (h_classical_MO), BDCA3+ cDC (h_BDCA3), BDCA1+ cDC (h_BDCA1), murine B cells (m_B), T cells (m_CD4_T and m_CD8_T), peritoneal cavity MP (m_PC_MPII-480HI), lung MP (m_LU_MP), non-classical monocytes (m_non-classical_MO), classical monocytes (m_classical_MO), splenic CD8α+ cDC (m_SP_DC1), suBcutaneous lymph node CD8α+ cDC (m_LN_DC1), splenic CD11B+ cDC (m_SP_DC2), suBcutaneous lymph node CD11B+ cDC (m_LN_DC2).
  • 1 SUPPLEMENTAL DATA Figure S1. Poly I:C Induces IFN-Β Expression

    1 SUPPLEMENTAL DATA Figure S1. Poly I:C Induces IFN-Β Expression

    SUPPLEMENTAL DATA Figure S1. Poly I:C induces IFN-β expression and signaling. Fibroblasts were incubated in media with or without Poly I:C for 24 h. RNA was isolated and processed for microarray analysis. Genes showing >2-fold up- or down-regulation compared to control fibroblasts were analyzed using Ingenuity Pathway Analysis Software (Red color, up-regulation; Green color, down-regulation). The transcripts with known gene identifiers (HUGO gene symbols) were entered into the Ingenuity Pathways Knowledge Base IPA 4.0. Each gene identifier mapped in the Ingenuity Pathways Knowledge Base was termed as a focus gene, which was overlaid into a global molecular network established from the information in the Ingenuity Pathways Knowledge Base. Each network contained a maximum of 35 focus genes. 1 Figure S2. The overlap of genes regulated by Poly I:C and by IFN. Bioinformatics analysis was conducted to generate a list of 2003 genes showing >2 fold up or down- regulation in fibroblasts treated with Poly I:C for 24 h. The overlap of this gene set with the 117 skin gene IFN Core Signature comprised of datasets of skin cells stimulated by IFN (Wong et al, 2012) was generated using Microsoft Excel. 2 Symbol Description polyIC 24h IFN 24h CXCL10 chemokine (C-X-C motif) ligand 10 129 7.14 CCL5 chemokine (C-C motif) ligand 5 118 1.12 CCL5 chemokine (C-C motif) ligand 5 115 1.01 OASL 2'-5'-oligoadenylate synthetase-like 83.3 9.52 CCL8 chemokine (C-C motif) ligand 8 78.5 3.25 IDO1 indoleamine 2,3-dioxygenase 1 76.3 3.5 IFI27 interferon, alpha-inducible