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Supplemental Table 1 Enriched Genes in Cortical Astrocytes from Aged

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Supplemental Table 1 Enriched genes in cortical astrocytes from aged and young-adult mice * Genes were present in the astrocyte module from the WGCNA analysis, and contains astrocyte enriched genes compared to microglia and oligodendrocytes # = Fold change of aged astrocyte expression over the average expression of all analyzed samples (microglia, astrocytes: young, old, with and without myelin contamination) $ ; aged = genes only present in the aged astrocyte top 1000 list (used to compare with lists from Cahoy, Lovatt, Doyle; see Fig. 4B), all = genes present in all astrocyte top 1000 lists Gene Symbol* Aged astr. (log2) Young astr.(log2) FC (aged/ aver.)# Location Ptprz1 15.37 15.02 18.76 Plasma Membrane Slc7a10 14.49 14.44 18.28 Plasma Membrane Gjb6 15.13 14.42 18.18 Plasma Membrane Dclk1 14.63 14.28 17.18 unknown Hes5 15.69 15.55 16.94 Nucleus Fgfr3 15.27 14.46 16.54 Plasma Membrane Entpd2 13.85 13.56 15.92 Cytoplasm Grin2c 14.93 14.87 15.75 Plasma Membrane Slc1a2 15.51 15.39 15.58 Plasma Membrane Fjx1 14.36 13.98 14.52 Extracellular Space Slc6a1 14.20 14.16 14.47 Plasma Membrane Kcnk1 12.93 13.49 14.43 Plasma Membrane Ppap2b 16.16 16.10 14.37 Plasma Membrane Fam20a 14.48 14.72 14.00 Extracellular Space Dbx2 13.68 13.32 13.99 Nucleus Itih3 13.93 13.93 13.94 Extracellular Space Htra1 17.12 16.91 13.92 Extracellular Space Atp1a2 14.59 14.48 13.73 Plasma Membrane Scg3 15.71 15.72 13.68 Extracellular Space F3 15.59 15.08 13.51 Plasma Membrane Mmd2 14.22 14.60 13.50 unknown Nrcam 13.73 13.88 13.47 Plasma Membrane Cldn10a 13.37 13.57 13.46 Ppp1r3g 13.18 12.49 13.45 Cytoplasm Atp1b2 15.28 13.92 13.45 Plasma Membrane Fzd2 13.07 13.48 13.38 Plasma Membrane Dtx1 13.81 13.94 13.37 Nucleus Acsl6 12.75 12.10 13.36 Cytoplasm Slc13a5 13.32 13.22 13.31 Plasma Membrane Nkain4 13.92 14.45 13.29 Extracellular Space Cspg5 15.69 15.96 13.29 Extracellular Space Ntsr2 15.61 15.85 13.15 Plasma Membrane Gja1 12.02 11.50 12.85 Plasma Membrane Scara3 13.19 13.73 12.85 Plasma Membrane Timp3 14.48 14.37 12.78 Extracellular Space Luzp2 12.66 12.77 12.70 unknown Rapgef3 14.90 14.72 12.68 Nucleus Cyp4f15 12.78 12.66 12.66 Cytoplasm C030009O12Rik 11.84 11.49 12.65 unknown Dkk3 13.75 12.89 12.53 Extracellular Space Nrxn1 13.85 13.65 12.46 Plasma Membrane ENSMUST00000000102 13.62 13.70 12.29 Cytoplasm Slc4a4 12.47 12.85 12.27 Plasma Membrane Bcan 16.32 15.28 12.25 Extracellular Space Slc6a11 12.45 13.09 11.99 Plasma Membrane Omg 14.01 14.35 11.97 Plasma Membrane Btbd17 14.09 14.23 11.97 Plasma Membrane Slc25a18 13.48 13.40 11.91 Cytoplasm Fkbp10 12.76 12.43 11.88 Cytoplasm Id4 12.51 12.13 11.74 Nucleus Fam181b 13.89 13.94 11.68 unknown ENSMUST00000066583 12.10 11.52 11.67 Cytoplasm Pdpn 12.60 13.03 11.48 Plasma Membrane Mfsd2a 13.09 12.88 11.47 unknown Mlc1 15.82 16.16 11.47 Plasma Membrane Prnp 15.77 15.75 11.40 Plasma Membrane Foxg1 13.14 12.48 11.38 Nucleus Cxcl14 14.80 15.12 11.38 Extracellular Space Bmpr1b 11.54 11.57 11.34 Plasma Membrane Trim9 14.41 14.67 11.24 Cytoplasm Gpm6a 13.32 13.63 11.17 Plasma Membrane Sdc2 11.44 11.15 11.14 Plasma Membrane Ptn 15.07 15.27 11.13 Extracellular Space Ntrk2 14.87 15.11 11.13 Plasma Membrane Ttyh1 15.43 15.17 11.04 Plasma Membrane Crym 13.77 14.31 10.98 Cytoplasm Cml5 10.87 10.03 10.98 unknown 2810432L12Rik 12.42 12.43 10.95 Aqp4 13.65 14.18 10.93 Plasma Membrane ENSMUST00000114270 12.73 12.95 10.87 Extracellular Space Gabrb1 11.92 12.08 10.84 Plasma Membrane Acsbg1 14.99 15.41 10.82 Cytoplasm Nr2f1 13.83 13.39 10.82 Nucleus Cyp2j9 13.52 12.71 10.72 Cytoplasm Ndp 12.02 12.28 10.72 Extracellular Space Itga7 13.18 12.89 10.71 Plasma Membrane Ngef 14.49 14.57 10.70 Cytoplasm Ephx2 11.56 11.23 10.69 Cytoplasm Fam59b 12.42 12.91 10.67 unknown Acsl3 12.54 11.15 10.60 Cytoplasm Slco1c1 12.72 11.98 10.53 Plasma Membrane Slc38a3 13.20 13.33 10.48 Plasma Membrane Sox9 11.57 11.58 10.42 Nucleus Lhx2 13.51 13.97 10.36 Nucleus Sox2 12.00 11.70 10.25 Nucleus Gli3 11.81 11.71 10.24 Nucleus Cdh2 13.30 13.20 10.21 Plasma Membrane AI464131 12.74 13.14 10.19 Nucleus LOC552874 11.93 12.19 10.05 Myh11 11.55 10.45 10.04 Cytoplasm Serpinh1 11.98 12.12 10.04 Extracellular Space 6030451C04Rik 12.43 12.37 9.94 unknown Gnao1 14.00 14.01 9.93 Plasma Membrane Hey1 12.32 12.00 9.88 Nucleus Nr2e1 11.60 11.41 9.84 Nucleus Sqle 13.63 13.37 9.78 Cytoplasm Cbs 14.72 15.00 9.75 Cytoplasm Gpr37l1 14.31 14.15 9.72 Plasma Membrane Megf10 11.87 11.65 9.72 Plasma Membrane Lrig1 12.28 12.14 9.54 Extracellular Space Gdf1 14.86 14.57 9.43 Extracellular Space Bdh1 11.85 12.13 9.39 Cytoplasm Tnfrsf19 12.78 13.18 9.29 Plasma Membrane Grm3 12.42 12.71 9.27 Plasma Membrane Aldh1l1 14.87 15.13 9.25 Cytoplasm Nat8 12.67 12.73 9.24 Nucleus Fermt2 11.96 11.66 9.17 Cytoplasm 2610017I09Rik 14.50 15.01 9.16 unknown Acta2 15.05 14.85 9.16 Cytoplasm LOC100047843 12.41 12.37 9.15 Gm11627 11.07 11.26 9.10 unknown Gabrg1 11.80 11.76 9.10 Plasma Membrane Gm266 10.69 10.30 9.07 unknown Ppp1r3c 12.30 12.22 9.05 Cytoplasm Frmpd1 12.18 12.30 9.04 Cytoplasm Gm6145 11.87 11.57 9.02 unknown Sod3 12.26 12.05 9.00 Extracellular Space Dio2 13.00 13.37 9.00 Cytoplasm Pou3f3 11.26 11.06 8.97 Nucleus Cntfr 11.29 12.23 8.96 Plasma Membrane Kcnn2 11.35 11.86 8.86 Plasma Membrane ENSMUST00000104895 8.96 7.96 8.84 Atp1b1 13.07 13.36 8.83 Plasma Membrane Tmem35 10.40 10.12 8.74 unknown Daam2 13.60 13.89 8.72 unknown Scrg1 13.12 14.12 8.71 Extracellular Space Astn1 11.90 12.23 8.70 unknown Slc25a34 11.70 11.74 8.69 Cytoplasm Mboat2 11.50 10.59 8.58 Cytoplasm Ntm 11.01 10.19 8.58 Plasma Membrane Clmn 12.32 12.22 8.55 Cytoplasm LOC100046032 10.57 10.06 8.52 Nfib 13.12 13.20 8.51 Nucleus Clu 16.95 16.48 8.44 Extracellular Space Efemp1 10.48 9.29 8.38 Extracellular Space 2900062L11Rik 11.69 12.17 8.37 Gucy1a3 11.14 10.47 8.34 Cytoplasm Hepacam 12.61 12.97 8.34 Plasma Membrane Sncg 11.51 10.30 8.32 Cytoplasm Tlcd1 11.44 11.56 8.32 unknown Elovl2 11.39 11.61 8.28 Cytoplasm Ak3l1 11.75 12.03 8.17 Epdr1 12.41 12.88 8.17 Nucleus Notch3 12.18 11.99 8.16 Plasma Membrane Ltbp1 10.06 9.75 8.16 Extracellular Space 6720482D04 9.89 9.52 8.16 unknown Wnk2 12.80 12.96 8.12 Cytoplasm Lrrc4b 14.53 14.97 8.11 unknown Rbpms2 11.52 11.27 8.09 unknown 2610034M16Rik 10.84 11.25 8.03 unknown Fabp7 12.50 13.17 8.02 Cytoplasm Nxn 12.83 12.77 8.00 Nucleus Alpl 10.58 9.39 7.98 Plasma Membrane Celsr1 11.07 11.12 7.97 Plasma Membrane 1190002H23Rik 13.86 14.61 7.97 Kctd15 11.61 11.52 7.94 unknown Cnn3 13.85 14.02 7.94 Cytoplasm Bmp7 10.95 10.89 7.94 Extracellular Space Baalc 13.15 14.16 7.92 Cytoplasm Fam171b 12.45 12.08 7.91 unknown Acot11 13.02 13.15 7.87 Cytoplasm Klf9 12.62 12.18 7.81 Nucleus Ndrg2 15.47 15.28 7.78 Cytoplasm Ptrf 15.06 14.94 7.78 Nucleus Adora2b 11.34 11.50 7.78 Plasma Membrane Rpe65 10.18 9.27 7.73 Cytoplasm Tagln3 12.06 12.24 7.65 Extracellular Space Syne1 11.08 10.42 7.63 Nucleus Gldc 12.83 13.59 7.60 Cytoplasm Dner 10.86 11.27 7.59 Plasma Membrane B3galt1 9.65 10.14 7.56 Cytoplasm Timp4 12.16 12.39 7.54 Extracellular Space Agxt2l1 11.85 11.52 7.54 unknown Efr3b 13.49 13.41 7.52 unknown Slc2a4 10.62 10.23 7.45 Plasma Membrane Angptl4 12.52 12.69 7.41 Extracellular Space Plcb1 10.87 10.32 7.41 Cytoplasm Lingo4 10.62 10.29 7.39 unknown Pamr1 11.97 12.05 7.36 Extracellular Space 2610301F02Rik 10.07 9.73 7.36 Cyp2j8 10.73 10.09 7.34 unknown Raver2 11.31 11.21 7.29 Nucleus Nhsl1 10.74 10.84 7.27 unknown Tst 13.02 13.45 7.25 Cytoplasm Dhcr24 13.27 13.80 7.24 Cytoplasm Fam163a 10.77 11.27 7.23 unknown Cyp4f14 10.92 11.60 7.23 Cytoplasm Fam59a 9.75 9.56 7.23 unknown 9430011C21Rik 9.28 8.54 7.21 unknown Mt2 16.46 16.45 7.20 unknown S1pr1 15.72 15.80 7.19 Plasma Membrane Limch1 12.97 12.84 7.18 unknown Abcb9 14.36 14.10 7.18 Cytoplasm Unc13c 8.84 8.27 7.16 Cytoplasm 1700084C01Rik 9.74 10.46 7.14 unknown 1200009O22Rik 10.41 10.62 7.13 Mfge8 17.58 17.45 7.13 Extracellular Space Caskin2 10.88 10.73 7.11 Cytoplasm Cmtm5 14.18 14.86 7.11 Extracellular Space Ednra 10.90 10.69 7.08 Plasma Membrane Chchd10 15.56 15.31 7.06 Cytoplasm Pcdh17 10.89 10.99 7.06 unknown Kank1 11.49 11.69 7.05 Nucleus Maob 11.46 12.23 7.03 Cytoplasm Lgi1 10.07 9.54 6.97 Plasma Membrane Tpm2 12.29 11.53 6.96 Cytoplasm Adcyap1r1 11.23 11.56 6.96 Plasma Membrane Ppp2r2b 11.25 11.73 6.95 Cytoplasm Pdk4 10.37 10.60 6.94 Cytoplasm Cpe 16.93 17.38 6.93 Plasma Membrane Tgfb2 11.13 10.99 6.87 Extracellular Space Tagln 14.93 15.29 6.86 Cytoplasm Gstm5 15.02 15.09 6.84 Cytoplasm Hapln1 10.52 11.05 6.81 Extracellular Space Iglon5 11.37 11.90 6.81 unknown Rnf182 10.57 10.74 6.80 Cytoplasm Nat8b 13.40 13.58 6.79 Lysmd2 11.45 11.40 6.78 unknown Aifm3 13.04 13.93 6.78 Cytoplasm Me1 11.45 11.99 6.77 Cytoplasm Prkcdbp 11.91 11.64 6.76 Cytoplasm Pik3ip1 13.03 12.62 6.75 unknown Bai1 13.14 13.63 6.75 Plasma Membrane Kcnj16 11.68 11.77 6.75 Plasma Membrane Fstl1 11.05 10.98 6.73 Extracellular Space Pdgfrb 11.25 11.60 6.73 Plasma Membrane Igdcc4 11.82 12.28 6.72 Plasma Membrane Gm715 9.89 9.86 6.71 unknown Kbtbd11 13.34 13.34 6.71 unknown LOC100047857 10.35 10.54 6.70 Gdpd2 11.46 12.26 6.67 Plasma Membrane Inhbb 10.51 10.64 6.67 Extracellular Space 6330418B08Rik 9.90 9.64 6.66 unknown Paqr6 12.23 12.55 6.65 unknown Ogn 9.02 7.19 6.65 Extracellular Space Sfxn5 13.72 13.87 6.65 Cytoplasm Igfbp2 11.22 11.61 6.63 Extracellular Space Ezr 13.27 13.18 6.62 Plasma Membrane Fzd1 10.57 10.41 6.62 Plasma Membrane Igsf1 11.12 11.34 6.61 Plasma Membrane ENSMUST00000110346 9.64 9.50 6.60 Plasma Membrane Fezf2 9.70 9.45 6.59 unknown Rab30 8.99 9.03 6.58 Cytoplasm Adk 13.99 13.93 6.54 Nucleus Paqr8 9.98 9.65 6.53 Plasma Membrane Me3 9.90 9.22 6.52 Cytoplasm XM_001474456
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    Nuclear Factor I/B is an Oncogene in Small Cell Lung Cancer The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Dooley, A. L. et al. “Nuclear factor I/B is an oncogene in small cell lung cancer.” Genes & Development 25 (2011): 1470-1475. As Published http://dx.doi.org/10.1101/gad.2046711 Publisher Cold Spring Harbor Laboratory Press in association with The Genetics Society Version Author's final manuscript Citable link http://hdl.handle.net/1721.1/66512 Terms of Use Creative Commons Attribution-Noncommercial-Share Alike 3.0 Detailed Terms http://creativecommons.org/licenses/by-nc-sa/3.0/ Dooley 1 Nuclear Factor I/B is an Oncogene in Small Cell Lung Cancer Alison L. Dooley1, Monte M. Winslow1, Derek Y. Chiang2,3,4, Shantanu Banerji2,3, Nicolas Stransky2, Talya L. Dayton1, Eric L. Snyder1, Stephanie Senna1, Charles A. Whittaker1, Roderick T. Bronson5, Denise Crowley1, Jordi Barretina2,3, Levi Garraway2,3, Matthew Meyerson2,3, Tyler Jacks1,6 1David H. Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA 2The Broad Institute, Cancer Program, Cambridge, Massachusetts, USA 3Dana-Farber Cancer Institute, Department of Medical Oncology and Center for Cancer Genome Discovery, Boston, Massachusetts, USA 4Current address: Lineberger Comprehensive Cancer Center, 450 West Drive, CB #7295, Chapel Hill, North Carolina, USA 5Department of Pathology, Tufts University School of Medicine and Veterinary Medicine, North Grafton, Massachusetts, USA 6Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Key Words: Small Cell Lung Cancer, Mouse model, Nuclear Factor I/B Dooley 2 Abstract Small cell lung cancer (SCLC) is an aggressive cancer often diagnosed after it has metastasized.
  • Guthrie Cdna Resource Center

    Guthrie Cdna Resource Center

    cDNA Resource Center cDNA Resource Center Catalog cDNA Resource Center Missouri University of Science and Technology 400 W 11th Rolla, MO 65409 TEL: (573) 341-7610 FAX: (573) 341-7609 EMAIL: [email protected] www.cdna.org September, 2008 1 cDNA Resource Center Visit our web site for product updates 2 cDNA Resource Center The cDNA Resource Center The cDNA Resource Center is a service provided by the faculty of the Department of Biological Sciences of Missouri University of Science and Technology. The purpose of the cDNA Resource Center is to further scientific investigation by providing cDNA clones of human proteins involved in signal transduction processes. This is achieved by providing high quality clones for important signaling proteins in a timely manner. By high quality, we mean that the clones are • Sequence verified • Propagated in a versatile vector useful in bacterial and mammalian systems • Free of extraneous 3' and 5' untranslated regions • Expression verified (in most cases) by coupled in vitro transcription/translation assays • Available in wild-type, epitope-tagged and common mutant forms (e.g., constitutively- active or dominant negative) By timely, we mean that the clones are • Usually shipped within a day from when you place your order. Clones can be ordered from our web pages, by FAX or by phone. Within the United States, clones are shipped by overnight courier (FedEx); international orders are shipped International Priority (FedEx). The clones are supplied for research purposes only. Details on use of the material are included on the Material Transfer Agreement (page 3). Clones are distributed by agreement in Invitrogen's pcDNA3.1+ vector.
  • Differential Gene Expression in Oligodendrocyte Progenitor Cells, Oligodendrocytes and Type II Astrocytes

    Differential Gene Expression in Oligodendrocyte Progenitor Cells, Oligodendrocytes and Type II Astrocytes

    Tohoku J. Exp. Med., 2011,Differential 223, 161-176 Gene Expression in OPCs, Oligodendrocytes and Type II Astrocytes 161 Differential Gene Expression in Oligodendrocyte Progenitor Cells, Oligodendrocytes and Type II Astrocytes Jian-Guo Hu,1,2,* Yan-Xia Wang,3,* Jian-Sheng Zhou,2 Chang-Jie Chen,4 Feng-Chao Wang,1 Xing-Wu Li1 and He-Zuo Lü1,2 1Department of Clinical Laboratory Science, The First Affiliated Hospital of Bengbu Medical College, Bengbu, P.R. China 2Anhui Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu, P.R. China 3Department of Neurobiology, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China 4Department of Laboratory Medicine, Bengbu Medical College, Bengbu, P.R. China Oligodendrocyte precursor cells (OPCs) are bipotential progenitor cells that can differentiate into myelin-forming oligodendrocytes or functionally undetermined type II astrocytes. Transplantation of OPCs is an attractive therapy for demyelinating diseases. However, due to their bipotential differentiation potential, the majority of OPCs differentiate into astrocytes at transplanted sites. It is therefore important to understand the molecular mechanisms that regulate the transition from OPCs to oligodendrocytes or astrocytes. In this study, we isolated OPCs from the spinal cords of rat embryos (16 days old) and induced them to differentiate into oligodendrocytes or type II astrocytes in the absence or presence of 10% fetal bovine serum, respectively. RNAs were extracted from each cell population and hybridized to GeneChip with 28,700 rat genes. Using the criterion of fold change > 4 in the expression level, we identified 83 genes that were up-regulated and 89 genes that were down-regulated in oligodendrocytes, and 92 genes that were up-regulated and 86 that were down-regulated in type II astrocytes compared with OPCs.
  • 140503 IPF Signatures Supplement Withfigs Thorax

    140503 IPF Signatures Supplement Withfigs Thorax

    Supplementary material for Heterogeneous gene expression signatures correspond to distinct lung pathologies and biomarkers of disease severity in idiopathic pulmonary fibrosis Daryle J. DePianto1*, Sanjay Chandriani1⌘*, Alexander R. Abbas1, Guiquan Jia1, Elsa N. N’Diaye1, Patrick Caplazi1, Steven E. Kauder1, Sabyasachi Biswas1, Satyajit K. Karnik1#, Connie Ha1, Zora Modrusan1, Michael A. Matthay2, Jasleen Kukreja3, Harold R. Collard2, Jackson G. Egen1, Paul J. Wolters2§, and Joseph R. Arron1§ 1Genentech Research and Early Development, South San Francisco, CA 2Department of Medicine, University of California, San Francisco, CA 3Department of Surgery, University of California, San Francisco, CA ⌘Current address: Novartis Institutes for Biomedical Research, Emeryville, CA. #Current address: Gilead Sciences, Foster City, CA. *DJD and SC contributed equally to this manuscript §PJW and JRA co-directed this project Address correspondence to Paul J. Wolters, MD University of California, San Francisco Department of Medicine Box 0111 San Francisco, CA 94143-0111 [email protected] or Joseph R. Arron, MD, PhD Genentech, Inc. MS 231C 1 DNA Way South San Francisco, CA 94080 [email protected] 1 METHODS Human lung tissue samples Tissues were obtained at UCSF from clinical samples from IPF patients at the time of biopsy or lung transplantation. All patients were seen at UCSF and the diagnosis of IPF was established through multidisciplinary review of clinical, radiological, and pathological data according to criteria established by the consensus classification of the American Thoracic Society (ATS) and European Respiratory Society (ERS), Japanese Respiratory Society (JRS), and the Latin American Thoracic Association (ALAT) (ref. 5 in main text). Non-diseased normal lung tissues were procured from lungs not used by the Northern California Transplant Donor Network.