Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

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[398] E. Poch, R. Miñambres, E. Mocholí, C. Ivorra, A. Pérez-Aragó, C. Guerri, I. Pérez- Roger, and R. M. Guasch. RhoE interferes with Rb inactivation and regulates the proliferation and survival of the U87 human glioblastoma cell line. Experimental cell research, 313(4):719–731, Feb. 2007. [399] S. Pollard, A. Benchoua, and S. Lowell. Neural stem cells, neurons, and glia. Methods in enzymology, 418:151–169, 2006. [400] S. Pollard and L. Conti. Investigating radial glia in vitro. Progress in neurobiology, 83(1):53–67, 2007. [401] S. Pollard, R. Wallbank, S. Tomlinson, L. Grotewold, and A. Smith. Fibroblast growth factor induces a neural stem cell phenotype in foetal forebrain progenitors and during embryonic stem cell differentiation. Molecular and Cellular Neuroscience, 38(3):393– 403, 2008. [402] S. Pollard, K. Yoshikawa, I. Clarke, D. Danovi, S. Stricker, R. Russell, J. Bayani, R. Head, M. Lee, M. Bernstein, et al. Glioma stem cell lines expanded in adherent culture have tumor-specific phenotypes and are suitable for chemical and genetic screens. Cell Stem Cell, 4(6):568–580, 2009. [403] S. M. Pollard. Adherent Neural Stem (NS) Cells from Fetal and Adult Forebrain. Cerebral Cortex, 16(Supplement 1):i112–i120, July 2006. [404] S. M. Pollard, K. Yoshikawa, I. D. Clarke, D. Danovi, S. Stricker, R. Russell, J. Bayani, R. Head, M. Lee, M. Bernstein, J. A. Squire, A. Smith, and P. Dirks. Glioma stem cell lines expanded in adherent culture have tumor-specific phenotypes and are suitable for chemical and genetic screens. Cell Stem Cell, 4(6):568–80, 2009. [405] K. Pollock, P. Stroemer, S. Patel, L. Stevanato, A. Hope, E. Miljan, Z. Dong, H. Hodges, J. Price, and J. Sinden. A conditionally immortal clonal stem cell line from human cortical neuroepithelium for the treatment of ischemic stroke. Experimental neurology, 199(1):143–155, 2006. [406] R. Popovic and J. Licht. Mek and maf in myeloma therapy. Blood, 117(8):2300–2302, 2011. [407] A. Popovi&cacute, A. Demirovi&cacute, B. Spaji&cacute, G. Štimac, and D. B Krušlin. Expression and prognostic role of syndecan-2 in prostate cancer. Prostate cancer and prostatic diseases, 13(1):78–82, 2009. [408] T. D. Portal. Tcga data portal: An integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in pdgfra, idh1, egfr and nf1. [409] K. Pruitt, T. Tatusova, and D. Maglott. Ncbi reference sequences (refseq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic acids research, 35(suppl 1):D61–D65, 2007. [410] PubMed. Pubmed. http://www.ncbi.nlm.nih.gov/pubmed. [411] R. Puca, L. Nardinocchi, G. Bossi, A. Sacchi, G. Rechavi, D. Givol, and G. D’Orazi. Restoring wtp53 activity in hipk2 depleted mcf7 cells by modulating metallothionein and zinc. Experimental cell research, 315(1):67–75, 2009. [412] Z. Qin, F. Ren, X. Xu, Y. Ren, H. Li, Y. Wang, Y. Zhai, and Z. Chang. Znf536, a novel zinc finger protein specifically expressed in the brain, negatively regulates neuron differentiation by repressing retinoic acid-induced gene transcription. Molecular and cellular biology, 29(13):3633, 2009. [413] A. Quiñones Hinojosa and N. Sanai. Cellular composition and cytoarchitecture of the adult human subventricular zone: a niche of neural stem cells. The Journal of comparative neurology, 2006. [414] F. Radtke and H. Clevers. Self-renewal and cancer of the gut: two sides of a coin. Science, 307(5717):1904, 2005. [415] B. Ragel, W. Couldwell, D. Gillespie, and R. Jensen. Identification of hypoxia-induced genes in a malignant glioma cell line (u-251) by cdna microarray analysis. Neurosurgical review, 30(3):181–187, 2007. [416] H. Rajagopalan, P. Jallepalli, C. Rago, V. Velculescu, K. Kinzler, B. Vogelstein, and C. Lengauer. Inactivation of hcdc4 can cause chromosomal instability. Nature, 428(6978):77–81, 2004.
[417] P. Rakic. Guidance of neurons migrating to the fetal monkey neocortex. Brain research, 33(2):471, 1971. [418] P. Rakic. Elusive radial glial cells: historical and evolutionary perspective. Glia, 43(1):19–32, 2003. [419] S. Ramaswamy, K. Ross, E. Lander, and T. Golub. A molecular signature of metastasis in primary solid tumors. Nature genetics, 33(1):49–54, 2002. [420] L. Rambhatla, S. Ram-Mohan, J. Cheng, and J. Sherley. Immortal dna strand cosegregation requires p53/impdh–dependent asymmetric self-renewal associated with adult stem cells. Cancer research, 65(8):3155, 2005. [421] L. B. Rangel, R. Agarwal, C. A. Sherman-Baust, V. Mello-Coelho, E. S. Pizer, H. Ji, D. D. Taub, and P. J. Morin. Anomalous expression of the HLA-DR alpha and beta chains in ovarian and other cancers. Cancer biology and therapy, 3(10):1021–7, 2004. [422] P. Rao, M. Jaggi, D. Smith, G. Hemstreet, and K. Balaji. Metallothionein 2a interacts with the kinase domain of pkcµ in prostate cancer. Biochemical and biophysical research communications, 310(3):1032–1038, 2003. [423] S. K. Rao, J. Edwards, A. D. Joshi, I.-M. Siu, and G. J. Riggins. A survey of glioblastoma genomic amplifications and deletions. Journal of neuro-oncology, 96(2):169–179, 2010. [424] W. A. Redmond WL, Ruby CE. The role of ox40-mediated co-stimulation in t-cell activation and survival. Crit Rev Immunol, 29:187–201, 2009. [425] J. Rehwinkel, J. Raes, and E. Izaurralde. Nonsense-mediated mRNA decay: Target genes and functional diversification of effectors. Trends Biochem Sci, 31(11):639–46, 2006. [426] K. Reilly, D. Loisel, and R. Bronson. Nf1; Trp53 mutant mice develop glioblastoma with evidence of strain-specific effects. Nature Genetics, 2000. [427] B. Reynolds and S. Weiss. Generation of neurons and astrocytes from isolated cells of the adult mammalian central nervous system. Science, 255(5052):1707, 1992. [428] S. Riaz, E. Jauniaux, G. Stern, and H. Bradford. The controlled conversion of human neural progenitor cells derived from foetal ventral mesencephalon into dopaminergic neurons in vitro. Developmental brain research, 136(1):27–34, 2002. [429] M. J. Riemenschneider, R. Büschges, M. Wolter, J. Reifenberger, J. Boström, J. A. Kraus, U. Schlegel, and G. Reifenberger. Amplification and overexpression of the MDM4 (MDMX) gene from 1q32 in a subset of malignant gliomas without TP53 mutation or MDM2 amplification. Cancer Research, 59(24):6091–6096, Dec. 1999. [430] A. Rizki, V. Weaver, S. Lee, G. Rozenberg, K. Chin, C. Myers, J. Bascom, J. Mott, J. Semeiks, L. Grate, et al. A human breast cell model of preinvasive to invasive transition. Cancer research, 68(5):1378, 2008. [431] D. Robinson, Y. Wu, and S. Lin. The protein tyrosine kinase family of the human genome. biomedical science, 19:5548–5557, 2000. [432] R. Roelofs, D. Fischer, S. Houtman, J. Sluijs, W. Van Haren, F. Van Leeuwen, and E. Hol. Adult human subventricular, subgranular, and subpial zones contain astrocytes with a specialized intermediate filament cytoskeleton. Glia, 52(4):289–300, 2005. [433] S. Rosen and H. Lemjabbar-Alaoui. Sulf-2: an extracellular modulator of cell signaling and a cancer target candidate. Expert opinion on therapeutic targets, 14(9):935–949, 2010. [434] L. Rosso and J. Mienville. Pituicyte modulation of neurohormone output. Glia, 57(3):235–243, 2009. [435] A. Rousseau, C. Nutt, R. Betensky, A. Iafrate, M. Han, K. Ligon, D. Rowitch, and D. Louis. Expression of oligodendroglial and astrocytic lineage markers in diffuse gliomas: use of ykl-40, apoe, ascl1, and nkx2-2. Journal of Neuropathology & Experimental Neurology, 65(12):1149, 2006. [436] N. Roy, A. Benraiss, S. Wang, R. Fraser, R. Goodman, W. Couldwell, M. Nedergaard, A. Kawaguchi, H. Okano, and S. Goldman. Promoter-targeted selection and isolation of neural progenitor cells from the adult human ventricular zone. Journal of neuroscience research, 59(3):321–331, 2000.
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Transcriptional Characterization of
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This dissertation is my own work an
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Acknowledgements I would like to th
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5.9 External Dataset Expression Cor
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Introduction 1
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1.1 Glial Cells in the Central Nerv
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1.2 Glioblastoma Multiforme Introdu
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1.3 Primary and Secondary Glioblast
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1.4 Pathways Involved in Glioblasto
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1.5 Pathway Crosstalk Introduction
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Chapter 2 Neurogenesis Contents 2.1
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2.1 Radial Glia Introduction VZ adj
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2.2 Neural Stem Cells Introduction
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Chapter 3 Brain Cancer Stem Cells C
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3.1 The Cancer Stem Cell Hypothesis
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3.1 The Cancer Stem Cell Hypothesis
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3.2 Brain Cancer Stem Cells Introdu
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3.3 Glioma Culture Systems Introduc
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Chapter 4 The Non-Coding RNA World
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4.1 MicroRNA regulation Introductio
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4.1 MicroRNA regulation Introductio
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4.2 Target Prediction and Validatio
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Methods 93
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5.1 Tag-sequencing Data Processing
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5.1 Tag-sequencing Data Processing
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5.2 Array Comparative Genomic Hybri
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5.4 Quantitative Real Time-PCR Vali
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5.5 Literature Mining Methods Figur
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5.5 Literature Mining Methods How m
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5.6 Differential Isoform Expression
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5.9 External Dataset Expression Cor
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5.10 Glioblastoma Pathway Construct
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5.11 MicroRNA Target Prediction Ana
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Results 119
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6.2 Tag mapping Results Table 6.1:
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6.2 Tag mapping Results 123 Figure
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6.3 Copy Number Aberrations Results
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6.3 Copy Number Aberrations Results
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6.4 Core Differentially Expressed G
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6.5 Large-scale qRT-PCR Validation
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6.6 Literature Mining for Different
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6.7 Isoform Differential Expression
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6.8 Long ncRNA Differential Express
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6.8 Long ncRNA Differential Express
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Chapter 7 Dataset Correlation Analy
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7.1 Enrichment Analysis Results Tab
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7.1 Enrichment Analysis Results Fig
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7.1 Enrichment Analysis Results Tab
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7.2 Glioblastoma Expression Signatu
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7.3 Tumour Expression Correlation R
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7.4 Survival Analysis Results Table
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7.4 Survival Analysis Results 867 g
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7.5 Glioblastoma Pathway Analysis R
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8.1 Principles Results say, this is
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8.3 Databases Results Figure 8.1: O
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8.3 Databases Results Figure 8.3: W
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8.4 Filters Results Bayesian method
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8.5 Target Prediction Ensemble Anal
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9.1. Digital Profiling of GNS Cell
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9.2. MicroRNA Target Prediction Ana
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9.3. Concluding Remarks Appendix pr
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A.1 Differential Expression Appendi
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A.2 Classified Differential Express
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A.3 Quantitative RT-PCR Appendix Ta
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A.3 Quantitative RT-PCR Appendix We
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A.3 Quantitative RT-PCR Appendix Ta
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A.3 Quantitative RT-PCR Appendix We
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A.4 Tag-seq vs qRT-PCR Correlation
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Appendix "BEX5", "DIAPH2", "GBP3",
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End Select End If End Sub Appendix
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If NameStr.ToLower().Equals("query"
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Appendix C Long ncRNAs We detected
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C. Long ncRNAs Appendix Tag Accessi
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D.1 Pathway Interactions Appendix F
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D.2 Pathway Images Appendix Figure
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Page 331 and 332: [153] T. Fujiwara, M. Bandi, M. Nit
Page 333 and 334: [192] M. Hernandez, M. Nieto, and M
Page 335 and 336: [231] T.-M. Kim, W. Huang, R. Park,
Page 337 and 338: [268] H. Lemjabbar-Alaoui, A. van Z
Page 339 and 340: [305] K. MAEDA, S. MATSUHASHI, K. T
Page 341 and 342: [342] H. Moon, M. Ahn, J. Park, K.
Page 343: [379] D. Park and J. Rich. Biology
Page 347 and 348: [456] T. Shima, N. Okumura, T. Taka
Page 349 and 350: [490] P. A. C. t’Hoen, Y. Ariyure
Page 351 and 352: [523] T. Watanabe, A. Takeda, T. Ts
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