Transcriptional Characterization of Glioma Neural Stem Cells Diva ...

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6.7 Isoform Differential Expression Results 154 Figure 6.19: Isoform detection by multi tag mapping of gene GAPVD1, a GTPase guanine nucleotide exchange factor essential during engulfment of apoptotic cells [238] and involved in the degradation of EGFR [473]. The expression levels across our GNS cell lines (top) are in blue (plus strand) and red (minus strand). Image adapted from the UCSC genome browser.
6.7 Isoform Differential Expression Results miR-34a transfected cells generated xenografts that were statistically significantly smaller than control miR transfected xenografts, demon- strating that miR-34a expression inhibits in vivo glioblastoma xenograft growth [278]. In our microRNA prediction analysis miR-34a is predicted to target C1orf9, an open reading frame 9 of chromosome 1 since no p53 targeting is predicted due to the deletion of the p53 genomic location within the GNS cell lines. · miR-26a is up-regulated in glioblastoma and targets PTEN through the direct binding in its 3'UTR of the B2 and B3 sites, mediating transla- tional repression and reduced steady-state levels of the protein. West- ern blotting demonstrated that miR-26a over-expression achieved a 50% knockdown of PTEN protein in two glioblastoma cell lines, accompa- nied by an enhanced Akt signaling pathway. In our microRNA microarray dataset we observe up-regulation of miR-26a as well. In addi- tion to enhancing tumourigenesis, miR-26a effectively represses endoge- nous PTEN protein in a relevant PDGF-driven glioma model system. The miR-26a-mediated knockdown of EZH2, a histone methylatrans- ferase, and SMAD1, a transcription factor, was also observed in glioblastoma [259,364]. In our analysis miR-26a was predicted to target the SMAD1 gene, of which two isoforms were detected through tag mapping (Fig 6.20). · miR-10b is up-regulated in glioblastomas but its function has not been described yet. Increased levels of miR-10b in breast cancer correlated with the disease’s progression [259,364]. In our microRNA microarray dataset miR-10b is also up-regulated. · miR-451 inhibited the growth of transfected glioblastoma cells, as detected by neurosphere formation assays [259,364]. We found miR-451 to be up-regulated in our microRNA microarray dataset, in line with its role as a cell cycle breaker and growth inhibitor. · miR-129-3p is found to be down-regulated in glioblastomas but its function remains unknown to date [259,364]. Interestingly, we observed miR- 129-3p to be up-regulated in our microRNA microarray dataset, possibly indicating a different regulation in action at the stem cell level. 155
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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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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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D.2 Pathway Images Appendix Figure
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E. Exon Array Data Appendix Average
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F. MicroRNA Array Data Appendix Tab
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F. MicroRNA Array Data Appendix GNS
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F. MicroRNA Array Data Appendix GNS
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Ln Natural logarithm LOH Loss of He
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3.3 Schematisation of cell cycle ph
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8.3 Workflows at the core of the pr
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7.1 Selected Gene Ontology terms an
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Bibliography [1] Cell signaling tec
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