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Tutorial RNASeq for detection of pre-tumoral biomarkers using a group case study of Proliferative Verrucous Leukoplakia

  1. Página Principal
  2. Nuestros cursos
  3. RNASeq Leukoplakia
  4. 5. BIBLIOGRAPHY
◄4. ACKNOWLEDGEMENTSCITE US►
  • CONTENTS
  • 1. PRELIMINARY INFORMATION
    • 1.1 - Tutorial objective
    • 1.2 - Tutorial material and case study
    • 1.3 - Experiment design and support
    • 1.4 - Installing and activating RNASeq and the Server-Side
  • 2. STEP-BY-STEP MODE TUTORIAL
    • 2.1. - TOPHAT/HISAT2 & CUFFLINKS
      • 2.1.1 - Preparing your experiment
      • 2.1.2 - Quality analysis and preprocessing
      • 2.1.3 - Mapping
      • 2.1.4 - Transcriptome Assembly
      • 2.1.5 - Differential Expression analysis
      • 2.1.6 - GOSeq
  • 3. PIPELINE MODE TUTORIAL
    • 3.1 - TopHat/Hisat2 & Cufflinks protocol
  • 4. ACKNOWLEDGEMENTS
  • 5. BIBLIOGRAPHY
  • CITE US
  • 5. BIBLIOGRAPHY

    - Andrews, S. 2016. FastQC: a quality control tool for high throughput sequence data. [URL]

    - Bolger, A.M., Lohse, M. and Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30(15):2114-2120. [URL]

    - Dobin, A., et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013;29(1):15-21. [URL]

    - Goff, L., Trapnell, C. and Kelley, D. 2019. CummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data. [URL]

    - Huntley, R.P., et al. The GOA database: gene Ontology annotation updates for 2015. Nucleic Acids Res 2015;43(Database issue):D1057-1063. [URL]

    - Kim, D., Langmead, B. and Salzberg, S.L. HISAT: a fast spliced aligner with low memory requirements. Nature methods 2015;12(4):357-360. [URL]

    - Kim, D., et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol.2013;14(4):R36. [URL]

    - Kotera, M., et al. The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals. Methods Mol.Biol. 2012;802:19-39. [URL]

    - Llorens, C., et al. Immune expression profile identification in a group of proliferative verrucous leukoplakia patients: a pre-cancer niche for oral squamous cell carcinoma development.Clin Oral Investig. 2021;25(5):2645-2657. [URL]

    - Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 2011;Vol 17(1). [URL]

    - Merkel, D. Docker: lightweight Linux containers for consistent development and deployment. Linux Journal 2014;2014:2. [URL]

    - Schmieder, R. and Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011;27(6):863-864. [URL]

    - Trapnell, C., et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat.Protoc. 2012;7(3):562-578. [URL]

    - Young, M.D., et al. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 2010;11(2):R14. [URL]


    ◄Pipeline mode: Tophat & Cufflinks protocol resultsCITE US►
    • Página Principal
    • Calendario
    • Secciones del curso
      • CONTENTS
      • 1. PRELIMINARY INFORMATION
      • 1.1 - Tutorial objective
      • 1.2 - Tutorial material and case study
      • 1.3 - Experiment design and support
      • 1.4 - Installing and activating RNASeq and the Server-Side
      • 2. STEP-BY-STEP MODE TUTORIAL
      • 2.1. - TOPHAT/HISAT2 & CUFFLINKS
      • 2.1.1 - Preparing your experiment
      • 2.1.2 - Quality analysis and preprocessing
      • 2.1.3 - Mapping
      • 2.1.4 - Transcriptome Assembly
      • 2.1.5 - Differential Expression analysis
      • 2.1.6 - GOSeq
      • 3. PIPELINE MODE TUTORIAL
      • 3.1 - TopHat/Hisat2 & Cufflinks protocol
      • 4. ACKNOWLEDGEMENTS
      • Pipeline mode: Tophat & Cufflinks protocol results
      • 5. BIBLIOGRAPHY
      • CITE US
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