• 00:00 1.
    Other Sequencing Technology
  • 02:24 2.
    BioNano Genomics (Irys System)
  • 05:56 3.
    Overview of RNA-seq Library Construction
  • 08:29 4.
    RNA Sample Preparation
  • 12:04 5.
    RNA Quality Assessment: Agilent 2100 BioAnalyzer (RIN)RNA Quantification:The UV-absorbance method uses a spectrophotometer to measure the natural absorbance of light at 260 nm (for DNA and RNA) or 280 nm (for proteins)(A260 - A320) x RNA extinction coeffi
  • 14:23 6.
    Input : 10 pg – 10 ng total RNA (RIN>8)
  • 15:52 7.
    QC / Demultiplexing
  • 18:01 8.
    Coverage
  • 21:17 9.
    NGS Experimental Considerations
  • 24:54 10.
    Phred - Quality Base Calling
  • 26:33 11.
    Phred Qualities
  • 28:40 12.
    N50 / L50
  • 33:01 13.
    Quality Control
  • 36:06 14.
    Quality Control – FastQC Tool for Quality Visualization
  • 38:38 15.
    Quality Control – FastQC Tool for Quality Visualization
  • 40:08 16.
    Quality Control – FastQC Tool for Quality Visualization
  • 40:29 17.
    Quality Control – FastQC Tool for Quality Visualization
  • 40:55 18.
    Quality Control – FastQC Tool for Quality Visualization
  • 41:32 19.
    PCR Duplicate
  • 42:35 20.
    Adapter Removal
  • 43:30 21.
    Example
  • 44:32 22.
    QC / Demultiplexing
  • 46:05 23.
    Differences Between RNA-Seq and DNA-Seq
  • 47:19 24.
    Alignment
  • 48:14 25.
    The Seed-Filter-Extend Approach
  • 48:33 26.
    Hash-Based Alignment Methods
  • 50:59 27.
    Burrows–Wheeler Transform
  • 56:22 28.
    Assembly
  • 58:38 29.
    Problems in DNA Sequencing
  • 1:00:45 30.
    Assemble algorithms
  • 1:01:29 31.
    de Bruijn Graph Approach
  • 1:03:27 32.
    de Bruijn Graph Approach
  • 1:04:03 33.
    QC / Demultiplexing
  • 1:05:09 34.
    RNA-Seq Data Normalization Methods
  • 1:07:42 35.
    RPKM
  • 1:07:57 36.
    Question
  • 1:08:12 37.
    Drawbacks of R/FPKM
  • 1:14:38 38.
    Evaluation of Normalization Methods
  • 1:15:57 39.
    Workflow for Analysis of RNA-Seq Data
  • 1:16:27 40.
    Tuxedo Pipeline
  • 1:17:51 41.
    Strategies for Reconstructing Transcripts from RNA-Seq Reads
  • 1:18:29 42.
    Differential Analysis
  • 1:19:26 43.
    Improving the Human Reference Genome
  • 1:21:28 44.
    Single Cell Database
  • 1:23:12 45.
    Single Sample GSEA (ssGSEA)
  • 1:24:53 46.
    GSVA Algorithm
  • 1:28:31 47.
    GSVA Algorithm
  • 1:34:05 48.
    Tools for NGS Data Analysis
  • 1:34:09 49.
    ONLINE ANALYSIS TOOLShttp://molbiol-tools.ca/
  • 1:34:13 50.
    Online Bioinformatics Resources Collection (OBRC)
  • 1:34:27 51.
    Tools for Visualizing Short Read Data
  • 1:34:42 52.
    Summary
  • 1:35:06 53.
    Microarrays vs RNA-seq
  • 1:36:24 54.
    Application of Sequence Census Assays
  • Index
  • Notes
  • Comment
  • Fullscreen
Comparative Gene-Expression Analysis III Sequence-based techniques (0420)
Duration: 1:37:12, Browse: 518, Last Updated: 2021-04-21
    • 00:00 1.
      Other Sequencing Technology
    • 02:24 2.
      BioNano Genomics (Irys System)
    • 05:56 3.
      Overview of RNA-seq Library Construction
    • 08:29 4.
      RNA Sample Preparation
    • 12:04 5.
      RNA Quality Assessment: Agilent 2100 BioAnalyzer (RIN)RNA Quantification:The UV-absorbance method uses a spectrophotometer to measure the natural absorbance of light at 260 nm (for DNA and RNA) or 280 nm (for proteins)(A260 - A320) x RNA extinction coeffi
    • 14:23 6.
      Input : 10 pg – 10 ng total RNA (RIN>8)
    • 15:52 7.
      QC / Demultiplexing
    • 18:01 8.
      Coverage
    • 21:17 9.
      NGS Experimental Considerations
    • 24:54 10.
      Phred - Quality Base Calling
    • 26:33 11.
      Phred Qualities
    • 28:40 12.
      N50 / L50
    • 33:01 13.
      Quality Control
    • 36:06 14.
      Quality Control – FastQC Tool for Quality Visualization
    • 38:38 15.
      Quality Control – FastQC Tool for Quality Visualization
    • 40:08 16.
      Quality Control – FastQC Tool for Quality Visualization
    • 40:29 17.
      Quality Control – FastQC Tool for Quality Visualization
    • 40:55 18.
      Quality Control – FastQC Tool for Quality Visualization
    • 41:32 19.
      PCR Duplicate
    • 42:35 20.
      Adapter Removal
    • 43:30 21.
      Example
    • 44:32 22.
      QC / Demultiplexing
    • 46:05 23.
      Differences Between RNA-Seq and DNA-Seq
    • 47:19 24.
      Alignment
    • 48:14 25.
      The Seed-Filter-Extend Approach
    • 48:33 26.
      Hash-Based Alignment Methods
    • 50:59 27.
      Burrows–Wheeler Transform
    • 56:22 28.
      Assembly
    • 58:38 29.
      Problems in DNA Sequencing
    • 1:00:45 30.
      Assemble algorithms
    • 1:01:29 31.
      de Bruijn Graph Approach
    • 1:03:27 32.
      de Bruijn Graph Approach
    • 1:04:03 33.
      QC / Demultiplexing
    • 1:05:09 34.
      RNA-Seq Data Normalization Methods
    • 1:07:42 35.
      RPKM
    • 1:07:57 36.
      Question
    • 1:08:12 37.
      Drawbacks of R/FPKM
    • 1:14:38 38.
      Evaluation of Normalization Methods
    • 1:15:57 39.
      Workflow for Analysis of RNA-Seq Data
    • 1:16:27 40.
      Tuxedo Pipeline
    • 1:17:51 41.
      Strategies for Reconstructing Transcripts from RNA-Seq Reads
    • 1:18:29 42.
      Differential Analysis
    • 1:19:26 43.
      Improving the Human Reference Genome
    • 1:21:28 44.
      Single Cell Database
    • 1:23:12 45.
      Single Sample GSEA (ssGSEA)
    • 1:24:53 46.
      GSVA Algorithm
    • 1:28:31 47.
      GSVA Algorithm
    • 1:34:05 48.
      Tools for NGS Data Analysis
    • 1:34:09 49.
      ONLINE ANALYSIS TOOLShttp://molbiol-tools.ca/
    • 1:34:13 50.
      Online Bioinformatics Resources Collection (OBRC)
    • 1:34:27 51.
      Tools for Visualizing Short Read Data
    • 1:34:42 52.
      Summary
    • 1:35:06 53.
      Microarrays vs RNA-seq
    • 1:36:24 54.
      Application of Sequence Census Assays
    Location
    Folder name
    2021
    Author
    賴亮全
    Branch
    賴亮全教授
    Created
    2021-04-20 16:17:17
    Last Updated
    2021-04-21 10:47:48
    Duration
    1:37:12