• 00:00 1.
    Tree of RNA Types
  • 01:29 2.
    Non-coding RNA
  • 02:15 3.
    Major Types of RNA endoribonucleases
  • 04:36 4.
    Comparative Gene-expression Analysis
  • 07:07 5.
    Question:Which hybridization technique can be used to detect the amount of polysaccharide?Eastern blottingWestern blottingSouthern blottingNorthern blotting
  • 08:18 6.
    Agarose gels to resolve large fragments of DNA Polyacrylamide gelsto separate shorter nucleic acids, generally in the range of 1−1000 base pairs, based on the concentration used Gels without a denaturant (e.g., SDS): native gelsSecondary structure affects
  • 12:09 7.
    Blurry bands Too much DNA (100−250 ng/mm well width) Too much saltBands in the wrong place Heat nucleic acids before running on a native gelRun gel >20 V/cm ( run gel slowly  sharper bands)Gel temp. >30 °CLoading buffer floats away Some salts built up i
  • 13:07 8.
    Question
  • 13:48 9.
    Hybridization-based techniques1
  • 15:43 10.
    Northen blotting
  • 18:47 11.
    Hybridization-based techniques2
  • 20:59 12.
    Microarray Platforms
  • 21:33 13.
    Advantages:Favor small sample sizeHigh throughput: gather data on thousands of genes (genome) in a single experimentQuantitative analysisApplication:Gene expressionGenotyping-polymorphisms (SNP) and copy number variationBinding site identification: ChIP-o
  • 22:28 14.
    High Throughput of Traditional Experiment
  • 23:27 15.
    Steps for Microarray Experiment
  • 25:04 16.
    Overview of the stages
  • 26:21 17.
    Guidelines
  • 26:59 18.
    Microarray Platforms
  • 27:12 19.
    In-House Spotted Arrays
  • 27:42 20.
    microarray animation
  • 32:47 21.
    URL for Building Microarrayer
  • 33:01 22.
    picture of arrayer
  • 34:03 23.
    microarray arrayer video
  • 36:01 24.
    HEEBO & MEEBO Genome Sets
  • 36:22 25.
    Microarray Platforms
  • 37:14 26.
    Prespotted Array Slides
  • 39:49 27.
    Question
  • 39:53 28.
    Phosphoamidite Reaction
  • 40:52 29.
    Feature (Spot) Morphology
  • 42:26 30.
    QuestionWhy did the samples need to be co-hybridized onto the same slide in two color platform?To reduce reagent costTo minimize microarray numberTo normalize unequal spot sizeTo simplify experimental protocol
  • 45:42 31.
    Microarray Platforms
  • 47:20 32.
    Affymetrix
  • 47:53 33.
    Probe Set and Probe Pair
  • 49:02 34.
    CheneChip – Affymetrix
  • 53:55 35.
    Overview of Target preparation
  • 54:53 36.
    In Vitro Transcription1
  • 57:10 37.
    In Vitro Transcription2
  • 57:30 38.
    QuestionIn DNA structure, coding strand (5’  3’) is also calledWatson strandAnti-sense strandTemplate strandCrick strand
  • 58:39 39.
    Anti-Sense RNA (Complementary RNA)
  • 1:04:55 40.
    Overview of target preparation
  • 1:05:30 41.
    QuestionThe purpose of fragmentation during the process of making cRNA is to reduceContaminationCross-hybridizationAmplification copiesFluorescent intensity
  • 1:06:15 42.
    Before Hybridization – cRNA Fragmentation1
  • 1:07:13 43.
    Microarray Platforms
  • 1:08:27 44.
    Maskless Array Synthesis – Nimblegen
  • 1:08:54 45.
    Digital Micromirror Device
  • 1:09:02 46.
    Maskless Array Synthesis
  • 1:09:53 47.
    QuestionWhat similarities and differences are there in manufacturing microarrays between Affymetrix and NimbleGen?
  • 1:10:26 48.
    Microarray Platforms
  • 1:10:34 49.
    BeadChip--Illumina
  • 1:11:40 50.
    Bead Preparation and Array Production
  • 1:13:36 51.
    Bead Array: Microwell Fabrication
  • 1:13:52 52.
    BeadChips
  • 1:15:06 53.
    Bead Design
  • 1:15:55 54.
    Decoding Randomly Ordered Bead Arrays
  • 1:21:31 55.
    Bead Decoding Example: 16 Bead Types
  • 1:22:11 56.
    BeadChip Products
  • 1:23:58 57.
    Types of Gene Expression Assays
  • 1:25:27 58.
    Types of Gene Expression Assays
  • 1:28:51 59.
    DASL Labeling1
  • 1:29:18 60.
    DASL Labeling2
  • 1:29:44 61.
    Whole Genome DASL Workflow
  • 1:30:02 62.
    QuestionWhat is the major differences of Illumina bead arrays as compared to other platforms?
  • 1:30:59 63.
    MicroArray Quality Control (MAQC) Project
  • 1:31:59 64.
    QuestionWhich value of same samples is smaller?Standard deviation (SD)Standard error of the mean (SEM)
  • 1:32:34 65.
    Coefficient of Variation
  • 1:36:21 66.
    Repeatability of Expression Signal Within Test Sites
  • 1:37:23 67.
    Interplatform Data Comparability
  • 1:38:25 68.
    Scatter Plot
  • 1:43:18 69.
    Correlation Between Microarray And TaqMan Data
  • 1:45:05 70.
    QuestionWhich factors will you consider to choose microarray platform? QualityPriceTurn-over rateAvailabilityAll of them
  • 1:45:48 71.
    Decoding Randomly Ordered Bead Arrays
  • Index
  • Notes
  • Comment
  • Fullscreen
Comparative Gene-Expression Analysis I: Hybridization-based techniques (0302)
Duration: 1:47:36, Browse: 664, Last Updated: 2021-03-10
    • 00:00 1.
      Tree of RNA Types
    • 01:29 2.
      Non-coding RNA
    • 02:15 3.
      Major Types of RNA endoribonucleases
    • 04:36 4.
      Comparative Gene-expression Analysis
    • 07:07 5.
      Question:Which hybridization technique can be used to detect the amount of polysaccharide?Eastern blottingWestern blottingSouthern blottingNorthern blotting
    • 08:18 6.
      Agarose gels to resolve large fragments of DNA Polyacrylamide gelsto separate shorter nucleic acids, generally in the range of 1−1000 base pairs, based on the concentration used Gels without a denaturant (e.g., SDS): native gelsSecondary structure affects
    • 12:09 7.
      Blurry bands Too much DNA (100−250 ng/mm well width) Too much saltBands in the wrong place Heat nucleic acids before running on a native gelRun gel >20 V/cm ( run gel slowly  sharper bands)Gel temp. >30 °CLoading buffer floats away Some salts built up i
    • 13:07 8.
      Question
    • 13:48 9.
      Hybridization-based techniques1
    • 15:43 10.
      Northen blotting
    • 18:47 11.
      Hybridization-based techniques2
    • 20:59 12.
      Microarray Platforms
    • 21:33 13.
      Advantages:Favor small sample sizeHigh throughput: gather data on thousands of genes (genome) in a single experimentQuantitative analysisApplication:Gene expressionGenotyping-polymorphisms (SNP) and copy number variationBinding site identification: ChIP-o
    • 22:28 14.
      High Throughput of Traditional Experiment
    • 23:27 15.
      Steps for Microarray Experiment
    • 25:04 16.
      Overview of the stages
    • 26:21 17.
      Guidelines
    • 26:59 18.
      Microarray Platforms
    • 27:12 19.
      In-House Spotted Arrays
    • 27:42 20.
      microarray animation
    • 32:47 21.
      URL for Building Microarrayer
    • 33:01 22.
      picture of arrayer
    • 34:03 23.
      microarray arrayer video
    • 36:01 24.
      HEEBO & MEEBO Genome Sets
    • 36:22 25.
      Microarray Platforms
    • 37:14 26.
      Prespotted Array Slides
    • 39:49 27.
      Question
    • 39:53 28.
      Phosphoamidite Reaction
    • 40:52 29.
      Feature (Spot) Morphology
    • 42:26 30.
      QuestionWhy did the samples need to be co-hybridized onto the same slide in two color platform?To reduce reagent costTo minimize microarray numberTo normalize unequal spot sizeTo simplify experimental protocol
    • 45:42 31.
      Microarray Platforms
    • 47:20 32.
      Affymetrix
    • 47:53 33.
      Probe Set and Probe Pair
    • 49:02 34.
      CheneChip – Affymetrix
    • 53:55 35.
      Overview of Target preparation
    • 54:53 36.
      In Vitro Transcription1
    • 57:10 37.
      In Vitro Transcription2
    • 57:30 38.
      QuestionIn DNA structure, coding strand (5’  3’) is also calledWatson strandAnti-sense strandTemplate strandCrick strand
    • 58:39 39.
      Anti-Sense RNA (Complementary RNA)
    • 1:04:55 40.
      Overview of target preparation
    • 1:05:30 41.
      QuestionThe purpose of fragmentation during the process of making cRNA is to reduceContaminationCross-hybridizationAmplification copiesFluorescent intensity
    • 1:06:15 42.
      Before Hybridization – cRNA Fragmentation1
    • 1:07:13 43.
      Microarray Platforms
    • 1:08:27 44.
      Maskless Array Synthesis – Nimblegen
    • 1:08:54 45.
      Digital Micromirror Device
    • 1:09:02 46.
      Maskless Array Synthesis
    • 1:09:53 47.
      QuestionWhat similarities and differences are there in manufacturing microarrays between Affymetrix and NimbleGen?
    • 1:10:26 48.
      Microarray Platforms
    • 1:10:34 49.
      BeadChip--Illumina
    • 1:11:40 50.
      Bead Preparation and Array Production
    • 1:13:36 51.
      Bead Array: Microwell Fabrication
    • 1:13:52 52.
      BeadChips
    • 1:15:06 53.
      Bead Design
    • 1:15:55 54.
      Decoding Randomly Ordered Bead Arrays
    • 1:21:31 55.
      Bead Decoding Example: 16 Bead Types
    • 1:22:11 56.
      BeadChip Products
    • 1:23:58 57.
      Types of Gene Expression Assays
    • 1:25:27 58.
      Types of Gene Expression Assays
    • 1:28:51 59.
      DASL Labeling1
    • 1:29:18 60.
      DASL Labeling2
    • 1:29:44 61.
      Whole Genome DASL Workflow
    • 1:30:02 62.
      QuestionWhat is the major differences of Illumina bead arrays as compared to other platforms?
    • 1:30:59 63.
      MicroArray Quality Control (MAQC) Project
    • 1:31:59 64.
      QuestionWhich value of same samples is smaller?Standard deviation (SD)Standard error of the mean (SEM)
    • 1:32:34 65.
      Coefficient of Variation
    • 1:36:21 66.
      Repeatability of Expression Signal Within Test Sites
    • 1:37:23 67.
      Interplatform Data Comparability
    • 1:38:25 68.
      Scatter Plot
    • 1:43:18 69.
      Correlation Between Microarray And TaqMan Data
    • 1:45:05 70.
      QuestionWhich factors will you consider to choose microarray platform? QualityPriceTurn-over rateAvailabilityAll of them
    • 1:45:48 71.
      Decoding Randomly Ordered Bead Arrays
    Location
    Folder name
    2021
    Author
    賴亮全
    Branch
    賴亮全教授
    Created
    2021-03-02 17:28:34
    Last Updated
    2021-03-10 12:41:57
    Duration
    1:47:36