• 01:29 1.
    Tree of RNA Types
  • 00:46 2.
    Non-coding RNA
  • 02:20 3.
    Major Types of RNA endoribonucleases
  • 02:31 4.
    Comparative Gene-expression Analysis
  • 01:10 5.
    Question:Which hybridization technique can be used to detect the amount of polysaccharide?Eastern blottingWestern blottingSouthern blottingNorthern blotting
  • 03:50 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
  • 00:58 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
  • 00:41 8.
    Question
  • 01:54 9.
    Hybridization-based techniques1
  • 03:04 10.
    Northen blotting
  • 02:11 11.
    Hybridization-based techniques2
  • 00:34 12.
    Microarray Platforms
  • 00:55 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
  • 00:59 14.
    High Throughput of Traditional Experiment
  • 01:36 15.
    Steps for Microarray Experiment
  • 01:16 16.
    Overview of the stages
  • 00:38 17.
    Guidelines
  • 00:12 18.
    Microarray Platforms
  • 00:30 19.
    In-House Spotted Arrays
  • 05:04 20.
    microarray animation
  • 00:14 21.
    URL for Building Microarrayer
  • 01:01 22.
    picture of arrayer
  • 01:58 23.
    microarray arrayer video
  • 00:21 24.
    HEEBO & MEEBO Genome Sets
  • 00:51 25.
    Microarray Platforms
  • 02:34 26.
    Prespotted Array Slides
  • 00:03 27.
    Question
  • 00:58 28.
    Phosphoamidite Reaction
  • 01:34 29.
    Feature (Spot) Morphology
  • 03:15 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
  • 01:38 31.
    Microarray Platforms
  • 00:32 32.
    Affymetrix
  • 01:09 33.
    Probe Set and Probe Pair
  • 04:52 34.
    CheneChip – Affymetrix
  • 00:58 35.
    Overview of Target preparation
  • 02:17 36.
    In Vitro Transcription1
  • 00:19 37.
    In Vitro Transcription2
  • 01:08 38.
    QuestionIn DNA structure, coding strand (5’  3’) is also calledWatson strandAnti-sense strandTemplate strandCrick strand
  • 06:16 39.
    Anti-Sense RNA (Complementary RNA)
  • 00:34 40.
    Overview of target preparation
  • 00:45 41.
    QuestionThe purpose of fragmentation during the process of making cRNA is to reduceContaminationCross-hybridizationAmplification copiesFluorescent intensity
  • 00:57 42.
    Before Hybridization – cRNA Fragmentation1
  • 01:14 43.
    Microarray Platforms
  • 00:26 44.
    Maskless Array Synthesis – Nimblegen
  • 00:08 45.
    Digital Micromirror Device
  • 00:51 46.
    Maskless Array Synthesis
  • 00:32 47.
    QuestionWhat similarities and differences are there in manufacturing microarrays between Affymetrix and NimbleGen?
  • 00:08 48.
    Microarray Platforms
  • 01:05 49.
    BeadChip--Illumina
  • 01:56 50.
    Bead Preparation and Array Production
  • 00:15 51.
    Bead Array: Microwell Fabrication
  • 01:13 52.
    BeadChips
  • 00:48 53.
    Bead Design
  • 05:36 54.
    Decoding Randomly Ordered Bead Arrays
  • 00:40 55.
    Bead Decoding Example: 16 Bead Types
  • 01:47 56.
    BeadChip Products
  • 01:28 57.
    Types of Gene Expression Assays
  • 03:23 58.
    Types of Gene Expression Assays
  • 00:27 59.
    DASL Labeling1
  • 00:25 60.
    DASL Labeling2
  • 00:18 61.
    Whole Genome DASL Workflow
  • 00:57 62.
    QuestionWhat is the major differences of Illumina bead arrays as compared to other platforms?
  • 00:59 63.
    MicroArray Quality Control (MAQC) Project
  • 00:35 64.
    QuestionWhich value of same samples is smaller?Standard deviation (SD)Standard error of the mean (SEM)
  • 03:46 65.
    Coefficient of Variation
  • 01:02 66.
    Repeatability of Expression Signal Within Test Sites
  • 01:01 67.
    Interplatform Data Comparability
  • 04:52 68.
    Scatter Plot
  • 01:47 69.
    Correlation Between Microarray And TaqMan Data
  • 00:43 70.
    QuestionWhich factors will you consider to choose microarray platform? QualityPriceTurn-over rateAvailabilityAll of them
  • 01:47 71.
    Decoding Randomly Ordered Bead Arrays
  • Index
  • Notes
  • Comment
  • Fullscreen
Comparative Gene-Expression Analysis I: Hybridization-based techniques (0302)
Duration: 1:47:36, Browse: 483, Last Updated: 2021-03-10
    • 01:29 1.
      Tree of RNA Types
    • 00:46 2.
      Non-coding RNA
    • 02:20 3.
      Major Types of RNA endoribonucleases
    • 02:31 4.
      Comparative Gene-expression Analysis
    • 01:10 5.
      Question:Which hybridization technique can be used to detect the amount of polysaccharide?Eastern blottingWestern blottingSouthern blottingNorthern blotting
    • 03:50 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
    • 00:58 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
    • 00:41 8.
      Question
    • 01:54 9.
      Hybridization-based techniques1
    • 03:04 10.
      Northen blotting
    • 02:11 11.
      Hybridization-based techniques2
    • 00:34 12.
      Microarray Platforms
    • 00:55 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
    • 00:59 14.
      High Throughput of Traditional Experiment
    • 01:36 15.
      Steps for Microarray Experiment
    • 01:16 16.
      Overview of the stages
    • 00:38 17.
      Guidelines
    • 00:12 18.
      Microarray Platforms
    • 00:30 19.
      In-House Spotted Arrays
    • 05:04 20.
      microarray animation
    • 00:14 21.
      URL for Building Microarrayer
    • 01:01 22.
      picture of arrayer
    • 01:58 23.
      microarray arrayer video
    • 00:21 24.
      HEEBO & MEEBO Genome Sets
    • 00:51 25.
      Microarray Platforms
    • 02:34 26.
      Prespotted Array Slides
    • 00:03 27.
      Question
    • 00:58 28.
      Phosphoamidite Reaction
    • 01:34 29.
      Feature (Spot) Morphology
    • 03:15 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
    • 01:38 31.
      Microarray Platforms
    • 00:32 32.
      Affymetrix
    • 01:09 33.
      Probe Set and Probe Pair
    • 04:52 34.
      CheneChip – Affymetrix
    • 00:58 35.
      Overview of Target preparation
    • 02:17 36.
      In Vitro Transcription1
    • 00:19 37.
      In Vitro Transcription2
    • 01:08 38.
      QuestionIn DNA structure, coding strand (5’  3’) is also calledWatson strandAnti-sense strandTemplate strandCrick strand
    • 06:16 39.
      Anti-Sense RNA (Complementary RNA)
    • 00:34 40.
      Overview of target preparation
    • 00:45 41.
      QuestionThe purpose of fragmentation during the process of making cRNA is to reduceContaminationCross-hybridizationAmplification copiesFluorescent intensity
    • 00:57 42.
      Before Hybridization – cRNA Fragmentation1
    • 01:14 43.
      Microarray Platforms
    • 00:26 44.
      Maskless Array Synthesis – Nimblegen
    • 00:08 45.
      Digital Micromirror Device
    • 00:51 46.
      Maskless Array Synthesis
    • 00:32 47.
      QuestionWhat similarities and differences are there in manufacturing microarrays between Affymetrix and NimbleGen?
    • 00:08 48.
      Microarray Platforms
    • 01:05 49.
      BeadChip--Illumina
    • 01:56 50.
      Bead Preparation and Array Production
    • 00:15 51.
      Bead Array: Microwell Fabrication
    • 01:13 52.
      BeadChips
    • 00:48 53.
      Bead Design
    • 05:36 54.
      Decoding Randomly Ordered Bead Arrays
    • 00:40 55.
      Bead Decoding Example: 16 Bead Types
    • 01:47 56.
      BeadChip Products
    • 01:28 57.
      Types of Gene Expression Assays
    • 03:23 58.
      Types of Gene Expression Assays
    • 00:27 59.
      DASL Labeling1
    • 00:25 60.
      DASL Labeling2
    • 00:18 61.
      Whole Genome DASL Workflow
    • 00:57 62.
      QuestionWhat is the major differences of Illumina bead arrays as compared to other platforms?
    • 00:59 63.
      MicroArray Quality Control (MAQC) Project
    • 00:35 64.
      QuestionWhich value of same samples is smaller?Standard deviation (SD)Standard error of the mean (SEM)
    • 03:46 65.
      Coefficient of Variation
    • 01:02 66.
      Repeatability of Expression Signal Within Test Sites
    • 01:01 67.
      Interplatform Data Comparability
    • 04:52 68.
      Scatter Plot
    • 01:47 69.
      Correlation Between Microarray And TaqMan Data
    • 00:43 70.
      QuestionWhich factors will you consider to choose microarray platform? QualityPriceTurn-over rateAvailabilityAll of them
    • 01:47 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
    Browse
    483
    Duration
    1:47:36