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00:00
1.
Tree of RNA Types
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01:29
2.
Non-coding RNA
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02:15
3.
Major Types of RNA endoribonucleases
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04:36
4.
Comparative Gene-expression Analysis
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07:07
5.
Question:Which hybridization technique can be used to detect the amount of polysaccharide?Eastern blottingWestern blottingSouthern blottingNorthern blotting
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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
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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
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13:07
8.
Question
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13:48
9.
Hybridization-based techniques1
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15:43
10.
Northen blotting
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18:47
11.
Hybridization-based techniques2
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20:59
12.
Microarray Platforms
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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
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22:28
14.
High Throughput of Traditional Experiment
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23:27
15.
Steps for Microarray Experiment
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25:04
16.
Overview of the stages
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26:21
17.
Guidelines
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26:59
18.
Microarray Platforms
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27:12
19.
In-House Spotted Arrays
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27:42
20.
microarray animation
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32:47
21.
URL for Building Microarrayer
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33:01
22.
picture of arrayer
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34:03
23.
microarray arrayer video
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36:01
24.
HEEBO & MEEBO Genome Sets
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36:22
25.
Microarray Platforms
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37:14
26.
Prespotted Array Slides
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39:49
27.
Question
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39:53
28.
Phosphoamidite Reaction
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40:52
29.
Feature (Spot) Morphology
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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
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45:42
31.
Microarray Platforms
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47:20
32.
Affymetrix
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47:53
33.
Probe Set and Probe Pair
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49:02
34.
CheneChip – Affymetrix
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53:55
35.
Overview of Target preparation
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54:53
36.
In Vitro Transcription1
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57:10
37.
In Vitro Transcription2
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57:30
38.
QuestionIn DNA structure, coding strand (5’ 3’) is also calledWatson strandAnti-sense strandTemplate strandCrick strand
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58:39
39.
Anti-Sense RNA (Complementary RNA)
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1:04:55
40.
Overview of target preparation
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1:05:30
41.
QuestionThe purpose of fragmentation during the process of making cRNA is to reduceContaminationCross-hybridizationAmplification copiesFluorescent intensity
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1:06:15
42.
Before Hybridization – cRNA Fragmentation1
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1:07:13
43.
Microarray Platforms
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1:08:27
44.
Maskless Array Synthesis – Nimblegen
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1:08:54
45.
Digital Micromirror Device
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1:09:02
46.
Maskless Array Synthesis
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1:09:53
47.
QuestionWhat similarities and differences are there in manufacturing microarrays between Affymetrix and NimbleGen?
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1:10:26
48.
Microarray Platforms
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1:10:34
49.
BeadChip--Illumina
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1:11:40
50.
Bead Preparation and Array Production
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1:13:36
51.
Bead Array: Microwell Fabrication
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1:13:52
52.
BeadChips
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1:15:06
53.
Bead Design
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1:15:55
54.
Decoding Randomly Ordered Bead Arrays
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1:21:31
55.
Bead Decoding Example: 16 Bead Types
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1:22:11
56.
BeadChip Products
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1:23:58
57.
Types of Gene Expression Assays
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1:25:27
58.
Types of Gene Expression Assays
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1:28:51
59.
DASL Labeling1
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1:29:18
60.
DASL Labeling2
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1:29:44
61.
Whole Genome DASL Workflow
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1:30:02
62.
QuestionWhat is the major differences of Illumina bead arrays as compared to other platforms?
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1:30:59
63.
MicroArray Quality Control (MAQC) Project
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1:31:59
64.
QuestionWhich value of same samples is smaller?Standard deviation (SD)Standard error of the mean (SEM)
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1:32:34
65.
Coefficient of Variation
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1:36:21
66.
Repeatability of Expression Signal Within Test Sites
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1:37:23
67.
Interplatform Data Comparability
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1:38:25
68.
Scatter Plot
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1:43:18
69.
Correlation Between Microarray And TaqMan Data
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1:45:05
70.
QuestionWhich factors will you consider to choose microarray platform? QualityPriceTurn-over rateAvailabilityAll of them
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1:45:48
71.
Decoding Randomly Ordered Bead Arrays