microarray technology
DESCRIPTION
MICROARRAY TECHNOLOGY. By Sehreen Saddique Ibtesam Riaz Bakhtawer Nasrullah University of Gujrat. OUTLINE. 1. Introduction of microarray. 2. Types of microarray. 3. Applications of microarray. DNA MICROARRAY. Gene expression. DNA MICROARRAY. - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/1.jpg)
MICROARRAY TECHNOLOGY
BySehreen Saddique
Ibtesam Riaz Bakhtawer NasrullahUniversity of Gujrat
![Page 2: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/2.jpg)
OUTLINE
1. Introduction of microarray1. Introduction of microarray
3. Applications of microarray3. Applications of microarray
2. Types of microarray 2. Types of microarray
![Page 3: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/3.jpg)
DNA MICROARRAY
![Page 4: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/4.jpg)
Gene expression
is used to measure the levels of gene expression DNA MICROARRAY
![Page 5: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/5.jpg)
If the hybridised DNA or RNA is labelled fluorescently it can be quantified by scanning of the chip.
![Page 6: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/6.jpg)
DNA microarrays can be manufactured by:
• Photolithography
• Robot spotting
![Page 7: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/7.jpg)
Photolithography
• Each probe 25 bp long• 22-40 probes per gene• Perfect Match (PM) as
well as MisMatch (MM) probes
![Page 8: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/8.jpg)
Robot Spotting
![Page 9: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/9.jpg)
DNA MICROARRAY TECHNIQUE
• Presynthesized DNA strands or synthesis of oligonuleotide sequence
• Spotting of DNA strands to plastic plate or glass plate
![Page 10: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/10.jpg)
DNA MICROARRAY TECHNIQUE
• The two samples to be compared are grown/acquired. In this example treated sample (case) and untreated sample (control).
• Extraction of mRNA material from cells
• Formation of complementary DNA through reverse transcription
• Labeling with fluorescent dyes with Cy3 or Cy5
• Mixing of labeled samples & presenting to microarray spots again by spotters
• Hybridization to a DNA Microarray
• Scanning the Hybridized Array
![Page 11: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/11.jpg)
![Page 12: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/12.jpg)
![Page 13: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/13.jpg)
ANALYSIS OF GENE EXPRESSION DATA
• Analyzing issues
• Different environmental conditions
![Page 14: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/14.jpg)
TYPES OF MICROARRAY
SEHREEN SADDIQUE
ROLL NO:08030614-045
![Page 15: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/15.jpg)
Types of microarray
• There are two types of DNA microarray
• c DNA
• Oligoneuclotide array
![Page 16: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/16.jpg)
c DNA MICROARRAY
1. Prepare sample.
Test Reference
2. Label with fluorescent dyes.
3. Combine cDNAs.
4. Print microarray.
5. Hybridize to microarray.
6. Scan.
![Page 17: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/17.jpg)
Nelzo ErefulCrop Bioinformatics
![Page 18: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/18.jpg)
cDNA Array Sample Preparation
![Page 19: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/19.jpg)
![Page 20: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/20.jpg)
![Page 21: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/21.jpg)
APPLICATIONS OF MICROOARRAY
BAKHTAWER
ROLL:08030614-047
![Page 22: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/22.jpg)
Applications of microarray
Drug Discovery and development
Evolutionary and ecological
genomics
Tiling array Tumor classification
Gene expression
(stress)
Microarray
SNP detection
![Page 23: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/23.jpg)
Applications of microarray
![Page 24: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/24.jpg)
Application in ecology
![Page 25: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/25.jpg)
Microarray and asthma
Disease discovery
![Page 26: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/26.jpg)
Medical application of microarray analysis
treatment of cancer may be tailored to the needs of that individual’s gene expression profile.
![Page 27: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/27.jpg)
Tumor classification
Quackenbush 2006; Retrieved from http://content.nejm.org/cgi/content/full/354/23/2463
![Page 28: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/28.jpg)
tolerant ATGTGTGGAGGAGAAGTGATCCCCGCCGACATGCCGGCGGCGCCGTTCACGCCACGCCAC 60 susceptible ------------------------------ATGCCGGCGGCGCCGTTCACGCCACGCCAC 30 ******************************
tolerant GGCGACGGCGAGACATGGGTTGACAGAAAGAGGAGGAACAAGAAGAAGAGGAAGCGCGGC 120 susceptible GGCGACGGCGAGACATGGGTTGACAGAAAGAGGAGGAACAAGAAGAAGAGGAAGCGCGGC 90 ************************************************************
tolerant GCCGACGAAGAATGGGAGGCCGCCTTCCAGGAGTTCATGGCTGCTGACGACGACGACGAC 180 susceptible GCCGACGAAGAATGGGAGGCCGCCTTCCAGGAGTTCATGGCTGCTGACGACGACGACGAC 150 ************************************************************
tolerant GGCGGCGGACTCGTGTTAAGTAGTAAATCTTTGGTGTTGAGGTCACCAGGTGAAAATGAT 240 susceptible GGCGGCGGACTCGTGTTAAGTAGTAAATCTTTGGTGTTGAGGTCACCAGGTGAAAATGAT 210 ************************************************************
tolerant GCAGGCCGGGGCGCCGCCGCCACCATGTCCATGCCGCTGGACCCCGTGACCGAGGAGGCC 300 susceptible GCAGGCCGGGGCGCCGCCGCCACCATGTCCATGCCGCTGGACCCCGTGACCGAGGAGGCC 270 ************************************************************
tolerant GAGCCGGCGGTGGCTGAGAAGCCTCGCCGGCGCCGGCCGAGGCGGAGCTACGAGTACCAC 360 susceptible GAGCCGGCGGTGGCTGAGAAGCCTCGCCGGCGCCGGCCGAGGCGGAGCTACGAGTACCAC 330 ************************************************************
tolerant GGCATCCGGCAGCGGCCGTGGGGGCGGTGGTCGTCGGAGATCCGCGACCCCGTCAAGGGC 420 susceptible GGCATCCGGCAGCGGCCGTGGGGGCGGTGGTCGTCGGAGATCCGCGACCCCGTCAAGGGC 390 ************************************************************
tolerant GTCCGCCTCTGGCTCGGCACCTTCGACACCGCCGTCGAAGCCGCGCTCGCCTACGACGCC 480 susceptible GTCCGCCTCTGGCTCGGCACCTTCGACACCGCCGTCGAAGCCGCGCTCGCCTACGACGCC 450 ************************************************************
tolerant GAGGCCCGCCGCATCCACGGCTGGAAAGCCCGGACAAACTTCCCACCCGCCGATCTTTCT 540 susceptible GAGGCCCGCCGCATCCACGGCTGGAAAGCCCGGACAAACTTCCCACCCGCCGATCTTTCT 510 ************************************************************
tolerant TCGCCGCCGCCGCCGTCGCAGCCGCTCTGCTTCTTGCTCAACGACAACGGCCTCATCACA 600 susceptible TCGCCGCCGCCGCCGCCGCAGCCGCTCTGCTTCTTGCTCAACGACAACGGCCTCATCACA 570 *************** ********************************************
tolerant ATCGGAGAAGCGCCGACCGACGACGCCGCGTCGACGTCGACGTCGACGACGGAGGCGTCC 660 susceptible ATCGGAGAAGCGCCGACCGACGACGCCGCGTCGACGTCGACGTCGACGACGGAGGCGTCC 630 ************************************************************
tolerant GGCGACGCGCGCATACAACTGGAGTGCTGCTCGGACGACGTGATGGACAGCCTCCTCGCC 720 susceptible GGCGACGCGCGCATACAGCTGGAGTGCTGCTCGGACGACGTGATGGACAGCCTCCTCGCC 690 ***************** ******************************************
tolerant GGCTACGACGTGGCCAGCGGCGACGACATATGGACATGGACATCTGGAGCCTCCTCCACC 780 susceptible GGCTACGACGTGGCCAGCGGCGACGACATATGGACATGGACATCTGGAGCCTCCTCCACC 750 ************************************************************
tolerant TCTGTTAACCAAGAGATCAAGACCCCATCGATCCACCAAAACATATCATATGCAGGTGCC 840 susceptible TCTGTTAACCAAGAGATCAAGACCCCATCGATCCACCAAAACATATCATATGCAGGTGCC 810 ************************************************************
tolerant CGCCCCATGACTTGTCACTTTAAGAATCATAAAAACACTTTTGTACAAATGGAGTGCTCA 900 susceptible CGCCCCATGACTTGTCACTTTAAGAATCATAAAAACACTTTTGTACAAATGGAGTGCTCA 870 ************************************************************
tolerant ACCATGCTAAACTTACTCAAAGGCCACAAACAATAA 936 susceptible ACCATGCTAAACTTACTCAAAGGCCACAAACAATAA 906 ************************************
CCGTCGC
CCGCCGC
tolerant ATGTGTGGAGGAGAAGTGATCCCCGCCGACATGCCGGCGGCGCCGTTCACGCCACGCCAC 60 susceptible ------------------------------ATGCCGGCGGCGCCGTTCACGCCACGCCAC 30 ******************************
tolerant GGCGACGGCGAGACATGGGTTGACAGAAAGAGGAGGAACAAGAAGAAGAGGAAGCGCGGC 120 susceptible GGCGACGGCGAGACATGGGTTGACAGAAAGAGGAGGAACAAGAAGAAGAGGAAGCGCGGC 90 ************************************************************
tolerant GCCGACGAAGAATGGGAGGCCGCCTTCCAGGAGTTCATGGCTGCTGACGACGACGACGAC 180 susceptible GCCGACGAAGAATGGGAGGCCGCCTTCCAGGAGTTCATGGCTGCTGACGACGACGACGAC 150 ************************************************************
tolerant GGCGGCGGACTCGTGTTAAGTAGTAAATCTTTGGTGTTGAGGTCACCAGGTGAAAATGAT 240 susceptible GGCGGCGGACTCGTGTTAAGTAGTAAATCTTTGGTGTTGAGGTCACCAGGTGAAAATGAT 210 ************************************************************
tolerant GCAGGCCGGGGCGCCGCCGCCACCATGTCCATGCCGCTGGACCCCGTGACCGAGGAGGCC 300 susceptible GCAGGCCGGGGCGCCGCCGCCACCATGTCCATGCCGCTGGACCCCGTGACCGAGGAGGCC 270 ************************************************************
tolerant GAGCCGGCGGTGGCTGAGAAGCCTCGCCGGCGCCGGCCGAGGCGGAGCTACGAGTACCAC 360 susceptible GAGCCGGCGGTGGCTGAGAAGCCTCGCCGGCGCCGGCCGAGGCGGAGCTACGAGTACCAC 330 ************************************************************
tolerant GGCATCCGGCAGCGGCCGTGGGGGCGGTGGTCGTCGGAGATCCGCGACCCCGTCAAGGGC 420 susceptible GGCATCCGGCAGCGGCCGTGGGGGCGGTGGTCGTCGGAGATCCGCGACCCCGTCAAGGGC 390 ************************************************************
tolerant GTCCGCCTCTGGCTCGGCACCTTCGACACCGCCGTCGAAGCCGCGCTCGCCTACGACGCC 480 susceptible GTCCGCCTCTGGCTCGGCACCTTCGACACCGCCGTCGAAGCCGCGCTCGCCTACGACGCC 450 ************************************************************
tolerant GAGGCCCGCCGCATCCACGGCTGGAAAGCCCGGACAAACTTCCCACCCGCCGATCTTTCT 540 susceptible GAGGCCCGCCGCATCCACGGCTGGAAAGCCCGGACAAACTTCCCACCCGCCGATCTTTCT 510 ************************************************************
tolerant TCGCCGCCGCCGCCGTCGCAGCCGCTCTGCTTCTTGCTCAACGACAACGGCCTCATCACA 600 susceptible TCGCCGCCGCCGCCGCCGCAGCCGCTCTGCTTCTTGCTCAACGACAACGGCCTCATCACA 570 *************** ********************************************
tolerant ATCGGAGAAGCGCCGACCGACGACGCCGCGTCGACGTCGACGTCGACGACGGAGGCGTCC 660 susceptible ATCGGAGAAGCGCCGACCGACGACGCCGCGTCGACGTCGACGTCGACGACGGAGGCGTCC 630 ************************************************************
tolerant GGCGACGCGCGCATACAACTGGAGTGCTGCTCGGACGACGTGATGGACAGCCTCCTCGCC 720 susceptible GGCGACGCGCGCATACAGCTGGAGTGCTGCTCGGACGACGTGATGGACAGCCTCCTCGCC 690 ***************** ******************************************
tolerant GGCTACGACGTGGCCAGCGGCGACGACATATGGACATGGACATCTGGAGCCTCCTCCACC 780 susceptible GGCTACGACGTGGCCAGCGGCGACGACATATGGACATGGACATCTGGAGCCTCCTCCACC 750 ************************************************************
tolerant TCTGTTAACCAAGAGATCAAGACCCCATCGATCCACCAAAACATATCATATGCAGGTGCC 840 susceptible TCTGTTAACCAAGAGATCAAGACCCCATCGATCCACCAAAACATATCATATGCAGGTGCC 810 ************************************************************
tolerant CGCCCCATGACTTGTCACTTTAAGAATCATAAAAACACTTTTGTACAAATGGAGTGCTCA 900 susceptible CGCCCCATGACTTGTCACTTTAAGAATCATAAAAACACTTTTGTACAAATGGAGTGCTCA 870 ************************************************************
tolerant ACCATGCTAAACTTACTCAAAGGCCACAAACAATAA 936 susceptible ACCATGCTAAACTTACTCAAAGGCCACAAACAATAA 906
************************************
CCGTCGC = tolerant (S186)
CCGCCGC = intolerant (P186)
ACAACTG = tolerant
ACAGCTG = intolerant
SNP
SNP detection using Microarray
![Page 29: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/29.jpg)
Generating DNA Sequence
base callingquality clippingvector clippingcontig assembly
chromatogram files
automatedsequencer
software pipeline
>GENE01
ACCTGTCAGTGTCAACTGCTTCAATAGCTAATGCTAGGCTCGATAATCGCTGGCCTCAGCTCAGTCTAGCATTACGATTACGGAGACCTATGCTTTAGCTAGTAGGAACCTCAGCTCAGTACCTGTCAGTGTCAACTGCTTCAATAGCTAATGCTACTC
>GENE01
ACCTGTCAGTGTCAACTGCTTCAATAGCTAATGCTAGGCTCGATAATCGCTGGCCTCAGCTCAGTCTAGCATTACGATTACGGAGACCTATGCTTTAGCTAGTAGGAACCTCAGCTCAGTACCTGTCAGTGTCAACTGCTTCAATAGCTAATGCTACTC
output
![Page 30: MICROARRAY TECHNOLOGY](https://reader035.vdocuments.us/reader035/viewer/2022081501/568143f6550346895db08224/html5/thumbnails/30.jpg)