types of microarray

1. DNA Microarrays Ms.ruchi yadav lecturer amity institute of biotechnology amity university lucknow(up)

6. Gene Expression Patrick Schmid

7. Uses and Applications

8. Microarrays: Universal Biochemistry Platforms Peptides Proteins Carbohydrates Lipids Small molecules DNA

12. MICROARRAY TYPES

15. I. Target and probe preparation

16. There are many ways to obtain a labeled target sample. ...GGCUUAAUGAGCCUUAAAAAA...A mRNA TTTTTT...T viral enzyme reverse transcriptase recognizes poly-T bound to poly-A and begins to add complementary DNA nucleotides. The C nucleotides are dyed. A A A G G C T C T T A A G C C ... poly-A tail cDNA target poly-T primer

17. Hybridization and Data Analysis

18. Spotted Array Synthesis.

19. Microarray Experiment

21. Robotic spotting

23. DNA Samples on 96 well plates

24. The PixSys 5500 Arraying Robot (Cartesian Technologies) Vacuum wash station The print head holds up to 32 pins in a 8x4 format Vacuum hold-down platform (50 slide capacity) Robotic arm

25. Contact Printing

26. Non Contact Printing InkJet (HP/Canon) technology • 1 drop = 100 picolitres

28. Spotting the Probes on the Microarray 8 X 4 Print Head microarray slide plate with wells holding probes in solution All spots of the same color are made at the same time. All spots in the same sector are made by the same pin.

29. Using cDNA Microarrays to Measure mRNA Levels ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? Sample 1 Sample 2 Microarray Slide Spots (Probes) Unknown mRNA Sequences (Target)

30. Extract mRNA ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G Sample 1 Sample 2 ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ??????????

31. Convert to cDNA and Label with Fluorescent Dyes ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G Sample 1 Sample 2 Sample 1 Sample 2 ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ??????????

32. Mix Labeled cDNA ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G Sample 1 Sample 2 ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ??????????

33. Hybridize cDNA to the Slide ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G Sample 1 Sample 2 ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ??????????

34. Excite Dyes with Laser Sample 1 Sample 2 ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G

35. Scan Sample 1 Sample 2 ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ACCTG...G ACCTG...G ACCTG...G TTCTG...A TTCTG...A TTCTG...A GGCTT...C GGCTT...C GGCTT...C ATCTA...A ATCTA...A ATCTA...A ACGGG...T ACGGG...T ACGGG...T CGATA...G CGATA...G CGATA...G

36. Quantify Signals ACCTG...G 7652 138 TTCTG...A 5708 4388 GGCTT...C 8566 765 ATCTA...A 1208 13442 ACGGG...T 6784 9762 CGATA...G 67 239 Sample 1 Sample 2

37. Patrick Schmid

42. Different Probe Pairs Represent Different Parts of the Same Gene gene sequence Probes are selected to be specific to the target gene and have good hybridization characteristics.

43. A Probe Set for Measuring Expression Level of a Particular Gene probe pair gene sequence ...TGCAATGGGTCAGAA G GACTCCTATGTGCCT... AATGGGTCAGAA G GACTCCTATGTG AATGGGTCAGAA C GACTCCTATGTG perfect match sequence mismatch sequence probe set probe cell

44. Affymetrix Chip

46. Photolithography The mask only allows light to pass to specific features on the chip

47. Photolithography

49. Photolithographic Approach

50. Patrick Schmid Affymetrix Arrays

52. Affymetrix GeneChip experiment

55. Photodeprotection without masks

56. Maskless Array Synthesis

57. NimbleGen Arrays

58. Microarray Experiment

59. Cancer and Microarray

60. * Measuring levels of gene expression * Creating diagnostic tests to predict whether a patient has a genetic predisposition to obesity * Designing Drugs Gene expression and obesity

61. Reading an array (cont.) Campbell & Heyer, 2003 Block Column Row Gene Name Red Green Red:Green Ratio 1 1 1 tub1 2,345 2,467 0.95 1 1 2 tub2 3,589 2,158 1.66 1 1 3 sec1 4,109 1,469 2.80 1 1 4 sec2 1,500 3,589 0.42 1 1 5 sec3 1,246 1,258 0.99 1 1 6 act1 1,937 2,104 0.92 1 1 7 act2 2,561 1,562 1.64 1 1 8 fus1 2,962 3,012 0.98 1 1 9 idp2 3,585 1,209 2.97 1 1 10 idp1 2,796 1,005 2.78 1 1 11 idh1 2,170 4,245 0.51 1 1 12 idh2 1,896 2,996 0.63 1 1 13 erd1 1,023 3,354 0.31 1 1 14 erd2 1,698 2,896 0.59

63. Clustering of example Campbell & Heyer, 2003

64. Clustering of entire yeast genome Campbell & Heyer, 2003

65. SMD Database

66. Microarray software

67. Microarray databases and tools

69. ARRAY EXPRESS (EBI)

70. GEO(NCBI)