1. Creating a Run

2. 1. Click the Create Run icon 2. Enter a unique run name 3. Select dye set 4. Click the Add/Remove sites button

3. 5. Select the protocol(s)-select a different protocol for each site. 6. Select sites – use ctrl and shift to select multiple sites 7. Click right-pointing arrow to transfer protocol and sites to the selections column. 8. Verify that selection is correct then click OK.

4. Defining a Protocol

5. 2. Click New Protocol button 1. Click Define Protocols icon 3. Enter a unique protocol name and click OK. 4. Enter thermal cycling protocol. 5. Click Save Protocol

6. Advance to Next Stage feature – the protocol will automatically advance to the next PCR stage after the threshold crossing.

7. Defining a Graph

8. 1. Click Define Graphs icon 2. Click New Graph button 3. Enter a unique graph name and click OK. 4. Enter graph definition 5. Click Save Graph

9. Viewing Results

10. Compare two runs Customize Views list View temperature and optical data in real time Customize data analysis

11. Viewing Results Table

13. Background subtraction

15. Background subtraction Background subtraction and drift correction started at cycle 5 and stopped at cycle 28.39.

16. Background subtraction Appearance of negative drift because positive slope of the growth curve was included in the background subtraction and drift correction calculation. Threshold set too high

17. Smart Cycler Menus

19. Melt Settings

24. Quantification 10 1 10 2 10 3 10 4 10 5 Unknown Sample Threshold

25. Quantification

26. SYBR ® Green – Standard Curve (Roche FastStart DNA SYBR Green kit; each dilution run in triplicate)

27. Setting up a Standard Curve

29. Importing a Standard Curve

30. Importing a Standard Curve

31. Importing a Standard Curve Imported standard curve is highlighted in yellow.

32. Saving an Imported Standard Curve

33. Quantitation of Unknowns

34. Maintenance Screen

35. Smart Cycler Menus User Administration Login/Logout

36. Login

37. Smart Cycler Menus Run and Specimen logs allow the user to search by run name or specimen name.

38. Run log

39. Run Report

40. Specimen report

41. Specimen report

42. Specimen report

44. User Administration tamlyn tamlyn **** **** Enter a User Name and Password

45. Configure User Select User name User Rights.

47. General

48. Analysis Setting

49. Automatic Backup

50. Default Export Settings

51. Default Export Settings

52. Default Export Settings

53. Export graph data

54. Export graph data

55. Melt Settings

57. Melt Settings

58. Melt Settings

59. Melt Settings

60. Melt Settings

61. Melt Settings

62. Melt Settings

63. Access Option

64. Smart Cycler Menus

65. Smart Cycler Menus

71. Signal Analysis - Version 1 and 2

72. Help Menus

73. Help Menus

74. Software Diagnostic

75. Software Diagnostic cmartcycleroolsyclerdiagnostics Tools used by technicians/engineers to perform functional testing and trouble-shooting of the smartcycler

76. Software Diagnostic Command Menu Site(s) activation table Cycler Diagnostic Rev.

77. Software Diagnostic GetDeviceSN : Reports the serial number of the instrument, backplane, the CPU board, the instrument model number and bootcode revision number

78. Software Diagnostic

79. Software Diagnostic

80. Troubleshooting examples

85. Frequently Asked Questions

87. Rules 1.White coat must be worn at all times in the laboratory. Coats are stored in the laboratory. Coats are removed before leaving the laboratory. 2.Never ingest any chemical from lab and, if a chemical is spilled on your hands, wash them immediately 3.You must ALWAYS thoroughly wash and scrub your hands before you leave the laboratory. 4.Follow the specific safety rules for each hazardous chemical. Each hazardous chemical will be given to you with specific instructions for its handling. These vary from chemical to chemical depending on the hazard each presents. Follow these instructions exactly and ask for assistance if you are unsure about how to proceed.

88. How remove gloves Wash your hands. finish turn the first glove inside out and discard it … turn completly the second glove inside out and discard it 6 5 4 With fingers wrapped in glove turned inside out take the second glove off… Remove glove till appearance. Seize glove few centimeters from glove rims. 3 2 1

89. Recommendations relating to hand washing Use towel to turn off water and discard in open bin Dry hands with disposable hand towel. Thoroughly rinse. 6 5 4 Rub hands together for 30 secondes, work all surfaces, insist on palms. Collect one dose of liquid soap. Roll up sleeves first and wet hands. 3 2 1