Agilent Technologies E5500 Series Guide de l'utilisateur

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USER GUIDE
Fragment Library Preparation Using the
AB Library Builder
System
5500 Series SOLiD
Systems
Publication Part Number 4460965 Rev. A
Revision Date March 2011
design experiment
X prepare libraries
prepare beads
run sequencer
analyze data
Vue de la page 0
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Résumé du contenu

Page 1 - AB Library Builder

USER GUIDEFragment Library Preparation Using theAB Library Builder™ System5500 Series SOLiD™ SystemsPublication Part Number 4460965 Rev. ARevision Dat

Page 2

10Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter1 About the ProductsProduct inform

Page 3 - Contents

11Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter1 About the ProductsKit contents a

Page 4

12Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter1 About the ProductsKit contents a

Page 5

13Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideCHAPTER2 Prepare to Build the LibraryWor

Page 6

14Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter2 Prepare to Build the LibraryQuan

Page 7 - About This Guide

15Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter2 Prepare to Build the LibraryShea

Page 8

16Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter2 Prepare to Build the LibraryShea

Page 9 - About the Products

17Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter2 Prepare to Build the LibrarySet

Page 10 - How to use the

18Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter2 Prepare to Build the LibrarySet

Page 11 - Kit contents

19Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter2 Prepare to Build the LibrarySet

Page 12 - Chapter1 About the Products

For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use.This user guide is the proprietary material of Applied Biosy

Page 13 - Procedural guidelines

20Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter2 Prepare to Build the LibrarySet

Page 14 - Quantitate the DNA

21Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter2 Prepare to Build the LibrarySet

Page 15

22Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter2 Prepare to Build the LibrarySet

Page 16 - 5. Remove the sheared DNA:

23Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter2 Prepare to Build the LibrarySet

Page 17 - System for size-selected or

24Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter2 Prepare to Build the LibrarySet

Page 18 - Insert or change

25Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter2 Prepare to Build the LibrarySet

Page 19 - Load the racks and

26Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter2 Prepare to Build the LibrarySet

Page 20 - Load the cartridge rack

27Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideCHAPTER3 Build the libraryWorkflowFor ad

Page 21

28Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter3 Build the librarySet up for a ne

Page 22

29Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideCHAPTER4 Nick-Translate the Library with

Page 23 - Insert the racks

Contents3Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User Guide About This Guide . . . . . . . .

Page 24

30Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter4 Nick-Translate the Library with

Page 25 - Insert the tip and tube rack

31Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter4 Nick-Translate the Library with

Page 26

32Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter4 Nick-Translate the Library with

Page 27 - Build the library

33Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter4 Nick-Translate the Library with

Page 28 - Set up for a new run

34Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter4 Nick-Translate the Library with

Page 29 - Optional Amplification

35Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideCHAPTER5 TroubleshootingFor symptoms oth

Page 30 - Purify the nick

36Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter5 TroubleshootingRun stops after a

Page 31 - Prepare the

37Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter5 Troubleshooting After the automa

Page 32

38Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideChapter5 TroubleshootingInstrument error

Page 33

39Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAAPPENDIXA Ordering InformationThis appe

Page 34

4Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideContentsAPPENDIX A Ordering Information .

Page 35 - Troubleshooting

40Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixA Ordering InformationRequired Ap

Page 36 - Chapter5 Troubleshooting

41Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixA Ordering InformationRequired Ap

Page 37

42Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixA Ordering InformationRequired eq

Page 38 - Instrument error codes

43Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixA Ordering InformationRequired eq

Page 39 - Ordering Information

44Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixA Ordering InformationOptional eq

Page 40

45Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixA Ordering InformationRequired co

Page 41

46Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixA Ordering InformationOptional co

Page 42 - Required equipment

47Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideBAPPENDIXB Supplemental ProceduresThis a

Page 43

48Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixB Supplemental ProceduresAB Libra

Page 44 - Replacement parts

49Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixB Supplemental ProceduresAB Libra

Page 45 - Required consumables

5Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideContents Glossary . . . . . . . . . . . . .

Page 46 - Optional consumables

50Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixB Supplemental ProceduresAB Libra

Page 47 - Supplemental Procedures

51Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixB Supplemental Procedures(Optiona

Page 48 - System operation

52Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixB Supplemental Procedures(Optiona

Page 49

53Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixB Supplemental Procedures(Optiona

Page 50 - Manage the run

54Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixB Supplemental Procedures(Optiona

Page 51 - Size-select the

55Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixB Supplemental ProceduresQuantita

Page 52

56Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixB Supplemental ProceduresQuantita

Page 53

57Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixB Supplemental ProceduresQuantita

Page 54 - Sample wells

58Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixB Supplemental ProceduresQuantita

Page 55 - Spectrophotometer

59Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideCAPPENDIXC Supplemental BackgroundInform

Page 56 - 2. Open the NanoDrop

6Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideContents

Page 57

60Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixC Supplemental Background Informa

Page 58

61Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixC Supplemental Background Informa

Page 59 - Information

62Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixC Supplemental Background Informa

Page 60 - Library molecule ligated

63Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideDAPPENDIXD Library ConstructionOligonucl

Page 61

64Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixD Library Construction Oligonucle

Page 62 - Guide (Part no. 4456991)

65Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixD Library Construction Oligonucle

Page 63 - Oligonucleotide Sequences

66Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixD Library Construction Oligonucle

Page 64

67Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixD Library Construction Oligonucle

Page 65

68Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixD Library Construction Oligonucle

Page 66

69Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixD Library Construction Oligonucle

Page 67

7Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User Guide About This GuideSafety informationNote: For

Page 68

70Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixD Library Construction Oligonucle

Page 69

71Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixD Library Construction Oligonucle

Page 70

72Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixD Library Construction Oligonucle

Page 71

73Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideEAPPENDIXE Checklist and workflow tracki

Page 72

74Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixE Checklist and workflow tracking

Page 73 - System Kit

75Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixE Checklist and workflow tracking

Page 74

76Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixE Checklist and workflow tracking

Page 75

77Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideFAPPENDIXF SafetyThis appendix covers:

Page 76

78Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixF SafetySDSsFChemical safety guid

Page 77 - Safety

79Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixF SafetyChemical waste safetyF WA

Page 78 - Chemical waste safety

8Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAbout This GuideSafety informationSDSs The S

Page 79 - Waste disposal

80Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideAppendixF SafetyBiological hazard safetyF

Page 80 - Biological hazard safety

81Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User Guide Documentation and SupportRelated documenta

Page 81 - Documentation and Support

82Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideDocumentation and SupportObtaining support

Page 82

83Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User Guide Glossarybarcode A short, unique sequence t

Page 83 - Glossary

84Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideGlossaryP1-T AdaptorA T-tailed double-stran

Page 84 - Standard Adaptor

85Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User Guide IndexAAB Library Builder Systemrunning 27A

Page 85

86Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideIndexNNanoDrop® ND-1000 Spectrophotometer 5

Page 86

4460965AHeadquarters5791 Van Allen Way | Carlsbad, CA 92008 USA | Phone +1 760 603 7200 | Toll Free in USA 800 955 6288For support visit www.app

Page 87 - Headquarters

9Fragment Library Preparation Using the AB Library Builder™ System: 5500 Series SOLiD™ Systems User GuideCHAPTER1 About the ProductsNote: For comp

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