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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
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Podsumowanie treści

Strona 1 - AB Library Builder

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

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

Strona 3 - Contents

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

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

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

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

Strona 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

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

Strona 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

Strona 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

Strona 11 - Kit contents

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

Strona 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

Strona 13 - Procedural guidelines

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

Strona 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

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

Strona 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

Strona 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

Strona 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

Strona 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

Strona 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

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

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

Strona 23 - Insert the racks

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

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

Strona 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

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

Strona 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

Strona 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

Strona 29 - Optional Amplification

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

Strona 30 - Purify the nick

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

Strona 31 - Prepare the

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

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

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

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

Strona 35 - Troubleshooting

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

Strona 36 - Chapter5 Troubleshooting

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

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

Strona 38 - Instrument error codes

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

Strona 39 - Ordering Information

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

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

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

Strona 42 - Required equipment

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

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

Strona 44 - Replacement parts

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

Strona 45 - Required consumables

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

Strona 46 - Optional consumables

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

Strona 47 - Supplemental Procedures

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

Strona 48 - System operation

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

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

Strona 50 - Manage the run

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

Strona 51 - Size-select the

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

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

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

Strona 54 - Sample wells

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

Strona 55 - Spectrophotometer

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

Strona 56 - 2. Open the NanoDrop

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

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

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

Strona 59 - Information

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

Strona 60 - Library molecule ligated

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

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

Strona 62 - Guide (Part no. 4456991)

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

Strona 63 - Oligonucleotide Sequences

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

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

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

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

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

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

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

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

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

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

Strona 73 - System Kit

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

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

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

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

Strona 77 - Safety

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

Strona 78 - Chemical waste safety

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

Strona 79 - Waste disposal

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

Strona 80 - Biological hazard safety

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

Strona 81 - Documentation and Support

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

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

Strona 83 - Glossary

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

Strona 84 - Standard Adaptor

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

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

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

Strona 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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