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主营:体外转录、基因克隆(BAC克隆试剂盒)、感受态细胞(TG1噬菌体文库构建感受态)、体外转录、转座子突变、蛋白表达
℡ 4000-520-616
℡ 4000-520-616
Lucigen/NxSeq® Long Mate Pair Index Kit/13200-1/12 indices (5 libraries each)
产品编号:13200-1
市  场 价:¥12620.00
场      地:美国(厂家直采)
联系QQ:1570468124
电话号码:4000-520-616
邮      箱: info@ebiomall.com
美  元  价:$631.00
品      牌: Lucigen
公      司:Lucigen
公司分类:
Lucigen/NxSeq® Long Mate Pair Index Kit/13200-1/12 indices (5 libraries each)
商品介绍

Closeandfinishyourmicrobialgenomewithtwolibraries

  • FlexIBLeinsertsizes:gel-based20kbandgel-free<8kb
  • Enablemicrobialgenomeclosureusing20kbprotocolwithyourexistingIlluminasequencer
  • IdealforNGSdenovogenomeassembly,closureandfinishing,chromosomalrearrangementdetection,haplotyping,andBACsequencing
  • IncreasedN50"sandlargerscaffoldsfromyourassemblyinNextGenSequencing

TableofContents

  • Moreaccurateassembliestocloseandfinishyourgenome
  • Howdoesitwork?
  • ChimeraCode™sequences
  • Insertsizeflexibility
  • Indicesformultiplexinglibraries
  • NxSeqScriptsandSampleDataSet
  • NxSeqGenomeClosureServices

Moreaccurateassembliestocloseandfinishyourgenome.

Fragmentlibrariesarenotsufficienttofullyassemblegenomesduetorepetitiveelementsthatmakethecorrectorderandorientationofcontigsimpossibletodetermine. Longspanreaddata(obtainedthroughmatepairlibraries,jumpinglibraries,orinformativematepairs)canbecombinedwithfragmentlibrariestoproperlyassemblenextgenerationsequencingdataintolargescaffolds,enablingeasiergenomeclosureandfinishing. Theadditionofmatepairlibrariescanmakecost-effectivegenomeclosureareality,withlimitedmanualsequencingrequiredforsmallgenomes.


Figure1:DenovoassemblyandclosingThermusaquaticus

 JGIPermanent
DraftGenome
Fragmentlibrary
NxSeq®MatePairs
+fragmentlibrary
Manuallyfinished
Thermusaquaticusgenome
#Contigs>500bp225422NA
ContigN50106kb79kb144kbNA
Maxcontigachieved343,213167,687260,181NA
Genomescaffolds>5kb0011

Maxscaffoldachieved

343,21302,161,6782,158,963
Genomesize2,338,1932,256,9232,161,6782,338,240
Plasmidscaffolds?024
Plasmidsizes?NA14.5kb,70.3kb14,047bp,16,597bp
78,727bp,and69,906bp
 

Figure2:SingleScaffoldAssemblyofE.coliK12
Fragment+8kbMatePairLibrary

Fragmentlibrary

5,001,861reads–4,656,638mappable
Assembled2.5MreadsinSPAdeswithK45

  • Contigs>1kb: 163
  • Contigs>500bp: 184
  • N50: 56,903
  • Maxcontig:179,213bp

8kbNxSeqlibrary

Megaruptorsheared

  • Rawreads: 6,909,356 
  • Truematepairs: 3,288,275(48%ofraw)
  • Matepairdistance: 8,310bp

K12 Scaffold

DenovoassemblyofE.coliK12genome.2.5Mfragmentreadswereassembleddenovointo163contigsover1kbbySPAdes3.1.Scaffoldingwasperformedwithcommercialsoftwareusing3.2M8kbmatepairs.Thesinglescaffoldwascomparedtoareference genomewithMauve2.3.1.

 

Figure3:AssemblyofRepeat-RichMouseBACs
AssemblyFormsOne171kbScaffold

Assembly Repeat-Rich Mouse BACs

Sequenceassemblyfortworepeat-richmouseBACs.ThesequenceswereassembledwithDNAStarsoftwareusingIonTorrent400bpfragmentsand5kbNxSeqsequencedata.Despitehavingover50%repeatsequence,twoBACswereeachassembledintosinglescaffoldsof171kb(shown)and143kb(notshown).

 

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Howdoesitwork?

LucigenhascreatedanewparADIgminlongspanreadtechnologyviahighlyefficientmatepairlibrarypreptechnology. GenomicDNAisshearedtothedesiredsize(2-8kbforbead-basedmethodsand10-20kbforgel-basedsizingmethods),endrepaired,A-tailedandligatedtobarcodeadaptorspriortosizeselection.TheinsertisligatedtoauniquemultiplexcouplerwithencryptedChimeraCode™sequences.SamplesarethentreatedwithexonucleasetoremoveunwantedDNA,andfinallydigestedwithaselectionofendonucleasestoproducethecorrectsizeddi-tags.BiotincaptureallowsfortheremovalofunwantedDNAfragmentspriortotheadditionofaJunctionCodeadaptorandre-circularization. LibrariesarethenPCRamplifiedandsequencedonanIlluminasequencer.

Figure4. NxSeqLongMatePairLibraryWorkflow

NxSeq Long Mate Pair Workflow

 

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ChimeraCode™Sequences

Lucigen'spatent-pendingChimeraCodesequencesarethekeytoachievingultra-highfrequenciesoftruematepairs,ensuringthemostaccurateassemblypossible. Softwareanalysisoffinalsequencesfiltersoutfalsematepairsformedbychimerasduringthelibraryprepprocess. Asaresult,mostlibrariesachieve>90%truematepairefficiency.


Figure5.ChimericReadDetection
Chimera Code Sequence Prevents False Mates

 

Figure6.

 E.coliDH10B
2kb
E.coliDH10B
5kb
E.coliDH10B
8kb
RawReads6,377,7925,995,9746,851,682
TotalMates2,167,2862,242,9303,091,359
TrueMatePairs2,071,267
(96%)
2,094,413
(93%)
2,938,426
(95%)
ChimericReads96,019
(4%)
148,517
(7%)
152,933
(5%)

Avg.ReadLength(aftersplit)

170b161b159b
TotalMatePairBases352,115,390337,200,493467,209,734
MappedMatePairDistance2,5435,1456,191
 

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InsertSizeFlexibility–YouChooseYourLibrarySize

TheNxSeqLongMatePairLibraryKitcanaccommodateawiderangeofinsertsizestofityourneeds. Bead-based,gel-freefragmentsizingprotocolsenablelibrariesupto8kbinsertsize,whilegel-basedsizingprotocolswillaccommodate10-20kbinsertsize.
Theresultistightsizingofyourmatepairs,enablingaccurateandcompletebioinformaticassembly.

Figure7.LongMatePairLibraries

Long Mate Pair Libiraries

An8kbNxSeqLongMatePairlibrarywasconstructedusingbead-based,gel-freemethods,anda10-20kbmatepairlibrarywasconstructedusinggelisolation. Resultingtruematepairsweremappedagainsttherespectivereferencegenometodeterminetheresultingmatepairdistances.

 

 

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Indicesfor
MultiplexingLibraries

Wanttomultiplexupto12librariesatonetime? LucigenofferstheNxSeqLongMatePairLibraryIndexkitwith12differentindexedamplificationprimersets(Illuminacompatible). Seetheorderinginformationtabformoredetails.

NxSeqScripts&
SampleDataSet

ToperformbioinformaticanalysisofyourIlluminaruns,scriptsmustberuntoconfirmChimeraCodeandJunctionCodesequencesaswellasfilteroutthesesequencespriortofinalassembly. Thesescripts,alongwithasampledatasetfortrialanalysiscanbefoundhere. 

NxSeqGenome
ClosureServices

WouldyouliketohaveaNxSeqLongMatePairlibrary,butdon'twanttodoityourself?ContactourCustomGenomicServicesgroupandwe'llprovideano-obligationquoteforarangeofservicesofferedbyLucigen.

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ORDERINFORMATION

Forafulllistofreagentsandcomponentsincludedinthisproduct,refertotheusermanual. TheNxSeqLongMatePairLibrarykitincludestwoboxes,eachofwhichcanbeorderedseparately. Box1containsallreagentsnecessaryforendrepairandtailingoffragmentedDNA,ligase,andaninternaladaptersequence. Box2containsreagentsforligationtothecouplerandJunctionCode™sequence,exonucleasedigestion,biotincapture,andamplification. 

TheNxSeqLongMatePairLibraryIndexkitcontains5reactionseachof12separateindexprimersets,foratotalof60indexreactions. Thekitmaybeorderedincombinationwiththelibrarykitorasaseparateitem.

Forresearchuseonly. Notforhumanordiagnosticuse.

1Thiskitcontainsthereagentsnecessarytogenerate10librariesof8kborless. Largerlibraries,10-20kb,willusemorereagentsandgeneratefewerlibrariesperkit. Instructionstogeneratematepairlibrariesusing10-20kbinsertsaredescribedinSP001:NxSeq20kbMatePairProtocol.

品牌介绍

Lucigen


美国Lucigen公司主要开发各类用于基因克隆的试剂盒及相关产品,凭借其独到的产品技术,过硬的产品质量,良好的产品服务赢得了全球广大用户的信赖。


Lucigen Corporation is working to improve people’s lives by providing quality products and services to life science and healthcare professionals. Founded in Wisconsin in 1998, Lucigen offers products and services that enable life-science professionals to perform their research and testing more efficiently and effectively. The company has grown to manufacture and sell over 325 biomedical research products and services to customers worldwide, all under an ISO 13485 compliant quality system. Core competencies include enzyme evolution, protein expression, cloning, competent cells, next gen sequencing, and molecular diagnostics.


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