Description: UltraIIDirectionalRNALibraryPrepwithSamplePurificationBeadsdeliverssignificantlyincreasedsensitivityandspecificityfromyourRNA-seqexperiments,fromever-decreasingamountsofinputRNA.InconjunctionwithribosomalRNA(rRNA)depletionorpoly(A)enrichment,thekitenablestheproductionofhighqualitylibrariesfrom5ngor10ngofTotalRNA,respectively,upto1µg. ThiskitcontainsNEB NextSamplePurificationBeads(SPRIselect® beadsfromBeckman Coulter)forsizeselectionandenzymereactioncleanup. Strand-specific/directionalmethodsforsequencingRNAprovideinformationontheDNAstrandfromwhichtheRNAstrandwastranscribed.Thisisusefulformanyreasonsincluding:Identificationofantisensetranscripts,determinationofthetranscribedstrandofnoncodingRNA,andmeasurementofexpressionlevelsofcodingornoncodingoverlappingtranscripts.Overall,theABI litytodeterminetheoriginatingstrandcansubstantiallyenhancethevalueofaRNA-seqexperiment. TheNEBNextUltraIIDirectionalRNALibraryPrepKitderivesitsdirectionalityfromthe“dUTP”methodforstrand-specificity,withprovensuperiorityforthisapplication. Features
Getmoreofwhatyouneed,withthehighestlibraryyields GeneratehighqualitylibrariesevenwhenyouhaveonlylimitedamountsofinputRNA:10ng–1µgTotalRNA(polyAmRNAworkflow) 5ng–1µgTotalRNA(rRNAdepletionworkflow) Minimizebias,withfewerPCRcyclesrequired Increasethecomplexityandtranscriptcoverageofyourlibraries Optimizeyourtimewithstreamlinedworkflows,reducedhands-ontime,andautomationcompatibility Relyonrobustperformance,evenwithlowqualityRNA,includingFFPE EnjoytheflexibilityandreliabilityofthegoldstandardSPRIselectsizeselectionandclean-upbeads,suppliedinjusttheamountsyouneed Alsoavailable
without SPRIselect
® beadsforclean-upandsize-selectionsteps.
Pleasenotethatadaptors,primers,rRNAdepletionreagentsandpoly(A)mRNAisolationreagentsarenotincludedinthekitandareavailableseparately.
ForextensiveNEBNextUltraIIperformancedata,clickthelinksintheFeaturesaboveanddownloadourtechnicalnoteforpoly(A)mRNAisolationorourtechnicalnoteforrRNAdepletion
. LIBRARYYIELDS Figure1.NEBNextUltraIIDirectionalRNAproducesthehighestyields,fromarangeofinputamounts Poly(A)-containingmRNAwasisolatedfromHumanUniversalReferenceRNA(Agilent #740000),andlibrariesweremadeusingtheNEBNextUltraIIDirectionalRNAKit(plustheNEBNextPoly(A)mRNAMagneticIsolationModule),KapaStrandedmRNA-SeqKit,KapamRNAHyperPrepKitandIllumina TruSeqStrandedmRNAKit.TheinputRNAamountandnumberofPCRcyclesareindicated.Libraryyieldsfromanaverageofthreereplicatesareshown. Viewadditionaldataonlibraryyields.
GCCONTENTDISTRIBUTIONFigure2.NEBNextUltraIIDirectionalRNAlibrariesprovideuniformGCcontentdistribution,atabroadrangeofinputamounts Poly(A)-containingmRNAwasisolatedfromHumanUniversalReferenceRNA(Agilent#740000),andlibrariesweremadeusingtheNEBNextUltraIIDirectionalRNAKit(plustheNEBNextPoly(A)mRNAMagneticIsolationModule),IlluminaTruSeqStrandedmRNAKit,KapaStrandedmRNA-SeqKitandKapamRNAHyperPrepKit.LibrariesweresequencedonanIlluminaNextSeq®500usingpaired-endmode(2x76bp).Readsweremappedtothehg19referencegenome.GCcontentdistributionforeachlibrarywascalculatedusingmappedreads.UltraIIDirectionalRNAlibrarieshaduniformGCcontentdistributionacrossarangeofinputamounts,whereasforotherkitstheGCcontentdistributionchangedwithdifferentinputamounts,indicatingtheintroductionofinput-dependentsequencebias. Viewadditionaldataonlibraryquality.
MAXIMIZINGTRANSCRIPTCOVERAGEFigure3.NEBNextUltraIIDirectionalRNAlibrariesprovideuniformcoverageacrossthegenebodyoftranscripts Poly(A)-containingmRNAwasisolatedfromHumanUniversalReferenceRNA(Agilent#740000),andlibrariesweremadeusingtheNEBNextUltraIIDirectionalRNAKit(plustheNEBNextPoly(A)mRNAMagneticIsolationModule),IlluminaTruSeqStrandedmRNAKit,KapaStrandedmRNA-SeqKitandKapamRNAHyperPrepKit.LibrariesweresequencedonanIlluminaNextSeq®500usingpaired-endmode(2x76bp).Thisviewofthe5´to3´coverageofRefSeqtranscriptsrevealsconsistentcoverageforUltraIIDirectionalRNAlibrariesasinputRNAisdecreasedfrom1μgto10ng.Thechangesapparentinotherkitsresultfromlossofcoverageatthe3´endofsometranscripts. Viewadditionaldataontranscriptcoverage.
SUPERIORLIBRARYCOMPLEXITYATLOWINPUTAMOUNTSFigure4.LowinputNEBNextUltraIIDirectionalRNAlibrariesretainsuperiorcomplexity Poly(A)-containingmRNAwasisolatedfromHumanUniversalReferenceRNA(Agilent#740000),andlibrariesweremadeusingtheNEBNextUltraIIDirectionalRNAKit(plustheNEBNextPoly(A)mRNAMagneticIsolationModule),IlluminaTruSeqStrandedmRNAKit,KapaStrandedmRNA-SeqKitandKapamRNAHyperPrepKit.LibrariesweresequencedonanIlluminaNextSeq®500usingpaired-endmode(2x76bp).Salmon0.4.0wasusedforreadmappingandquantificationofallGENCODEv25transcripts.TPM=TranscriptsPerKilobaseMillion.R2 valuesforthelinearfitareshown.CorrelationanalysisofthetranscriptsindicatessuperiortranscriptexpressioncorrelationbetweenthedifferentinputsforUltraIIDirectionalRNAlibraries. Viewadditionaldataonlibrarycomplexity.
SUPERIORPERFORMANCEWITHFFPERNA Figure5.NEBNextUltraIIDirectionalRNAwithNEBNextrRNADepletionresultsinthelowestremainingribosomalRNAlevelswithFFPEsamples RibosomalRNAwasdepletedfromhumanadultnormallivertissueFFPETotalRNA(Biochain#R2234149.RIN2.5)andlibrariesweremadeusingNEBNextUltraIIDirectionalRNAKit(plustheNEBNextrRNADepletionKit(Human/Mouse/Rat)),KapaStrandedRNA-SeqKitwithRiboErase,KapaHyperPrepKitwithRiboErase,andIlluminaTruSeqStrandedTotalRNALibraryPrepKitwithRibo-Zero™Gold.LibrariesweresequencedonanIlluminaNextSeq®500usingpaired-endmode(2x76bp).ReadpairswereassessedtoberRNAiftheycontain6ormore32basematchesto18S,28S,5S,5.8S,16Sor12ShumanrRNAsequences(mirabait4.9).PercentrRNAremainingwascalculatedbydividingrRNAreadsbythetotalnumberofreadspassinginstrumentqualityfiltering.AveragepercentrRNAremainingisshownforthreereplicates.TheNEBNextrRNADepletionUltraIIDirectionalRNAworkflowisthemostefficientinremovingrRNAfromtotalFFPERNA. Figure6.UniformityofCoverageacrosstheAP000769.1-201transcript RibosomalRNAwasdepletedfromhumanadultnormallivertissueFFPETotalRNA(Biochain#R2234149.RIN2.5),andlibrariesweremadeusingNEBNextUltraIIDirectionalRNAKit(plustheNEBNextrRNADepletionKit(Human/Mouse/Rat)),IlluminaTruSeqStrandedTotalRNALibraryPrepKitwithRibo-Zero™Gold,KapaStrandedRNA-SeqKitwithRiboEraseandKapaHyperPrepKitwithRiboErase.LibrariesweresequencedonanIlluminaNextSeq®500usingpaired-endmode(2x76bp).Coverageacrossthelengthofthisindividualtranscript(ENST00000625158.1;AP000769.1-201)wasassessedbymappingreadsdirectlytotheGENCODEv25transcriptsandexamining100binsalongthetranscriptlength.NEBNextUltraIIDirectionalRNAlibrariesprovidedcoverageacrosstheentirelengthofthetranscriptevenasinputwasdecreasedfrom100ngto10ng. ViewadditionaldataonFFPERNAsamples.
KitComponents Thefollowingreagentsaresuppliedwiththisproduct:
Storeat(°C) Concentration NEBNextFirstStrandSynthesisEnzymeMix -20 NEBNextStrandSpecificityReagent -20 NEBNextSecondStrandSynthesisReactionBufferwithdUTPMix -20 10X NEBNextUltraIIEndPrepEnzymeMix -20 NEBNextUltraIIEndPrepReactionBuffer -20 NEBNext® Ultra™ IILigationMasterMix -20 NEBNext® LigationEnhancer -20 NEBNextUSER® Enzyme -20 NEBNext®UltraIIQ5®MasterMix -20 2X NEBNextAdaptorDilutionBuffer -20 NEBNext® SamplePurificationBeads 25 NEBNextFirstStrandSynthesisReactionBuffer -20 RandomPrimers -20 NEBNextSecondStrandSynthesisEnzymeMix -20 (0.1X)TEBuffer -20 0.1X Nuclease-freeWater -20