A.1TheRNAiConsortium ThepLKO.1cloningvectoristhebackboneuponwhichTheRNAiConsortium(TRC)hasbuiltalibraryofshRNAsdirectedagainst15,000humanand15,000mousegenes.AddgeneisworkingwiththeTRCtomakethisshRNAcloningvectoravailabletothescientificcommunity.PleaseciteMoffatetal.,Cell2006Mar;124(6):1283-98(PubMed)inallpublicationsarisingfromtheuseofthisvector. A.2MapofpLKO.1 pLKO.1isareplication-incompetentlentiviralvectorchosenbytheTRCforexpressionofshRNAs.pLKO.1canbeintroducedintocellsviadirecttransfection,orcanbeconvertedintolentiviralparticlesforsubsequentinfectionofatargetcellline.Onceintroduced,thepuromycinresistanceMarkerencodedinpLKO.1allowsforconvenientstableselection. Figure1:MapofpLKO.1containinganshRNAinsert.TheoriginalpLKO.1-TRCcloningvectorhasa1.9kbstufferthatisreleasedbydigestionwithAgeIandEcoRI.shRNAoligosareclonedintotheAgeIandEcoRIsitesinplaceofthestuffer.TheAgeIsiteisdestroyedinmostcases(dependingonthetargetsequence),whiletheEcoRIsiteispreserved.ForacompletemapofpLKO.1containingthe1.9kbstuffer,visitwww.addgene.org/10878. Figure2:DetailofshRNAinsert.TheU6promoterdirectsRNAPolymeraseIIItranscriptionoftheshRNA.TheshRNAcontains21"sense"basesthatareidenticaltothetargetgene,aloopcontaininganXhoIrestrictionsite,and21"antisense"basesthatarecomplementarytothe"sense"bases.TheshRNAisfollowedbyapolyTterminationsequenceforRNAPolymeraseIII. A.3RelatedProducts ThefollowingplasmidsavailablefromAddgenearerecommendedforuseinconjunctionwiththepLKO.1TRC-cloningvector. Note:pLKO.1canalsobeusedwithpackagingplasmidpCMV-dR8.2dvpr(Addgene#8455)andenvelopeplasmidpCMV-VSVG(Addgene#8454)fromRobertWeinberg""slab.Formoreinformation,visitAddgene""sMammalianRNAiToolspage. SeveralotherlaboratorieshavedepositedpLKOderivedvectorsthatmayalsobeusefulforyourexperiment.Toseethesevectors,visitAddgene""swebsiteandsearchfor"pLKO". BacktoTop B.1DeterminingtheOptimal21-merTargetsinyourGene Selectionofsuitable21-mertargetsinyourgeneisthefirststeptowardefficientgenesilencing.Methodsfortargetselectionarecontinuouslybeingimproved.Belowaresuggestionsfortargetselection. 1.UseansiRNAselectiontooltodetermineasetoftop-scoringtargetsforyourgene.Forexample,theWhiteheadInstituteforBiomedicalResearchhostsansiRNASelectionProgramthatcanbeaccessedafterafreeregistration(http://jura.wi.mit.edu/bioc/siRNAext/).IfyouhaveMacOSX,anotherexcellentprogramisiRNAi,whichisprovidedfreebythecompanyMekentosj(http://www.mekentosj.com/irnai/). AsummaryofguidelinesfordesigningsiRNAswitheffectivegenesilencingisincludedhere: 2.Tominimizedegradationofoff-targetmRNAs,useNCBI""sBLASTprogram.Selectsequencesthathaveatleast3nucleotidemismatchestoallunrelatedgenes. B.2OrderingOligosCompatiblewithpLKO.1 TogenerateoligosforcloningintopLKO.1,insertyoursenseandantisensesequencesfromstepB.1intotheoligosbelow.Donotchangetheends;thesebasesareimportantforcloningtheoligosintothepLKO.1TRC-cloningvector. Forwardoligo: 5""CCGG—21bpsense—CTCGAG—21bpantisense—TTTTTG3"" Reverseoligo: 5""AATTCAAAAA—21bpsense—CTCGAG—21bpantisense3"" Forexample,ifthetargetsequenceis(AA)TGCCTACGTTAAGCTATAC,theoligoswouldbe: Forwardoligo: 5""CCGGAATGCCTACGTTAAGCTATACCTCGAGGTATAGCTTAACGTAGGCATTTTTTTG3"" Reverseoligo: 5""AATTCAAAAAAATGCCTACGTTAAGCTATACCTCGAGGTATAGCTTAACGTAGGCATT3"" BacktoTop ThepLKO.1-TRCcloningvectorcontainsa1.9kbstufferthatisreleasedupondigestionwithEcoRIandAgeI. TheoligosfromsectionBcontaintheshRNAsequenceflankedbysequencesthatarecompatiblewiththestickyendsofEcoRIandAgeI.ForwardandreverseoligosareannealedandligatedintothepLKO.1vector,producingafinalplasmidthatexpressestheshRNAofinterest. C.1RecommendedMaterials C.2AnnealingOligos 1.ResuspendoligosinddH2Otoaconcentrationof20μM,thenmix: 2.Incubatefor4minutesat95oCinaPCRmachineorinabeakerofboilingwater. 3.IfusingaPCRmachine,incubatethesampleat70oCfor10minutesthenslowlycooltoroomtemperatureovertheperiodofseveralhours.Ifusingabeakerofwater,removethebeakerfromtheflame,andallowthewatertocooltoroomtemperature.Thiswilltakeafewhours,butitisimportantforthecoolingtooccurslowlyfortheoligostoanneal. C.3DigestingpLKO.1TRCCloningVector 1.DigestpLKO.1TRC-cloningvectorwithAgeI.Mix: >Incubateat37oCfor2hours. 2.PurifywithQiaquickgelextractionkit.Elutein30μLofddH2O. 3.DigesteluatewithEcoRI.Mix: >Incubateat37oCfor2hours. 4.RundigestedDNAon0.8%lowmeltingpointagarosegeluntilyoucandistinctlysee2bands,one7kbandone1.9kb.Cutoutthe7kbbandandplaceinasterilemicrocentrifugetube. 5.PurifytheDNAusingaQiaquickgelextractionkit.Elutein30μLofddH2O. 6.MeasuretheDNAconcentration. C.4LigatingandTransformingintoBacteria 1.Useyourligationmethodofchoice.ForastandardT4ligation,mix: >Incubateat16oCfor4-20hours. 2.Transform2μLofligationmixinto25μLcompetentDH5alphacells,followingmanufacturer""sprotocol.PlateonLBagarplatescontaining100μg/mLampicillinorcarbenicillin(anampicillinanalog). BacktoTop Youmayscreenforplasmidsthatweresuccessfullyligatedbyrestrictionenzymedigestion.However,onceyouhaveidentifiedthepositiveclones,itisimportanttoverifytheinsertbyconductingasequencingreaction. D.1RecommendedMaterials D.2ScreeningforInserts Day1: Day2: 3.ConductarestrictiondigestwithEcoRIandNcoI: >Incubateat37oCfor1-2hours. 4.Runthedigestionproductsona1%agarosegel.Youshouldseetwofragments,a2kbfragmentanda5kbfragment. 5.SequencepositivecloneswithpLKO.1sequencingprimer(5""CAAGGCTGTTAGAGAGATAATTGGA3""). BacktoTop Fortransientknockdownofproteinexpression,youmaytransfectplasmidDNAdirectlyintothetargetcells.TheshRNAwillbeexpressed,buttheDNAisunlikelytobeintegratedintothehostgenome. Forstableloss-of-functionexperiments,Addgenerecommendsthatyougeneratelentiviralparticlesandinfectthetargetcells.AdditionofpuromycinwillallowyoutoselectforcellsthatstablyexpressyourshRNAofinterest. E.1RecommendedMaterials Note:pLKO.1couldalsobepackagedusingpCMV-dR8.2dvprandpCMV-VSVGfromtheRobertWeinberglab.Formoreinformation,visitAddgene""sMammalianRNAiToolspage. E.2ProtocolforProducingLentiviralParticles Thisprotocolisfortransfectionina6cmplate.Theprotocolcanbescaledtoproducedifferentamountsofvirusasneeded. Day1: Day2: c.Inpolypropylenemicrofugetubes(doNOTusepolystyrenetubes),makeacocktailforeachtransfection: d.CreateamastermixofFuGENE®6transfectionreagentinserum-freeOPTI-MEM.CalculatetheamountofFugene®andOPTI-MEMnecessarygiventhateachreactionwillrequire6μLFuGENE®+74μLOPTI-MEM.Forexample: e.Add80μLofFuGENE®mastermixtoeachtubefromstepcforatotalvolumeof100μL.Pipettemastermixdirectlyintotheliquidandnotontothewallsofthetube.Mixbyswirlingorgentlyflickingthetube. f.Incubatefor20-30minutesatroomtemperature. g.RetrieveHEK-293Tcellsfromincubator.Thecellsshouldbe50-80%confluentandinDMEMthatdoesnotcontainantibiotics. h.Withouttouchingthesidesofthedish,gentlyaddDNA:FuGENE®mixdropwisetocells.Swirltodispersemixtureevenly.Donotpipetteorswirltoovigorously,asyoudonotwanttodislodgethecellsfromtheplate. i.Incubatecellsat37oC,5%CO2for12-15hours. Day3: k.Incubatecellsat37oC,5%CO2for24hours. Day4: m.Add5mLoffreshmediacontainingantibioticstothecellsandincubateat37oC,5%CO2for24hours. Day5: o.Virusmaybestoredat4oCforafewdays,butshouldbefrozenat-20oCor-80oCforlong-termstorage. BacktoTop Lentiviralparticlescanefficientlyinfectabroadrangeofcelltypes,includingbothdividingandnon-dividingcells.AdditionofpuromycinwillallowyoutoselectforcellsthatarestablyexpressingyourshRNAofinterest. F.1.RecommendedMaterials *Detailedprotocolsforpreparingpolybrene,protaminesulfate,andpuromycinarelocatedintheAppendix. F.2.DeterminingtheOptimalPuromycinConcentration Eachcelllinerespondsdifferentlytopuromycinselection.Addgenestronglyrecommendsthatyoudeterminetheoptimalpuromycinconcentrationforyourcelllinebeforeinitiatingyourexperiment. Day1: Day2: c.Dilutepuromycininthepreferredculturemediaforyourtargetcells.Thefinalconcentrationofpuromycinshouldbefrom1-10μg/mLin1μg/mLincrements. d.Labelplatesfrom1-10andaddappropriatepuromycin-containingmediatocells. Days3+: f.Theminimumconcentrationofpuromycinthatresultsincompletecelldeathafter3-5daysistheconcentrationthatshouldbeusedforselectioninyourexperiments.(Youmaywishtorepeatthistitrationwithfinerincrementsofpuromycintodetermineamorepreciseoptimalpuromycinconcentration.) F.3.ProtocolforLentiviralInfectionandSelection Day1: Day2: c.AddlentiviralparticlesolutionfromstepE.Fora6cmtargetplate,addbetween0.05-1mLvirus(add≥0.5mLforahighMOI,and≤0.1mLforalowMOI).Scaletheamountofvirusaddeddependingonthesizeofyourtargetplate. d.Incubatecellsat37oC,5%CO2overnight. Day3: f.Toselectforinfectedcells,addpuromycintothemediaattheconcentrationdeterminedinstepE.2. Days4+: h.Assayinfectedcells.Thefollowingrecommendationsareguidelinesforthenumberofdaysyoushouldwaituntilharvestingyourcells.However,youshouldoptimizethetimebasedonyourcelllineandassay: BacktoTop BL2safetypracticesshouldbefollowedwhenpreparingandhandlinglentiviralparticles.Personalprotectiveclothingshouldbewornatalltimes.Useplasticpipettesinplaceofglasspipettesorneedles.Liquidwasteshouldbedecontaminatedwithatleast10%bleach.Laboratorymaterialsthatcomeincontactwithviralparticlesshouldbetreatedasbiohazardouswasteandautoclaved.PleasefollowallsafetyguidelinesfromyourinstitutionandfromtheCDCandNIHforworkinaBL2facility. Ifyouhaveanyquestionsaboutwhatsafetypracticetofollow,pleasecontactyourinstitution""ssafetyoffice. ToobtaintheMSDSforthisproduct,visitwww.addgene.org/sitemapandfollowtheMSDSlink. BacktoTop H.1.PublishedArticles KhvorovaAet.al.2003.FunctionalsiRNAsandmiRNAsexhibitstrandbias.Cell115:209-216.(PubMed) MoffatJet.al.2006.AlentiviralRNAilibraryforhumanandmousegenesappliedtoanarrayedviralhigh-contentscreen.Cell124:1283-1298.(PubMed) NaldiniLet.al.1996.Invivogenedeliveryandstabletransductionofnondividingcellsbyalentiviralvector.Science272:263-267.(PubMed) SchwarzDSet.al.2003.AsymmetryintheassemblyoftheRNAienzymecomplex.Cell115:199-208.(PubMed) StewartSAet.al.2003.Lentivirus-deliveredstablegenesilencingbyRNAiinprimarycells.RNA9(4):493-501.(PubMed) ZuffereyRet.al.1997.Multiplyattenuatedlentiviralvectorachievesefficientgenedeliveryinvivo.NatBiotechnol15(9):871-5.(PubMed) ZuffereyRet.al.1998.Self-inactivatinglentivirusvectorforsafeandefficientinvivogenedelivery.JVirol72(12):9873-80.(PubMed) H.2.Webresources Addgene""smammalianRNAiwebsite:www.addgene.org/rnaitools TheRNAiConsortium(TRC):www.broad.mit.edu/genome_bio/trc/rnai.html BackgroundonRNAimechanism:www.nature.com/focus/rnai/animations/animation/animation.htm WhiteheadsiRNASelectionProgram:jura.wi.mit.edu/bioc/siRNAext/ MekentosjiRNAiProgram:www.mekentosj.com/irnai/ BacktoTop I.1.SequenceofpLKO.1TRC-CloningVector Clickhere(http://www.addgene.org/10878)toseethesequenceofpLKO.1TRC-cloningvector.Thevectoris8901basepairstotal,andthestufferinsertisshowninallcapitalletters. I.2.Recipes LuriaBrothAgar(LBagar)+antibiotic Per40gramsofpowderfromAmericanBioanalyticalcatalog#AB01200-02000,LBcontains: >PrepareLBagarsolutionbydissolving40gofLBpowderin1Lofdistilledwater.Autoclaveandcoolto55oC.Add1mLof100mg/mLampicillinorcarbenicillintoobtainafinalconcentrationof100μg/mLantibiotic.Pourplatesandstoreat4oC. HexadimethrineBromide(Polybrene) Preparea1mg/mLsolutionofpolybrene(Sigma-Aldrichcatalog#H9268)in0.9%NaCl.Autoclavetosterilize.Stocksolutionisstableat4oCforuptooneyear.Thepowderformofpolybreneisstableat4oCforseveralyears. ProtamineSulfate Storeprotaminesulfate(MPBiomedicalscatalog#194729)at4oC.Freelysolubleinhotwaterandslightlysolubleincoldwater. Puromycin Preparea50mg/mLstocksolutionofpuromycin(Sigma-Aldrichcatalog#P8833)indistilledwater.Sterilizebypassingthrougha0.22μmfilter.Storealiquotsat-20oC. I.3.WarrantyInformation Addgeneiscommittedtoprovidingscientistswithhigh-qualitygoodsandservices.Addgenemakeseveryefforttoensuretheaccuracyofitsliterature,butrealizesthattypographicalorothererrorsmayoccur.Addgenemakesnowarrantyofanykindregardingthecontentsofanyliterature.Literatureareprovidedtoyouasaguideandonan"ASIS""ASAVAILABLE"basiswithoutwarrantyofanykindeitherexpressedorimplied,includingbutnotlimitedtotheimpliedwarrantiesoffitnessforaparticularpurpose,non-infringement,typicality,safetyandaccuracy. ThedistributionofanyliteraturebyAddgeneisnotmeanttocarrywithit,anddoesnotgrantanylicenseorrightsofaccessorusetothematerialsdescribedintheliterature. ThedistributionofmaterialsbyAddgeneisnotmeanttocarrywithit,anddoesnotgrantanylicense,expressorimplied,underanypatent.AlltransfersofmaterialsfromAddgenetoanypartyaregovernedbyAddgene""sTermsofUse,Addgene""sTermsofPurchase,andapplicableMaterialTransferAgreementsbetweenthepartythatdepositedthematerialatAddgeneandthepartyreceivingthematerial.
Description VectorElement U6 HumanU6promoterdrivesRNAPolymeraseIIItranscriptionforgenerationofshRNAtranscripts. cPPT Centralpolypurinetract,cPPT,improvestransductionefficiencybyfacilitatingnuclearimportofthevector""spreintegrationcomplexinthetransducedcells. hPGK Humanphosphoglyceratekinasepromoterdrivesexpressionofpuromycin. PuroR PuromycinresistancegeneforselectionofpLKO.1plasmidinmammaliancells. sin3""LTR 3""Self-inactivatinglongterminalrepeat. f1ori f1bacterialoriginofreplication. AmpR AmpicillinresistancegeneforselectionofpLKO.1plasmidinbacterialcells pUCori pUCbacterialoriginofreplication. 5""LTR 5""longterminalrepeat. RRE Revresponseelement. 
Plasmid(AddgeneID#) Description pLKO.1-TRCcontrol(10879) Negativecontrolvectorcontainingnon-hairpininsert. pLKO.1-scrambleshRNA(1864) NegativecontrolvectorcontainingscrambledshRNA. psPAX2(12260) Packagingplasmidforproducingviralparticles. pMD2.G(12259) Envelopeplasmidforproducingviralparticles.
Addgenerecommendsthatyouselectmultipletargetsequencesforeachgene.Somesequenceswillbemoreeffectivethanothers.Inaddition,demonstratingthattwodifferentshRNAsthattargetthesamegenecanproducethesamephenotypewillalleviateconcernsaboutoff-targeteffects.Material Vendorandcatalog# AgeI NewEnglandBiolabs(NEB)#R0552S EcoRI NEB#R0101S T4DNAligase NEB#M0202S NEBbuffer2 NEB#B7002S DH5alphacompetentcells Invitrogen#18258-012 Qiaquickgelextractionkit Qiagen#28704 Lowmeltingpointagarose Sigma#A9414 LuriaBrothAgar(LBagar) AmericanBioanalytical:#AB01200-02000 Ampicillin VWR:#7177-48-2.Useat100μg/mL. Carbenicillin VWR:#80030-956.Useat100μg/mL. 5μL Forwardoligo 5μL Reverseoligo 5μL 10xNEBbuffer2 35μL ddH2O 6μg pLKO.1TRC-cloningvector(maxipreporminiprepDNA) 5μL 10xNEBbuffer1 1μL AgeI to50μL ddH2O 30μL pLKO.1TRC-cloningvectordigestedwithAgeI 5μL 10xNEBbufferforEcoRI 1μL EcoRI 14μL ddH2O
WhenvisualizingDNAfragmentstobeusedforligation,useonlylong-wavelengthUVlight.ShortwavelengthUVlightwillincreasethechanceofdamagingtheDNA.2μL annealedoligofromstepC.2. 20ng digestedpLKO.1TRC-cloningvectorfromstepC.3.(IfyouwereunabletomeasuretheDNAconcentration,use1μL) 2μL 10xNEBT4DNAligasebuffer 1μL NEBT4DNAligase to20μL ddH2O Material Vendorandcatalog# DNAMiniprepKit Qiagen#27104 EcoRI NEB#R0101S NcoI NEB#R0193S Agarose Sigma#A9539 1.Innoculate5coloniesfromeachligationintoLB+100μg/mLampicillinorcarbenicillin.
2.SpindowntheculturesanduseaminiprepkittoobtainDNA.
1μg miniprepDNA 2μL 10xNEBbufferforEcoRI 0.8μL EcoRI 0.8μL NcoI to20μL ddH2O
YoumayneedtoadjustthesequencingconditionsiftheDNApolymerasehasdifficultyreadingthroughthesecondarystructureofthehairpinsequence.Beforethisstep,youmustcontactyourinstitution""sBio-Safetyofficetoreceivepermissionandinstitution-specificinstructions.Youmustfollowsafetyproceduresandworkinanenvironment(e.g.BL2+)suitableforhandlingHIV-derivativeviruses. Material Vendorandcatalog# psPAX2 Addgene#12260 pMD2.G Addgene#12259 HEK-293Tcells GenHunter:#Q401 FuGENE®6TransfectionReagent RocheAppliedBiosciences:#11814443001 OPTI-MEM®serum-freemedia Invitrogen:#31985 Dulbecco""sModifiedEagleMedium(DMEM) Invitrogen:#11995 FetalBovineSerum(FBS) Invitrogen:#16000 Penicillin/Streptomycin Invitrogen:#15140-122 Polypropylenetubes VWR:#87003-290 a.Foreachplasmidtobetransfected,plate7x105HEK-293Tcellsin5mLofmediaina6cmtissuecultureplate.Incubatecellsat37oC,5%CO2overnight.
AlthoughcellsshouldregularlybepassagedinDMEM+10%FBSwithpenicillin/streptomycin,cellsshouldbeplatedatthisstepinDMEM+10%FBSwithoutantibiotics(nopenicillinorstreptomycin).
b.Performthetransfectioninthelateafternoonbecausethetransfectionmixshouldonlybeincubatedwiththecellsfor12-15hours.
1μg pLKO.1shRNAplasmid 750ng psPAX2packagingplasmid 250ng pMD2.Genvelopeplasmid to20μl serum-freeOPTI-MEM
YoumaywanttovarytheratioofshRNAplasmid,packagingplasmid,andenvelopeplasmidtoobtaintheratiothatgivesyoutheoptimalviralproduction.
Inapolypropylenetube,addOPTI-MEMfirst.PipetteFuGENE®directlyintotheOPTI-MEM-donotallowFuGENE®tocomeincontactwiththewallsofthetubebeforeithasbeendiluted.Mixbyswirlingorgentlyflickingthetube.Incubatefor5minutesatroomtemperature.1xmastermix: 6μLFuGENE®+74μLOPTI-MEM 5xmastermix: 30μLFuGENE®+370μLOPTI-MEM 10xmastermix: 60μLFuGENE®+740μLOPTI-MEM j.Inthemorning,changethemediatoremovethetransfectionreagent.Replacewith5mLfreshDMEM+10%FBS+penicillin/streptomycin.Pipettethemediaontothesideoftheplatesoasnottodisturbthetransfectedcells.
l.Harvestmediafromcellsandtransfertoapolypropylenestoragetube.Themediacontainsyourlentiviralparticles.Storeat4oC.
n.HarvestmediafromcellsandpoolwithmediafromDay4.Spinmediaat1,250rpmfor5minutestopelletanyHEK-293Tcellsthatwereinadvertentlycollectedduringharvesting.
Inlieuofcentrifugation,youmayfilterthemediathrougha0.45μmfiltertoremovethecells.Donotusea0.2μmfilter,asthisislikelytosheartheenvelopeofyourvirus.
Freeze/thawcyclesdecreasetheefficiencyofthevirus,soAddgenerecommendsthatyouusethevirusimmediatelyoraliquotthemediaintosmallertubestopreventmultiplefreeze/thawcycles.Material Vendorandcatalog# Hexadimethrinebromide(polybrene)* Sigma-Aldrich:#H9268 ProtamineSulfate* MPBiomedicals:#194729 Puromycin* Sigma-Aldrich:#P8833 Targetcells Variesbasedonyourexperiment Culturemediafortargetcells Variesbasedonyourexperiment Materialsforassay Variesbasedonyourexperiment a.Platetargetcellsinten6cmplatesandgrowat37oC,5%CO2overnight.
b.Thetargetcellsshouldbeapproximately80-90%confluent.
e.Examinecellseachdayandchangetofreshpuromycin-containingmediaeveryotherday.
a.Platetargetcellsandincubateat37oC,5%CO2overnight.
b.Targetcellsshouldbeapproximately70%confluent.Changetofreshculturemediacontaining8μg/mLpolybrene.
Polybreneincreasestheefficiencyofviralinfection.However,polybreneistoxictosomecelllines.Inthesecelllines,substituteprotaminesulfateforpolybrene.
MOI(multiplicityofinfection)referstothenumberofinfectingviralparticlespercell.AddgenerecommendsthatyoutestarangeofMOIstodeterminetheoptimalMOIforinfectionandgenesilencinginyourtargetcellline.e.Changetofreshmedia24hoursafterinfection.
Ifviraltoxicityisobservedinyourcellline,youmaydecreasetheinfectiontimetobetween4-20hours.Removethevirus-containingmediaandreplacewithfreshmedia.Donotaddpuromycinuntilatleast24hoursafterinfectiontoallowforsufficientexpressionofthepuromycinresistancegene.
Addgenerecommendsthatyoumaintainoneuninfectedplateofcellsinparallel.Thisplatewillserveasapositivecontrolforthepuromycinselection.g.Changetofreshpuromycin-containingmediaasneededeveryfewdays.
Assay Dayspost-infection mRNAknockdown(quantitativePCR) ≥3days Proteinknockdown(westernblot) ≥4days Phenotypicassay ≥4days 10g tryptone 5g yeastextract 10g sodiumchloride 15g agar