DNA Technologies Core | UC Davis

Contact us at [email protected] with any remaining questions. ... PacBio and Oxford Nanopore long read DNA sequencing and Iso-Seq RNA sequencing library ... PacBio_Sequel_II_1620x540_3 PacBioSequelIIlong-readsequencer Bionano_Genome_Mapping_1620x540 OpticalwholegenomemappingwiththeBionanoSaphyr PromethIONforHeader2_1620x540 NanoporesequencingonthePromethION 10XGenomicsChromiumSingle-Cell&Genome 10XGenomicsChromiumforsingle-cell&genomestudies DNATechCore CBSNewsreportingoutofourlaboratory Long-readandlinked-readsequencingforhighqualitygenomeassemblies FluidigmAccessArray Chips UCDGBSFAug2013 WelcometotheDNATechnologies&ExpressionAnalysisCore ApartoftheDNATechnologiesCorelabiscurrentlydedicatedtoCOVIDtestingfortheUCDcampus.SofarwehaveperformedmorethantwomillionCovid19tests.Theturnaroundtimesformostofoursequencingandgenotypingprojectshavereturnedbacktonormal. Wearecurrentlyofferingallourstandardservices. Sequencing samples(non-Covid)canbeshippedtousviaFedExandUPSasnormal.Todrop-offsamplesinperson(between9amand5pm),pleasecallthelabphoneonceyouareoutsidetheGenomeCenter(530-754-9143).Wewillmeetyouatthefrontentrancetoacceptyoursamplesandprintedsubmissionform. Inordertomeettheclinicallaboratoryrequirementsthefollowingchangestoouroperationsremaininplace: Thelabdoorsarelockedandonlystaffmembershaveaccesstothelabs. Thesharedequipmentisnotaccessibleuntilfurthernotice.Weoffersampleprocessingonthisequipmentasaservice(pleasecontactSiranooshAshtari[[email protected]]orcallthelab). ConsultationsarecarriedoutviaZoomonlinecalls. Pleasepickatimeforafreeconsultationhere TheDNATechnologiesandExpressionAnalysisCoreattheGenomeCenteroffershigh-throughputsequencing,genotyping,andmicroarrayservices,aswellastrainingandconsultation.Ourgoalistoenableaccesstohighthroughputgenome-wideanalysesateconomicalrechargerates,asafunctionalextensionofyourlaboratory.Weoperateonthecost-recoveryprinciple.Weemployliquidhandlingrobotstominimizesamplehandlingvariationandtoprovidefastturnaroundtimes.WeareadesignatedCampusResearchCoreFacility. WeofferallimportantNextGenerationSequencing(NGS)technologies:IlluminaandElementBiosciencesshort-readsequencing,PacBioandNanoporelong-readsequencing,providingthefullspectrumofsequencingoptionsandawiderangeoflibrarypreparationservicesfortheseplatforms.GenotypingisperformedontheFluidigmEP1Systemforlowtomediumassaynumbers,genotyping-by-sequencingassays,andwithIlluminaInfiniumarraysforhigh-densityarraySNPgenotyping.GeneexpressionanalysisiscarriedoutbyRNA-seqonshort-readsequencersaswellasfull-lengthtranscriptsequencingonlong-readsystems.Single-celltranscriptome(high-throughputsingle-cellgeneexpressionprofiling)areenabledbyour10XGenomicsChromiumXsystemandParseBiosciences(SPLiT-seq)assays. WeofferannualIlluminaandPacBiosequencinglibrarypreparationworkshops,freeconsultationsonprojectconsiderationsandexperimentaldesign,andcustomsequencinglibraryprepsolutions.TheCore’sequipment(withexceptionofthesequencersandthegenotypingsystems)isavailabletoscientistsoncampusasSharedEquipmentforasmallusagefee. WeoperatePacBioSequelII, SequelIIe, OxfordNanoporePromethION,ElementBiosciencesAviti,andIllumina NextSeq500, and MiSeq sequencers,andalsosequenceonanIllumina NovaSeq6000.Thesequencersarecomplementedbya10XGenomicsChromiumXsingle-cellprocessor,liquidhandlingrobots(PerkinElmer’sScicloneNGSG3,twoCybioFeliX,IntegraAssistPlusandViaflo96),aCovarisE220sonicator,andaFluidigmAccessArraySystemforhigh-throughputsampleandsequencinglibrarypreparation.WemaintainaLIMSthatallowsusersfastaccesstosequencedata. PleaseseeourFAQsandinformationonhowtogetstartedwithyoursequencingandgenotypingprojectsattheCore.Contactusatdnatech@ucdavis.eduwithanyremainingquestions. OurneighborsattheBioinformaticsCoreprovidesequencedataanalysis,statisticalevaluations,consulting,andtrainingworkshopstohelpyougetthemostoutofyourdata.PleasecontactusforjointconsultationswiththeBioinformaticsCorestaff;completeanalysispackages,includingsequencingandbioinformatics(e.g.differentialgeneexpression,variantcalling),arealsoavailable. Ourservicesinclude: MiSeq,andNextSeqsequencing:allruntypes ElementBiosiciencesAVITIsequencing(PE150) IlluminaNovaSeq6000sequencing:S4(PE150),S1(PE100),andSp500(PE250) DNAsequencing(whole-genomeshotgun,targeted,amplicon,exome,ChIP,reduced-representation,custom) RNAsequencing(mRNA,totalRNA,miRNA,smallRNA,3′Tag-Seq,custom) Methyl-Seq:WGBS(WholeGenomeBisulfiteSeq)andRRBS(ReducedRepresentationBisulfiteSeq) PacBioSequelII(e)sequencing (whole-genomeshotgun long-read,amplicon,andRNA-sequencing) NanoporesequencingontheONTPromethION GeneExpressionProfiling via3′Tag-Seq—includingDifferentialGeneExpression(DGE)dataanalysis FluidigmEP1Genotyping IlluminaInfiniumGenotyping(microarrays) 10XGenomicsChromiumGenomeLinked-Read-Sequencing 10XGenomicsChromiumSingle-CellExpressionProfiling FluidigmAccessArraytargetedmultiplexedamplifications High-Molecular-WeightDNAisolations SequencingLibraryConstruction andassociatedservices: PacBioandOxfordNanoporelongreadDNAsequencingandIso-SeqRNAsequencinglibrarypreparations Illuminasequencinglibrarypreps,including: GenomicDNAlibrarypreps RNA-Seqlibrarypreps(poly-Aenrichmentorribo-depletion) High-Throughput(HT)librarypreps(DNAorRNA;startingfrom24libraries) miRNA-Seqlibrarypreps Methyl-seq:WGBS(WholeGenomeBisulfiteSeq)andRRBS(ReducedRepresentationBisulfiteSeq) Reducedrepresentationlibrarypreps(e.g.,genotypingbysequencing) LibraryprepsfromChIPsamples Customlibrarypreparationsandsequencing Librarypooling NucleicacidQC(fromsinglesamplesto96-wellplates) Nucleicacidandlibraryquantification BluePippinnucleicacidsizeselection PleaseseetheGettingStarted pagetolearnhowtoworkwithourCore.PleasealsoseeourInstrumentList.WeencourageyoutoconsultourextensiveFAQsincaseofquestions.IlluminahaspostedNGStutorialsinthis“Beginner’sGuidetoNGS”. Our SharedEquipmentincludes: Bioanalyzer–microcapillarynucleicacidfragmentanalysisforsampleandlibraryQC CaliperLabChipGX–a“high-­throughputbioanalyzer”(1-­384samples) AgilentFemtoPulse–largefragmentanalyzerusingpulsed-fieldtechnology,ultralowinput CaliperScicloneG3–liquidhandlerrobotforhigh-throughputlibrarypreps(upto96samplesatatime) CovarisE220–high-­throughputsonicator(1-­96samples) DiagenodeMegaruptor –longinsertsizeDNAshearingforPacBiolibrarypreps BluePippinandPippinHTsystems–50bpto50KbDNAautomatedsizeselection FluidigmAccessArray–targetamplificationforsequencing-­readylibraryprep FilterMaxF5PlateReader–DNA/RNAquantification Nanodrop–microvolumeDNA/RNAquantification TheSharedEquipment pageexplainshowtogettrained. AcknowledgingOur Services Pleasesupportusbyacknowledgingourservicesinyourpublications.WehavereceivedNIHfundingforthepurchaseofsomeofourinstrumentsandthissupportshouldbementioned.Pleaseadda sentencelikethistoyouracknowledgments:“ThesequencingwascarriedbytheDNATechnologiesandExpressionAnalysisCoreattheUCDavisGenomeCenter,supportedbyNIHSharedInstrumentationGrant1S10OD010786-01.”AcknowledgmentssuchasthisconstitutebigsupportforfutureNIHinstrumentationgrantapplications.Pleasealsoseeour FAQs. SupportingYourGrantApplications Wesupportthegenerationofproof-of-principledatabyprovidingseedgrants(pleaseseebelow) andbyofferingfree-of-chargeconsultations.Wewillgladlyprovidelettersofsupportforyour grantapplication.PleasealsoseeourFacilitiesandEquipmentdescription. SeedGrants TheGenomeCenterinvitesproposalsforpilotprojectsthatmeritsupportbytheGenomeCenter.Theseseedgrantsawardupto$2000perprojecttospendatanyoftheCores;itisalsopossibletoapplyforgrantsatmultipleCores.TheGenomeCenterseedgrantsareavailableyear-round.TheyaremeanttoeitherintroduceUCDavislabstohigh-throughputsequencingorgenotypingmethods,ortohelpestablishnewmethods.PleaseseetheseedgrantFAQ.  AssociatedServicesByCollaboratingCores Bioinformatics: TheBioinformaticsCorewillhelpyouwiththeanalysisofalldatageneratedbyourCoresaswellaswiththestatisticalinterpretation.WehighlyrecommendjointconsultationswithusandtheBioinformaticsCorestaffwhileplanningyourresearchproject. DNAandRNA sample isolationservicescanbearrangedthroughtheTaqmanCore. 16SSequencing:Wesequence16Slibrariesdaily.Thevastmajorityofthesearecustomerpreparedsamples.Wedonotgenerate16SlibrariesourselvesbecauseUCDavishasafacilityspecializingin16Sanalysis:theHostMicrobeBiologySystemsCore (HSMBC;alsolocatedinourbuilding).TheHSMBCoffersacompleteservicerangingfromDNAisolation,16Samplification,sequencing(carriedoutbytheDNATechCore),todataanalysis.Youcanalsopickselectedpartsoftheirservicethatyourequire.PleasecontacttheHSMBCmanagerfordetails. TillingBySequencing:TheTILLINGCorecarriesouthigh-throughputmutationscreeningforrice,wheat,Arabidopsis,andtomatopopulations. YeastOneHybridscreening:TheYeastOneHybridCoreoffersascreeningservicebetweenpromotersandcollectionsofArabidopsisormaizetranscriptionfactors. Bionano SaphyrWholeGenomeMapping:TheLuoLab atUCDavisofferswholegenomemappingservices usingthe BionanoSaphyropticalmappingtechnology.Thisisofspecialvalueifthegenomeassemblyforyour organismofinterestisalreadyofhighquality.PleaseinquirewithMing-ChengLuo. SangerSequencing:TheDNASequencingFacilitywillhelpyouhelpyouwithallSangersequencingprojects. CancerGenomics:TheGenomicsSharedResourceontheSacramentocampusprovidesgeneral genomics supportandcustomservices forcancerstudies. FlowCytometry&FlowSorting: WeworkwiththeFlowCytometryCoretoenablesingle-cellexpressionprofilingfromselectedcellpopulations. TheDNATechnologiesandExpressionAnalysisCoreisaUCDavisCampusResearchCoreFacility.Pleasesubscribetoournewsletter. Thegeneralcontactaddressis [email protected].  Follow@DNATech_Lutz Follow@DavisCores RecentPosts HolidaySchedule CoreoperationsresumeinPhase2oftheCOVIDresponse DNATechnologiesCorehastorampdownlabwork AdjustingDNATechCoreoperationtotheCOVID-19guidelines JoinusforthePacBioDaySymposium—February26th LatestTweets AnupdatetothebesteverNGSposter,the"Forallyouseq..."poster! Thistimeexpandedtothreeversions:DNA,…https://t.co/PWpoki8JzT,Oct4Ialwayshadtheidea,Illuminaputsaboutasmucheffortandmathinto"designing/optimizing"thepricesoftheir…https://t.co/TkDh9dQKCd,Oct3Ohh,...Iamquoted. 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