SiC-Seq:Single-cellgenomesequencingatultrahigh-throughputwithmicrofluidicdropletbarcodingFreemanLan1,2,BenjaminDemaree1,2,NoorsherAhmed1,andAAbate1,2,*1DepartmentofBioengineeringandTherapeuticSciences,CaliforniaInstituteforQuantitativeBiosciences,UniversityofCalifornia,SanFrancisco,CA94158,USA2UCBerkeley-UCSFGraduatePrograminBioengineering,UniversityofCalifornia,SanFrancisco,CA94158,USATheapplicationofsingle-cellgenomesequencingtolargecellpopulationshasbeenhinderedbytechnicalchallengesinisolatingsinglecellsduringgenomepreparation.Herewepresentsingle-cellgenomicsequencing(SiC-seq),whichusesdropletmicrofluidicstoisolate,fragment,andbarcodethegenomesofsinglecells,followedbyIlluminasequencingofpooledDNA.Wedemonstrateultra-highsequencingthroughputof>50,000cellsperruninasyntheticcommunityofGramnegativeandGram-positivebacteriaandfungi.Thesequencedgenomescanbesortedinsilicobasedoncharacteristicsequences.Weusethisapproachtoanalyzethedistributionsofantibioticresistancegenes,virulencefactors,andphagesequencesinmicrobialcommunitiesfromanenvironmentalsample.Theabilitytoroutinelysequencelargepopulationsofsinglecellswillenablethede-convolutionofgeneticheterogeneityindiversecellpopulations.Organismsarelivingexpressionsoftheirgenomesand,hence,genomesequencingisapowerfulwaytostudyhowtheygrowandfunction.Organismsarephenotypicallydiverse,andthisdiversityismirroredbyheterogeneityatthegenomiclevelandplaysimportantrolesinpopulationsasawhole,particularlyamongpopulationsofsinglecells.Acommonchallengewhenapplyingsinglecellsequencingtoheterogeneoussystemsisthattheyoftencontainmassivenumbersofcells:acentimeter-sizedtumorcancontainhundredsofmillionsofcancercells1,whileamilliliterofseawatercancontainmillionsofmicrobes2.Moreover,eachcellhasatinyquantityofDNA,makingitchallengingtoaccuratelyamplifyandUsersmayview,print,copy,anddownloadtextanddata-minethecontentinsuchdocuments,forthepurposesofacademicresearch,subjectalwaystothefullConditionsofuse:http://www.nature.com/authors/editorial_policies/l...
