Supplemental_Figures_Tables

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1、7%!6%!5%!4%!3%!2%!%ofduplicatereads!1%!0%!BxC!CxB!BxC!CxB!CTCF!cohesin!FigureS1:ReadduplicatesareshownforeachChIP-seqexperiment.Clonalreadswereremovedpriortofurtheranalysisbutoverallthesewereasmallproportion(<7%)ofthetotalnumberofreads,indicativeoftherobustnessoftheChIP-seqdata.80000&73159&67443!

2、70000&Bindingpeakscalledat50813!FDR<13!60000&47138!52928&50249!49358&46470!50000&Peaksexpandedby+/-500bpandoverlappingpeaks40000&merged!30000&Expandedpeaksoverlappingnumberofpeaks!20000&aSNP!10000&Testedpeaks!0&CTCF!Rad21!FigureS2:CTCFandcohesinbindingregionswereidentifiedusingUseqandresultedinth

3、eidentificationof67,443CTCFand73,159(Rad21)cohesinbindingatanFDR<13(bluebars).Totestmono-allelicbindingCTCFandRad21bindingregionswereexpandedby500bpandoverlappingregionsmerged(redbars).MergedregionsoverlappingaSNPandthuswhereitistheoreticallypossibletotestmono-allelicbindingareshown(greenbars).Wh

4、eretwoormorereadswithgoodenoughqualityoverlappedtheSNPabinomialtestwasconducted,andmono-allelicexpressionwasassessed(purplebars).FigureS3:Toidentifythecorrectsizeofpeaktomakeappropriatecomparisonsbetweendatasets,theoptimumsizeforthebindingpeakwasdeterminedbyiterativecomparisonofoverlapsinbrain,li

5、ver(Schmidtetal.2010)andEScell(Chenetal.2008)datasets:Graph(A)indicatesthataboveapeaksizeof1kb,anyincreaseinoverlapbetweenthedatasetisduetonoise.Graph(B)isthecontrolfor(A)wherebyarandomlycreateddatasetisplottedagainstbrainCTCFChIP-seqdata.OverlapofCTCFbindingbetweentissues:3545!9016!4431!19158!18

6、030!3183!1516!FigureS4:OverlapofCTCFbindingbetweenEScells,liverandbrainwasrepeatedusingCTCFChIP-seqdatafromShenetal(2012).CTCFbindingforbrainfromShenwasnotusedduetothepaucityofdataavailable.Overlapofbindingconfirmstheresultseenintheoriginalcomparisonindicatingsignificantoverlapofbindingbetweenall

7、threetissues(Fig.4A).CTCF!cohesin!1&0.9&0.8&0.7&reads!0.6&0.5&mat:pat0.4&Ratioof0.3&0.2&0.1&0&FigureS5:Plotof95%confidenceintervalsforratioofmaternal:paternalreadsofCTCF(left)andcohesin(right).Theseplotsillustratethatt