[{"smoothwindow":11,"tracks":{"forward":{"CG":{"color":"rgb(100,139,216)","bg":"#d9d9d9","url":"http://vizhub.wustl.edu/public/hg18/pmid19829295/imr90.f.cg.gz"},"CHG":{"color":"rgb(255,148,77)","bg":"#ffe0cc","url":"http://vizhub.wustl.edu/public/hg18/pmid19829295/imr90.f.chg.noZero.gz"},"CHH":{"color":"rgb(255,0,255)","bg":"#ffe5ff","url":"http://vizhub.wustl.edu/public/hg18/pmid19829295/imr90.f.chh.noZero.gz"},"ReadDepth":{"color":"#525252","url":"http://vizhub.wustl.edu/public/hg18/pmid19829295/IMR90.forward.readDepth.bedGraph.gz"}},"reverse":{"CG":{"color":"rgb(100,139,216)","bg":"#d9d9d9","url":"http://vizhub.wustl.edu/public/hg18/pmid19829295/imr90.r.cg.gz"},"CHG":{"color":"rgb(255,148,77)","bg":"#ffe0cc","url":"http://vizhub.wustl.edu/public/hg18/pmid19829295/imr90.r.chg.noZero.gz"},"CHH":{"color":"rgb(255,0,255)","bg":"#ffe5ff","url":"http://vizhub.wustl.edu/public/hg18/pmid19829295/imr90.r.chh.noZero.gz"},"ReadDepth":{"color":"#525252","url":"http://vizhub.wustl.edu/public/hg18/pmid19829295/IMR90.reverse.readDepth.bedGraph.gz"}}},"type":"methylC","name":"IMR90 methylome","public":true,"mode":1,"qtc":{"height":70,"smooth":11},"custom_annotation":["IMR90","WGBS","methylC"],"details":{"Publication":"Human DNA methylomes at base resolution show widespread epigenomic differences. <a href=http://www.nature.com/nature/journal/vaop/ncurrent/full/nature08514.html target=_blank>doi:10.1038/nature08514</a>","Source":"http://neomorph.salk.edu/human_methylome/data.html","Download date":"Feb 2014","Note":"The CG track contains data for both methylated and unmethylated cytosines.<br><br>The CHG and CHH tracks contain data for only methylated cytosines.<br>Unmethylated CHG and CHH cytosines were excluded."}},{"type":"bedGraph","name":"CpG Sample_met12STK.raw","url":"http://linaria.man.poznan.pl/bio/methyl-0/Sample_met12STK.raw.CpG.bedGraph.gz","mode":1,"qtc":{"anglescale":1,"pr":100,"pg":139,"pb":216,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":0,"thmax":1,"thpercentile":90,"height":40,"summeth":1,"barplotbg":"#d9d9d9"},"custom_annotation":["CpG","RRBS","bedGraph"]},{"type":"bedGraph","name":"Density Sample_met12STK.raw","url":"http://linaria.man.poznan.pl/bio/methyl-0/Sample_met12STK.raw.density.bedGraph.gz","mode":1,"qtc":{"anglescale":1,"pr":100,"pg":139,"pb":216,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":0,"thmax":1,"thpercentile":90,"height":40,"summeth":1,"barplotbg":"#d9d9d9"},"custom_annotation":["Density","RRBS","bedGraph"]},{"type":"bedGraph","name":"CpG Sample_met12STO.raw","url":"http://linaria.man.poznan.pl/bio/methyl-0/Sample_met12STO.raw.CpG.bedGraph.gz","mode":1,"qtc":{"anglescale":1,"pr":100,"pg":139,"pb":216,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":0,"thmax":1,"thpercentile":90,"height":40,"summeth":1,"barplotbg":"#d9d9d9"},"custom_annotation":["CpG","RRBS","bedGraph"]},{"type":"bedGraph","name":"Density Sample_met12STO.raw","url":"http://linaria.man.poznan.pl/bio/methyl-0/Sample_met12STO.raw.density.bedGraph.gz","mode":1,"qtc":{"anglescale":1,"pr":100,"pg":139,"pb":216,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":0,"thmax":1,"thpercentile":90,"height":40,"summeth":1,"barplotbg":"#d9d9d9"},"custom_annotation":["Density","RRBS","bedGraph"]},{"type":"bedGraph","name":"CpG Sample_metIPS26-6.raw","url":"http://linaria.man.poznan.pl/bio/methyl-0/Sample_metIPS26-6.raw.CpG.bedGraph.gz","mode":1,"qtc":{"anglescale":1,"pr":100,"pg":139,"pb":216,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":0,"thmax":1,"thpercentile":90,"height":40,"summeth":1,"barplotbg":"#d9d9d9"},"custom_annotation":["CpG","RRBS","bedGraph"]},{"type":"bedGraph","name":"Density Sample_metIPS26-6.raw","url":"http://linaria.man.poznan.pl/bio/methyl-0/Sample_metIPS26-6.raw.density.bedGraph.gz","mode":1,"qtc":{"anglescale":1,"pr":100,"pg":139,"pb":216,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":0,"thmax":1,"thpercentile":90,"height":40,"summeth":1,"barplotbg":"#d9d9d9"},"custom_annotation":["Density","RRBS","bedGraph"]},{"type":"bedGraph","name":"CpG Sample_metPHDF.raw.","url":"http://linaria.man.poznan.pl/bio/methyl-0/Sample_metPHDF.raw.CpG.bedGraph.gz","mode":1,"qtc":{"anglescale":1,"pr":100,"pg":139,"pb":216,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":0,"thmax":1,"thpercentile":90,"height":40,"summeth":1,"barplotbg":"#d9d9d9"},"custom_annotation":["CpG","RRBS","bedGraph"]},{"type":"bedGraph","name":"Density Sample_metPHDF.raw","url":"http://linaria.man.poznan.pl/bio/methyl-0/Sample_metPHDF.raw.density.bedGraph.gz","mode":1,"qtc":{"anglescale":1,"pr":100,"pg":139,"pb":216,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":0,"thmax":1,"thpercentile":90,"height":40,"summeth":1,"barplotbg":"#d9d9d9"},"custom_annotation":["Density","RRBS","bedGraph"]},{"type":"native_track","list":[{"name":"rmsk_ensemble","mode":1,"qtc":{"anglescale":1,"height":15},"categories":{"1":["SINE - short interspersed nuclear elements","#cc0000"],"2":["LINE - long interspersed nuclear element","#FF6600"],"3":["LTR - long terminal repeat element","#006600"],"4":["DNA transposon","#4A72E8"],"5":["Simple repeat, micro-satellite","#AB833B"],"6":["Satellite repeat","#660000"],"7":["Low complexity repeat","#663333"],"8":["RNA repeat","#cc33ff"],"9":["Other repeats","#488E8E"],"10":["Unknown","#5C5C5C"],"-1":["no information","transparent"]}},{"name":"refGene","mode":3,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":0,"ng":0,"nb":230,"pth":"#800000","nth":"#000099","thtype":0,"thmin":0,"thmax":10,"thpercentile":95,"height":50,"summeth":1,"textcolor":"rgb(0,0,0)","fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"bedcolor":"rgb(0,77,153)"}}]},{"type":"coordinate_override","coord":"chr7,27053086,chr7,27373143"},{"type":"geneset_ripe","list":[{"name":"pluri","lst":[{"c":"chr6","a":31132377,"b":31138397,"isgene":true,"type":"xenoRefGene","name":"POU5F1","id":71382,"strand":"-","struct":{"thick":[[31132377,31132644],[31132904,31133063],[31133347,31133478],[31133703,31133824],[31137992,31138397]]},"desc":"POU domain, class 5, transcription factor 1","a1":31132377,"b1":31138397},{"c":"chr12","a":7941994,"b":7948655,"isgene":true,"type":"refGene","name":"NANOG","id":30273,"strand":"+","struct":{"thin":[[7941994,7942210],[7947691,7948655]],"thick":[[7942210,7942361],[7945545,7945808],[7947052,7947139],[7947274,7947691]]},"desc":"Homo sapiens Nanog homeobox (NANOG), mRNA.","a1":7941994,"b1":7948655}],"gss_down":2500,"gss_opt":"genebody","gss_origin":"txstart","gss_up":2500}]},{"type":"metadata","vocabulary":{"Sample":["H1","IMR90"],"Assay":["WGBS","RRBS","450K"],"Data format":["BED","bigWig","bedGraph","interaction","categorical","methylC","annotation","BAM"]},"show":["Sample","Assay"],"source":"http://linaria.man.poznan.pl/bio/methyl-0/rrbs-raw0-cpg.json","termname":{},"termcolor":{},"termdesc":{}}]