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000125420 041__ $$aeng
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000125420 1001_ $$aÄijö, Tarmo$$b0
000125420 245__ $$aA probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways.
000125420 260__ $$aLondon$$bBioMed Central$$c2016
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000125420 520__ $$aWe present a generative model, Lux, to quantify DNA methylation modifications from any combination of bisulfite sequencing approaches, including reduced, oxidative, TET-assisted, chemical-modification assisted, and methylase-assisted bisulfite sequencing data. Lux models all cytosine modifications (C, 5mC, 5hmC, 5fC, and 5caC) simultaneously together with experimental parameters, including bisulfite conversion and oxidation efficiencies, as well as various chemical labeling and protection steps. We show that Lux improves the quantification and comparison of cytosine modification levels and that Lux can process any oxidized methylcytosine sequencing data sets to quantify all cytosine modifications. Analysis of targeted data from Tet2-knockdown embryonic stem cells and T cells during development demonstrates DNA modification quantification at unprecedented detail, quantifies active demethylation pathways and reveals 5hmC localization in putative regulatory regions.
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000125420 650_7 $$2NLM Chemicals$$aDNA-Binding Proteins
000125420 650_7 $$06R795CQT4H$$2NLM Chemicals$$a5-Methylcytosine
000125420 650_7 $$08J337D1HZY$$2NLM Chemicals$$aCytosine
000125420 650_7 $$09007-49-2$$2NLM Chemicals$$aDNA
000125420 7001_ $$aHuang, Yun$$b1
000125420 7001_ $$aMannerström, Henrik$$b2
000125420 7001_ $$0P:(DE-HGF)0$$aChavez, Lukas$$b3
000125420 7001_ $$aTsagaratou, Ageliki$$b4
000125420 7001_ $$aRao, Anjana$$b5
000125420 7001_ $$aLähdesmäki, Harri$$b6
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