MassIVE MSV000090568

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Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS

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Description

Analysis of nucleosides (dC, dG, 5mdC and 5hmdC) using mass spectrometry and digested DNA samples. Experimental data description: - 12 h restoration (corresponding to EDFig2 b, EDFig5 b,c,h), E14 mESCs, labelled samples and followed for 12h, total DNA and stranded, 4 biological replicates (rep1, rep2, rep3 and rep4) and 2 technical replicates (_1, _2). - KST061-62-63 (corresponding to Fig1 e-f, Fig2 b-g, Fig5 b-e, EDFig5 a,f), E14 mESCs, labelled samples and followed for 8h, total DNA and stranded, 3 biological replicates (KST061, KST062 and KST063) and 2 technical replicates (_1, _2). - KST73-74-75 (corresponding to EDFig5 d,e,g), NIH3T3 cell line, labelled samples and followed for 8h, total DNA and stranded, 3 biological replicates (KST073, KST074 and KST075) and 2 technical replicates (_1, _2). - KST76-77-78 (corresponding to Fig6 b-e, EDFig6 b-c), E14 mESCs, ChIP mass spectrometry samples for several histone modifications antibodies, total DNA and ChIP DNA, 3 biological replicates (KST076, KST077 and KST078) and 2 technical replicates (_1, _2). - KST035 (corresponding to Fig1 c-d), E14 mESCs, DNA abundance and methylation levels, 2 technical replicates (_1, _2) - KST045-46-47 (corresponding to Fig3 b, EDFig3 a), E14 mESCs, labelled early S phase samples and followed for 8h, total DNA and EdU+ pull down, 3 biological replicates (KST045, KST046 and KST047) and 2 technical replicates (_1, _2). - KST050-51-52 (corresponding to Fig3 c, EDFig3 b), E14 mESCs, labelled late S phase samples and followed for 8h, total DNA and EdU+ pull down, 3 biological replicates (KST050, KST051 and KST052) and 2 technical replicates (_1, _2). - KST056-57-60 (corresponding to EDFig4 a), E14 mESCs, cell cycle phases sorted using EdU labelling, 3 biological replicates (KST056, KST057 and KST060) and 2 technical replicates (_1, _2). Standard curve data used for quantification are named as MM1-MM10, 2 technical replicates (_1, _2). [doi:10.25345/C5MK65D2N] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Epigenetics ; DNA methylation ; Chromatin

Contact

Principal Investigators:
(in alphabetical order) 		Anja Groth, 1Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark. 2 Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark., Denmark
Petra Hajkova, 3MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK 4Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK, United Kingdom
Submitting User: cristinarequena
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