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Series GSE116163 Query DataSets for GSE116163
Status Public on Jun 26, 2018
Title DNA methylation oscillations at CpG poor enhancers in primed embryonic stem cells [amplicon-Seq]
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary Mouse embryonic stem cells (ESCs) primed for differentiation display dynamic heterogeneity characterised by stochastic switching between transcriptional states, and recent advances have highlighted the heterogeneous and dynamic nature of DNA methylation in these. Using single cell sequencing we report global oscillations in ESC DNA methylation that affect particularly CpG poor regions including distal enhancers. These oscillations are dependent on DNA methylation turnover by Dnmt3 and Tet enzymes and influence the probability of transcriptional state switching. Our observations suggest that regulated DNA methylation heterogeneity may contribute to lineage priming in cells poised for differentiation.
Overall design 2i ES cells transferred into serum media and collected at 48 time points. Control cells were 2i ES cells collected at the same time points (i.e. without changing to serum media)
Contributor(s) Rulands S, Lee HJ, Clark SJ, Angermueller C, Smallwood SA, Krueger F, Kelsey G, Stegle O, Simons BD, Reik W
Citation(s) 30031774
Submission date Jun 22, 2018
Last update date Jan 27, 2019
Contact name Felix Krueger
Organization name Altos Labs
Department Bioinformatics
Street address Granta Park
City Cambridge
ZIP/Postal code CB21 6GP
Country United Kingdom
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (96)
GSM3211611 Amplicon_BS_2i_0
GSM3211612 Amplicon_BS_2i_100
GSM3211613 Amplicon_BS_2i_10
This SubSeries is part of SuperSeries:
GSE75975 Genome-scale DNA methylation oscillations in pluripotent cells
BioProject PRJNA477530
SRA SRP151135

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE116163_RAW.tar 780.0 Kb (http)(custom) TAR (of COV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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