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Series GSE38216 Query DataSets for GSE38216
Status Public on Nov 04, 2013
Title Dynamic changes of DNA methylome and hydroxymethylome during neural differentiation of hES cells (Methylation BeadChip)
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary DNA methylation and hydroxymethylation have been implicated in normal development and differentiation, but our knowledge about the genome-wide distribution of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) during cellular differentiation remains limited. Using in vitro model system of gradual differentiation of human embryonic stem (hES) cells into ventral midbrain-type neural precursor (NP) cells and terminally into dopamine (DA) neurons, we explored changes in 5mC or 5hmC patterns during lineage commitment. We used three techniques, 450K DNA methylation array, MBD-seq, and hMeDIP-seq, and found combination of these methods can provide comprehensive information on the genome-wide 5mC or 5hmC patterns. We observed dramatic changes of 5mC patterns during differentiation of hES cells into NP cells. Although genome-wide 5hmC distribution was more stable than 5mC, coding exons, CpG islands and shores showed dynamic 5hmC patterns during differentiation. In addition to the role of DNA methylation as a mechanism to initiating gene silencing, we also found DNA methylation as a locking system to maintain gene silencing. More than 1,000 genes including mesoderm development related genes acquired promoter methylation during neuronal differentiation even though they were already silenced in hES cells. Finally, we found that activated genes lost 5mC in transcription start site (TSS) but acquired 5hmC around TSS and gene body during differentiation. Our findings may provide clues for elucidating the molecular mechanisms underlying lineage specific differentiation of pluripotent stem cells during human embryonic development.
Overall design Examination of genome-wide DNA methylation in 3 cell types (human embryonic stem, neural precursor, and dopamine neuron cells)
Contributor(s) Kim M, Park Y, Kang T, Lee S, Rhee Y, Park J, Kim HJ, Kim S, Lee D, Lee D, Kim YS
Citation(s) 24087792
Submission date May 24, 2012
Last update date May 15, 2019
Contact name Mirang Kim
Organization name KRIBB(Korea Research Institute of Bioscience and Biotechnology
Department Personalized Genomic Medicine Research Center
Street address 125 Gwahak-ro, Yuseong-gu
City Daejeon
ZIP/Postal code 34141
Country South Korea
Platforms (2)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (12)
GSM936817 H9 Embryonic stem (ES) cells hMeDIP-Seq
GSM936818 H9 ES-derived neural precursor cells hMeDIP-Seq
GSM936819 H9 ES-derived dopamine neuron cells hMeDIP-Seq
This SubSeries is part of SuperSeries:
GSE38217 Dynamic changes of DNA methylome and hydroxymethylome during neural differentiation of hES cells
BioProject PRJNA167472

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Supplementary file Size Download File type/resource
GSE38216_RAW.tar 346.0 Mb (http)(custom) TAR (of BED)
GSE38216_signal_intensities.txt.gz 14.8 Mb (ftp)(http) TXT
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Raw data are available on Series record
Processed data included within Sample table

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