GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE137098 Query DataSets for GSE137098
Status Public on Jul 25, 2023
Title Embryonic stem cell-derived neurons as a model system for epigenome maturation during development
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Third-party reanalysis
Expression profiling by high throughput sequencing
Summary DNA methylation in neurons is directly linked to neuronal genome regulation and maturation. Unlike other tissues, vertebrate neurons accumulate high levels of atypical DNA methylation in the CH sequence context (mCH) during early postnatal brain development. Here we investigate to what extent neurons derived in vitro from both mouse and human pluripotent stem cells recapitulate in vivo DNA methylation patterns. While human ESC-derived neurons did not accumulate mCH in either 2D culture or 3D organoid models, even after prolonged culture, neurons derived from mouse ESCs in vitro acquire in vivo levels of mCH over a similar time period as both primary neuron cultures and in vivo development. mESC-derived neuron mCH deposition occurs concurrently with a transient increase in Dnmt3a expression, is preceded by expression of the post-mitotic marker Rbfox3 (NeuN), is enriched at the nuclear lamina, and negatively correlates with gene expression. We further show that CG- and CH-methylation patterning subtly differs between in vitro mES-derived and in vivo neurons, suggesting the involvement of additional non-cell autonomous processes. As our findings show mouse ESC-derived neurons are capable of recapitulating the unique DNA methylation landscape of adult mammalian neurons in vitro over experimentally tractable timeframes, identification of such external cues, and elucidation of the writing-reading mechanisms and functional consequences of these different types and patterns of DNA methylation events, is now achievable.
Overall design Whole genome bisulfite sequencing of 49 different mouse cell culture and primary cell samples, and RNA-seq of a subset of samples
Contributor(s) Martin S, Poppe D, Olova N, O'Leary C, Ivanova E, Pflueger J, Dechka J, Simmons RK, Cooper HM, Reik W, Lister R, Wolvetang EJ
Citation(s) 37239317
Submission date Sep 09, 2019
Last update date Jul 26, 2023
Contact name Ryan Lister
Phone 61864884407
Organization name The University of Western Australia
Street address 35 Stirling Highway
City Perth
State/province WA
ZIP/Postal code 6009
Country Australia
Platforms (3)
GPL16417 Illumina MiSeq (Mus musculus)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (53)
GSM4066867 HPC_1div
GSM4066868 HPC_14div
GSM4066869 HPC_14div_50mMKCl_6h
Reanalysis of GSM1173786
Reanalysis of GSM1173787
Reanalysis of GSM1173779
BioProject PRJNA564548
SRA SRP221040

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

Supplementary file Size Download File type/resource
GSE137098_7wkNeuNneg.CG.coverage.bigWig 260.1 Mb (ftp)(http) BIGWIG
GSE137098_7wkNeuNneg.CH.coverage.bigWig 4.3 Gb (ftp)(http) BIGWIG
GSE137098_7wkNeuNneg.mCG.percent.bigWig 278.1 Mb (ftp)(http) BIGWIG
GSE137098_7wkNeuNneg.mCH.percent.bigWig 3.7 Gb (ftp)(http) BIGWIG
GSE137098_7wkNeuNneg.stacks.txt.gz 11.6 Gb (ftp)(http) TXT
GSE137098_7wkNeuNpos.CG.coverage.bigWig 254.0 Mb (ftp)(http) BIGWIG
GSE137098_7wkNeuNpos.CH.coverage.bigWig 4.6 Gb (ftp)(http) BIGWIG
GSE137098_7wkNeuNpos.mCG.percent.bigWig 251.8 Mb (ftp)(http) BIGWIG
GSE137098_7wkNeuNpos.mCH.percent.bigWig 3.9 Gb (ftp)(http) BIGWIG
GSE137098_7wkNeuNpos.stacks.txt.gz 11.3 Gb (ftp)(http) TXT
GSE137098_CG_DMRs.txt.gz 483.9 Kb (ftp)(http) TXT
GSE137098_CH_DMRs.txt.gz 357.2 Kb (ftp)(http) TXT
GSE137098_RAW.tar 91.2 Gb (http)(custom) TAR (of BIGWIG, GTF, TXT)
GSE137098_fetalBrain.CG.coverage.bigWig 244.5 Mb (ftp)(http) BIGWIG
GSE137098_fetalBrain.CH.coverage.bigWig 3.9 Gb (ftp)(http) BIGWIG
GSE137098_fetalBrain.mCG.percent.bigWig 250.9 Mb (ftp)(http) BIGWIG
GSE137098_fetalBrain.mCH.percent.bigWig 3.2 Gb (ftp)(http) BIGWIG
GSE137098_fetalBrain.stacks.txt.gz 11.0 Gb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap