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Series GSE50798 Query DataSets for GSE50798
Status Public on Sep 13, 2013
Title Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites [methylation array]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary We applied Illumina Human Methylation450K array to perform a genomic-scale single-site resolution DNA methylation analysis in neuronal and nonneuronal (primarily glial) nuclei separated from the orbitofrontal cortex of postmortem human brain. The findings were validated using enhanced reduced representation bisulfite sequencing. We identified thousands of sites differentially methylated (DM) between neuronal and nonneuronal cells. The DM sites were depleted within CpG island–containing promoters but enriched in predicted enhancers. Classification of the DM sites into those undermethylated in neurons (neuronal type) and those undermethylated in nonneuronal cells (glial type), combined with findings of others that methylation within control elements typically negatively correlates with gene expression, yielded large sets of predicted neuron-specific and non– neuron-specific genes. These sets of predicted genes were in excellent agreement with the available direct measurements of gene expression in human and mouse. We also found a distinct set of DNA methylation patterns that were unique for neuronal cells. In particular, neuronal-type differential methylation was overrepresented in CpG island shores, enriched within gene bodies but not in intergenic regions, and preferentially harbored binding motifs for a distinct set of transcription factors, including neuron-specific activity-dependent factors. Finally, non-CpG methylation was substantially more prevalent in neurons than in nonneuronal cells.
Overall design Genomic DNA was isolated from FACS-sorted human brain neuronal and nonneuronal nuclei. DNA was bisulfite converted and hybridised to the Illumina Infinium 450K Human Methylation Beadchip array. Six subjects in two technical replicate expriments were analyzed.
Contributor(s) Kozlenkov A, Dracheva S
Citation Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites; Alexey Kozlenkov, Panos Roussos, Alisa Timashpolsky, Mihaela Barbu, Sergei Rudchenko, Marina Bibikova, Brandy Klotzle, William Byne, Rebecca Lyddon, Antonio Fabio Di Narzo, Yasmin L. Hurd, Eugene V. Koonin and Stella Dracheva; Accepted for publication in Nucleic Acids Research (28-Aug-2013)
Submission date Sep 11, 2013
Last update date Mar 22, 2019
Contact name Stella Dracheva
Organization name Icahn School of Medicine at Mount Sinai
Department Dept. of Psychiatry
Street address James J. Peters VA Medical Center,130 W Kingsbridge Rd
City Bronx
State/province New York
ZIP/Postal code 10468
Country USA
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (24)
This SubSeries is part of SuperSeries:
GSE50853 Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites
BioProject PRJNA219103

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
GSE50798_RAW.tar 183.1 Mb (http)(custom) TAR
GSE50798_unmethylated_methylated_signal_intensities.txt.gz 57.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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