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Series GSE38604 Query DataSets for GSE38604
Status Public on Sep 03, 2013
Title The developmental patterning of 5-hydroxymethylcytosine during neuronal differentiation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Recent analyses of 5-hydroxymethylcytosine (5hmC) suggest that the modified base influences transcription by acting as an intermediate to demethylation. However, elevated levels of 5hmC within neural tissues suggest that the mark is stable and may directly contribute to gene regulation. Here, we characterize the in vivo genomic patterning and stability of 5hmC in three defined developmental states of the mouse main olfactory epithelium – multipotent stem cells, neuronal progenitors, and mature olfactory sensory neurons. 5hmC is globally enriched in neuronal progenitors and neurons relative to the stem population with significant enrichment on the bodies of transcriptionally active genes and intergenic enhancers. Although gene body 5hmC levels are positively correlated with cell type-specific gene expression in all developmental stages, genes that are commonly expressed within both neuronal progenitors and mature neurons experience the greatest increases in 5hmC levels. Moreover, enriched levels of the modified base on intergenic conserved regions correlate with cell type-specific expression of nearby genes and coincide with developmentally regulated enhancer-promoter interaction at one locus examined. Finally, an analysis of two-month old neurons indicates that elevated 5hmC levels persist in fully differentiated neurons. Together, these data suggest that 5hmC stabilizes the expression of developmentally active genes through effects at both gene bodies and intergenic regulatory elements.
Overall design 9 Samples
Contributor(s) Colquitt BM, Lomvardas S
Citation(s) 23969834
Submission date Jun 08, 2012
Last update date May 15, 2019
Contact name Michael Brainard
Organization name University of California, San Francisco
Street address 675 Nelson Rising Ln
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
Platforms (3)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (9)
GSM945988 mOSN 5hmC
GSM945989 GBC 5hmC
GSM945990 HBC 5hmC
BioProject PRJNA168207
SRA SRP013625

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE38604_RAW.tar 45.8 Mb (http)(custom) TAR (of TXT, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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