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Series GSE55249 Query DataSets for GSE55249
Status Public on Feb 22, 2014
Title Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary 5-Hydroxymethylcytosine (hmC) is particularly abundant in mammalian brains with yetto be revealed functions. Here, we present genome-wide and single-base-resolutionmaps of hmC and mC in the human brain. We demonstrated that hmCs increasemarkedly from the fetal to the adult stage, and in the adult brain, 13.4% of all CpGs arehighly hydroxymethylated with strong enrichment at genic regions and distal regulatoryelements. Notably, hmC peaks were identified at the 5' splicing sites at the exon-intronboundary, suggesting a mechanistic link between hmC and splicing. We also report asurprising transcription-correlated hmC bias toward the sense strand and an mC biastoward the antisense strand of gene bodies. Furthermore, hmC is negatively correlatedwith H3K27me3-marked repressive genomic regions, and is more enriched in poisedenhancers than active enhancers. Our results provide insights into understanding themultiple potential functions of hmC in the human brain.
Overall design A cell type specific hydroxymethylome sample of NeuN+ neurons in frontal lobe from the same adult individual, whose TAB-Seq data was deposited in GSE46710
Contributor(s) Wen L, Li X, Yan L, Tan Y, Tang F, Qiao J
Citation(s) 24594098
Submission date Feb 21, 2014
Last update date May 15, 2019
Contact name Xianlong Li
Organization name Peking University
Department Biodynamic Optical Imaging Center, College of Life Sciences
Street address 5, Yiheyuan Rd., Haidian District
City Beijing
ZIP/Postal code 100871
Country China
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (1)
GSM1332603 Ad_Front_NeuN_pos.TARRBS
BioProject PRJNA238997
SRA SRP038730

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Supplementary file Size Download File type/resource
GSE55249_RAW.tar 41.7 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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