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Series GSE17972 Query DataSets for GSE17972
Status Public on Sep 04, 2010
Title The DNA methylome of human peripheral blood mononuclear cells
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary DNA methylation plays a vital role in genome dynamics and, in the human genome, occurs predominantly at cytosine guanine dinucleotide (CpG) sites. The diploid haploid human genome analysed here contains around 2060 million CpG sites (methylome) where DNA methylation can vary, affecting many biological processes in health and disease. Using whole-genome bisulfite sequencing, we report the essentially complete (92.6282%) methylome of human peripheral blood mononuclear cells (PBMC) which constitute an important source for clinical blood tests world-wide. We find the majority of CpG sites (68.4% at false positive rate of 0.46%) and only <0.2% of non-CpG sites to be methylated, demonstrating that non-CpG cytosine methylation is negligible in human PBMC. Analysis of the PBMC methylome revealed a rich landscape of epigenomic data for 20 distinct features including regulatory, protein-coding, RNA gene coding, non-coding and repeat sequences. Alu element mobility, for instance, was found to negatively correlate with their methylation levels, emphasizing the critical role of DNA methylation in genome stability. Integration of our methylome data with the previously determined genome sequence of the same Asian individual analysed here, enabled a first assessment of allele-specific methylation (ASM) differences between the two haploid methylomes of any individual. Using a conservative cut-off (p <0.001), we identified 599 haploid differentially methylated regions (hDMRs) covering 287 genes. Of these, 76 genes had hDMRs within 2kb of their transcriptional start sites of which >80% displayed allele-specific expression (ASE) after random testing using TA clone sequencing of the same PBMC sample. These data show, that ASM is a recurrent phenomenon and highly correlated with ASE, suggesting that imprinting may be more common than previously thought. Our study not only provides a comprehensive resource for future epigenomic research but also demonstrates a paradigm of large-scale epigenomics studies through new sequencing technology.
Overall design We report the essentially complete (92.6282%) methylome of human peripheral blood mononuclear cells (PBMC) which constitute an important source for clinical blood tests world-wide.
Contributor(s) Cao HZ
Citation(s) 21085693
Submission date Sep 04, 2009
Last update date May 15, 2019
Contact name Hong zhi Cao
Phone 8675525274032
Organization name BGI-SHENZHEN
Department Bioinformatics
Street address F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District
City Shenzhen
State/province Guangdong
ZIP/Postal code 518083
Country China
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (77)
GSM450016 YanHuang1_methy_rep1
GSM450017 YanHuang1_methy_rep2
GSM450018 YanHuang1_methy_rep3
SRA SRP002339
BioProject PRJNA119949

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

Supplementary file Size Download File type/resource
GSE17972_HUMtg5lib.qmap.chr1.txt.gz 1.2 Gb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr10.txt.gz 688.3 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr11.txt.gz 689.4 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr12.txt.gz 691.5 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr13.txt.gz 497.9 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr14.txt.gz 466.3 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr15.txt.gz 429.0 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr16.txt.gz 418.4 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr17.txt.gz 407.3 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr18.txt.gz 389.5 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr19.txt.gz 299.9 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr2.txt.gz 1.2 Gb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr20.txt.gz 309.4 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr21.txt.gz 183.2 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr22.txt.gz 179.0 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr3.txt.gz 1.0 Gb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr4.txt.gz 992.4 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr5.txt.gz 933.3 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr6.txt.gz 881.5 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr7.txt.gz 821.5 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr8.txt.gz 749.0 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chr9.txt.gz 627.4 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chrM.txt.gz 71.2 Kb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chrX.txt.gz 610.2 Mb (ftp)(http) TXT
GSE17972_HUMtg5lib.qmap.chrY.txt.gz 114.2 Mb (ftp)(http) TXT
GSE17972_HumMethy.qmap.chr_format.txt.gz 379 b (ftp)(http) TXT
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Raw data are available in SRA

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