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Series GSE79277 Query DataSets for GSE79277
Status Public on Feb 19, 2017
Title Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tissue-of-origin mapping from plasma DNA [Plasma RRBS]
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary Adjacent CpG sites in mammalian genomes tend to be co-methylated due to the processivity of enzymes responsible for adding or removing the methyl group. Yet discordant methylation patterns have also be observed, and found to be related to stochastic or uncoordinated molecular processes. Here we focused on a systematic search and investigation of regions in the human genome that exhibit highly coordinated methylation. By examining the co-methylation patterns of multiple adjacent CpG sites, termed methylation haplotypes, in single bisulfite sequencing reads, we applied a greedy-searching strategy to defined blocks of tightly coupled CpG sites, called Methylation Haplotype Blocks (MHBs), based on 53 sets of whole genome bisulfite sequencing (WGBS) data, including 43 published sets from human adult tissues, ESC and in vitro differentiated cell lines, as well as 10 sets from human adult tissues generated in this study. The MHBs were then further validated with 101 sets of RRBS ENCODE data, and 637 sets of Illumina 450k methylation array data from TCGA tumor and normal samples. Globally, MHBs are enriched in but only partially overlap with several well-known genomic features, including CpG islands, promoters, enhancers and VMRs. To perform quantitative analysis of the MHBs, we defined a metric called Methylation Haplotype Load (MHL), which is covered both average methylation level and methylation complexity and therefore more informative than average methylation level or Shannon entropy. Using a feature selection strategy, we identified a set of tissue-specific MHBs that cluster by developmental germ-layers. Interestingly, examination of these MHBs revealed two distinct mechanisms for fate commitment during development: epigenetic silencing of pluripotent genes, such as NANOG, for mesoderm induction; and epigenetic induction (or de-suppression) of lineage-specific factors for ectoderm commitment.
Overall design Examination of co-methylation in human cfDNA
Contributor(s) Guo S, Diep DH, Zhang K
Citation(s) 28263317
Submission date Mar 16, 2016
Last update date May 15, 2019
Contact name Kun Zhang
Organization name University of California, San Diego
Department Bioengineering
Lab Integrative Genomics Laboratory
Street address 9500 Gilman Dr Mailcode: 0412
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
Platforms (2)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (134)
GSM2090507 CRC-P-1
GSM2090508 CRC-P-10
GSM2090509 CRC-P-11
This SubSeries is part of SuperSeries:
GSE79279 Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tissue-of-origin mapping from plasma DNA
BioProject PRJNA315379
SRA SRP071841

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

Supplementary file Size Download File type/resource
GSE79277_RAW.tar 454.2 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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