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Series GSE19418 Query DataSets for GSE19418
Status Public on Dec 29, 2009
Title Dynamic Changes in the Human Methylome During Differentiation
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary DNA methylation is a critical epigenetic regulator in mammalian development. Here, we present a whole genome comparative view of DNA methylation using bisulfite sequencing of three cultured cell types representing progressive stages of differentiation: human embryonic stem cells (hESCs), a fibroblastic differentiated derivative of the hESCs, and neonatal fibroblasts. As a reference, we compared our maps with a methylome map of a fully differentiated adult cell type, mature peripheral blood mononuclear cells (monocytes). We observed many notable common and cell type-specific features among all cell types. Promoter hypomethylation (both CG and CA) and higher levels of gene body methylation were positively correlated with transcription in all cell types. Exons were more highly methylated than introns and sharp transitions of methylation occurred at exon-intron boundaries, suggesting a role for differential methylation in transcript splicing. Developmental stage was reflected in both the level of global methylation and extent of non-CpG methylation, with hESC highest, fibroblasts intermediate, and monocytes lowest. Differentiation-associated differential methylation profiles were observed for developmentally regulated genes, including the HOX clusters, other homeobox transcription factors, and pluripotence-associated genes such as POU5F1, TCF3, and KLF4. Our results highlight the value of high-resolution methylation maps, in conjunction with other systems-level analyses, for investigation of previously undetectable developmental regulatory mechanisms.
Overall design Examination of 3 cell types DNA methylation profile
Contributor(s) Li G, Wei C, Rigoutsos I
Citation(s) 20133333
Submission date Dec 10, 2009
Last update date Feb 11, 2020
Contact name Chia-Lin Wei
Phone 65 64788074
Fax 65 64789059
Organization name Genome Institute of Singapore
Department Genome Technology & Biology
Street address 60 Biopolis Street #02-01
City Singapore
ZIP/Postal code 138672
Country Singapore
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (3)
GSM491349 Embryonic stem cells: Bisulfite sequencing
GSM491350 Fibroblasts derived from human embryonic stem cells: Bisulfite sequencing
GSM491351 Newborn Human Foreskin Fibroblasts: Bisulfite sequencing
SRA SRP001720
BioProject PRJNA120353

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
GSE19418_Fibro_HumMethy.qmap.chr1.txt.gz 531.0 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr10.txt.gz 306.1 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr11.txt.gz 301.5 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr12.txt.gz 299.4 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr13.txt.gz 199.3 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr14.txt.gz 202.1 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr15.txt.gz 195.0 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr16.txt.gz 209.0 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr17.txt.gz 206.7 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr18.txt.gz 160.8 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr19.txt.gz 169.0 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr2.txt.gz 524.3 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr20.txt.gz 146.5 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr21.txt.gz 79.3 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr22.txt.gz 99.5 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr3.txt.gz 423.0 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr4.txt.gz 393.4 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr5.txt.gz 384.5 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr6.txt.gz 363.3 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr7.txt.gz 358.5 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr8.txt.gz 315.6 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chr9.txt.gz 282.0 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chrM.txt.gz 146.5 Kb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chrX.txt.gz 294.2 Mb (ftp)(http) TXT
GSE19418_Fibro_HumMethy.qmap.chrY.txt.gz 58.9 Mb (ftp)(http) TXT
GSE19418_README.txt 1.5 Kb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr1.txt.gz 486.0 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr10.txt.gz 280.3 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr11.txt.gz 276.0 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr12.txt.gz 273.6 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr13.txt.gz 183.3 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr14.txt.gz 185.4 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr15.txt.gz 179.1 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr16.txt.gz 191.2 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr17.txt.gz 188.3 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr18.txt.gz 147.7 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr19.txt.gz 153.9 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr2.txt.gz 480.2 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr20.txt.gz 134.3 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr21.txt.gz 73.1 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr22.txt.gz 90.9 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr3.txt.gz 387.1 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr4.txt.gz 360.4 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr5.txt.gz 352.5 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr6.txt.gz 332.5 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr7.txt.gz 327.6 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr8.txt.gz 288.7 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chr9.txt.gz 259.2 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chrM.txt.gz 154.1 Kb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chrX.txt.gz 311.0 Mb (ftp)(http) TXT
GSE19418_hESC-Fibro_HumMethy.qmap.chrY.txt.gz 38.5 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr1.txt.gz 562.3 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr10.txt.gz 321.6 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr11.txt.gz 316.9 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr12.txt.gz 317.5 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr13.txt.gz 208.6 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr14.txt.gz 213.7 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr15.txt.gz 207.1 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr16.txt.gz 221.7 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr17.txt.gz 224.4 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr18.txt.gz 168.0 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr19.txt.gz 183.0 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr2.txt.gz 550.5 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr20.txt.gz 154.8 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr21.txt.gz 82.9 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr22.txt.gz 105.9 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr3.txt.gz 445.1 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr4.txt.gz 411.2 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr5.txt.gz 404.2 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr6.txt.gz 382.5 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr7.txt.gz 378.5 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr8.txt.gz 330.0 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chr9.txt.gz 297.7 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chrM.txt.gz 152.5 Kb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chrX.txt.gz 355.4 Mb (ftp)(http) TXT
GSE19418_hESC_HumMethy.qmap.chrY.txt.gz 43.7 Mb (ftp)(http) TXT
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Raw data are available in SRA

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