|
| 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 |
| E-mail(s) |
weicl@gis.a-star.edu.sg
|
| Phone |
65 64788074
|
| Fax |
65 64789059
|
| URL |
http://www.gis.a-star.edu.sg/internet/site/investigators.php?f=cv&user_id=9
|
| 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 |
|
| Relations |
| SRA |
SRP001720 |
| BioProject |
PRJNA120353 |
| 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 |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
