Genomics

Dataset Information

296

Transcriptome profiling of wild type and Tet1-null primordial germ cells (PGC) by Bisulfite-seq


ABSTRACT: Purpose: To investigate the effect of Tet1 depletion on global DNA methylation, we performed whole-genome bisulfite sequencing (WGBS). Methods: Starting with as little as 1400-5251 manually micro-dissected PGCs, we used an ultra-low input method, Tn5mC-seq. Results: We generated 945 million reads for Tet1Gt/Gt PGCs and 302 million reads for wild-type PGCs. We obtained 14-16 million CpG sites per genotype at 1.76-2.66x genome coverage, which enables a comprehensive view of genome-wide DNA methylation patterns in E13.5 PGCs. PGCs are almost completely unmethylated genome-wide. Loss of Tet1 led to a subtle increase of methylation level in various genomic elements including promoters, exons, introns and repetitive elements in Tet1Gt/Gt PGCs (p<0.01). Local analysis identified 4,337 differentially methylated regions (DMRs) between Tet1-/- PGCs and wild-type cells. These DMRs are associated with 5,261 genes, among which 271 genes also exhibited differential gene expression and enriched for the cell cycle pathway (FDR=0.02). Conclusions: This result revealed that demethylation of certain set of cell cycle genes is largely abolished in the Tet1-/- PGCs. Genome-wide methylation profiles of primordial germ cells derived from the wild type (WT) and Tet1-null female embryos at E13.5 were generated by whole genome bisulfite sequencing using Illumina Hiseq.

ORGANISM(S): Mus musculus  

SUBMITTER: Dinh Hue Diep  

PROVIDER: E-GEOD-41912 | ArrayExpress | 2012-11-20

SECONDARY ACCESSION(S): SRP016883GSE41912PRJNA181955

REPOSITORIES: GEO, ArrayExpress, ENA

altmetric image

Publications

Tet1 controls meiosis by regulating meiotic gene expression.

Yamaguchi Shinpei S   Hong Kwonho K   Liu Rui R   Shen Li L   Inoue Azusa A   Diep Dinh D   Zhang Kun K   Zhang Yi Y  

Nature 20121114 7429


Meiosis is a germ-cell-specific cell division process through which haploid gametes are produced for sexual reproduction. Before the initiation of meiosis, mouse primordial germ cells undergo a series of epigenetic reprogramming steps, including the global erasure of DNA methylation at the 5-position of cytosine (5mC) in CpG-rich DNA. Although several epigenetic regulators, such as Dnmt3l and the histone methyltransferases G9a and Prdm9, have been reported to be crucial for meiosis, little is kn  ...[more]

Similar Datasets

2013-06-27 | E-GEOD-42923 | ArrayExpress
2014-06-04 | E-GEOD-44038 | ArrayExpress
2014-07-01 | E-GEOD-55752 | ArrayExpress
2011-04-21 | E-GEOD-28533 | ArrayExpress
2013-02-14 | E-GEOD-44092 | ArrayExpress
2016-06-01 | E-GEOD-77828 | ArrayExpress
2014-05-12 | E-GEOD-56697 | ArrayExpress
2014-07-08 | E-GEOD-56712 | ArrayExpress
2015-09-21 | E-GEOD-72247 | ArrayExpress
2013-08-18 | E-GEOD-44638 | ArrayExpress