Genomics

Dataset Information

154

The transcriptome and chromatin accessbility landscape of mammalian germline


ABSTRACT: We first isolate the PGCs from the Oct4-Gfp knock-in mice, and KIT-positive PGCs from the post-implantation human fetus. Then we use the Nome-seq (Nucleosome Occupancy and Methylome Sequencing), using a in vitro GpC methyltransferase (M.CviPI) and next generation sequencing to generate the endogenous DNA methylation information and chromatin accessibility of the same DNA molecules in these mammalian germ cells. Overall design: Together, we isolated the E6.5 epiblast, E11.5 PGC, E13.5 PGC, E16.5 PGC and their surrounding somatic cells from mouse embryos, and week5 heart, week7 PGC, week11 PGC, week12 PGC, week17 PGC and week26 PGC, and also their gonadal somatic cells from human fetus.

INSTRUMENT(S): Illumina HiSeq 2500 (Homo sapiens)

SUBMITTER: Hongshan Guo  

PROVIDER: GSE79552 | GEO | 2016-11-14

SECONDARY ACCESSION(S): PRJNA316148

REPOSITORIES: GEO

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Publications


Chromatin remodeling is important for the epigenetic reprogramming of human primordial germ cells. However, the comprehensive chromatin state has not yet been analyzed for human fetal germ cells (FGCs). Here we use nucleosome occupancy and methylation sequencing method to analyze both the genome-wide chromatin accessibility and DNA methylome at a series of crucial time points during fetal germ cell development in both human and mouse. We find 116 887 and 137 557 nucleosome-depleted regions (NDRs  ...[more]

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