GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE66582 Query DataSets for GSE66582
Status Public on Jun 15, 2016
Title The landscape of accessible chromatin in mammalian pre-implantation embryos (RNA-Seq)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development.

Overall design Mouse preimplantation embryos were obtained from crosses of C57BL/6N and DBA/2N. RNA-seq was performed in these embryos at various stages in preimplantation development.
Contributor(s) Wu J, Huang B, Chen H, Xie W
Citation(s) 27309802
Submission date Mar 05, 2015
Last update date May 15, 2019
Contact name Wei Xie
Organization name Tsinghua University
Street address zhongguancun beidajie
City Beijing
ZIP/Postal code 100086
Country China
Platforms (1)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (32)
GSM1625860 RNA-Seq zygote rep1
GSM1625861 RNA-Seq zygote rep2
GSM1625862 RNA-Seq 2-cell rep1
This SubSeries is part of SuperSeries:
GSE66390 The landscape of accessible chromatin in mammalian pre-implantation embryos
BioProject PRJNA277361
SRA SRP055882

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
GSE66582_FPKM_blastocyst.txt.gz 443.7 Kb (ftp)(http) TXT
GSE66582_nr5a2_8cell_KD_fpkm.txt.gz 492.3 Kb (ftp)(http) TXT
GSE66582_stage_FPKM.txt.gz 639.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap