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Series GSE66581 Query DataSets for GSE66581
Status Public on Jun 15, 2016
Title The landscape of accessible chromatin in mammalian pre-implantation embryos (ATAC-Seq)
Organism Mus musculus
Experiment type Genome binding/occupancy 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. ATAC-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 (17)
GSM1625847 ATAC-Seq 4-cell rep1
GSM1625858 ATAC-Seq 200 mESC
GSM1933921 ATAC-Seq early 2-cell rep1
This SubSeries is part of SuperSeries:
GSE66390 The landscape of accessible chromatin in mammalian pre-implantation embryos
BioProject PRJNA277362
SRA SRP055881

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Supplementary file Size Download File type/resource
GSE66581_RAW.tar 2.6 Gb (http)(custom) TAR (of BEDGRAPH)
GSE66581_atac_1k_mESC.bedGraph.gz 168.2 Mb (ftp)(http) BEDGRAPH
GSE66581_atac_200_mESC.bedGraph.gz 214.9 Mb (ftp)(http) BEDGRAPH
GSE66581_atac_2cell.bedGraph.gz 342.2 Mb (ftp)(http) BEDGRAPH
GSE66581_atac_2cell_early.bedGraph.gz 296.3 Mb (ftp)(http) BEDGRAPH
GSE66581_atac_2cell_early_trx_inhibitor.bedGraph.gz 198.4 Mb (ftp)(http) BEDGRAPH
GSE66581_atac_4cell.bedGraph.gz 552.6 Mb (ftp)(http) BEDGRAPH
GSE66581_atac_4cell_reciprocal.bedGraph.gz 425.5 Mb (ftp)(http) BEDGRAPH
GSE66581_atac_50k_mESC.bedGraph.gz 192.6 Mb (ftp)(http) BEDGRAPH
GSE66581_atac_8cell.bedGraph.gz 476.3 Mb (ftp)(http) BEDGRAPH
GSE66581_atac_ICM.bedGraph.gz 400.4 Mb (ftp)(http) BEDGRAPH
GSE66581_bed_files.tar.gz 5.9 Mb (ftp)(http) TAR
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