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Series GSE76505 Query DataSets for GSE76505
Status Public on Dec 05, 2017
Title Dynamic epigenomic landscapes during early lineage specification in mouse embryos
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary In mammals, all somatic development originates from lineage segregation in early embryos. However, the dynamics of transcriptomes and epigenomes in concert with initial cell fate commitment remains poorly characterized. Here, we report comprehensive investigation of transcriptomes and base-resolution methylomes for early lineages in peri- and postimplantation mouse embryos. We found allele- and lineage-specific de novo methylation at CG and CH sites, leading to differential methylation between embryonic and extraembryonic lineages at promoters of lineage regulators, gene bodies, and DNA methylation valleys. By determining chromatin architecture using Hi-C across the same developmental period, we showed both global demethylation and remethylation in early development correlate with chromatin compartments. Dynamic local methylation is evident during gastrulation, which revealed maps of putative regulatory elements. Finally, we found that de novo methylation patterning does not strictly require implantation. These data unveiled dynamic transcriptomes, DNA methylomes, and 3D chromatin landscapes during the earliest mammalian lineage specification.
Overall design Mouse preimplantation, periimplantation and postimplantation embryos were obtained from crosses of C57BL/6N and DBA/2N as well as C57BL/6N and PWK/PhJ. STEM-seq, RNA-seq and Hi-C were performed in these embryos at various stages in development. STEM-seq was also performed on Tet1/2 double knockout embryos and in vitro culture embryos.
Contributor(s) Zhang Y, Xiang Y, Yin Q, Du Z, Xie W
Citation(s) 29203909
Submission date Jan 04, 2016
Last update date May 15, 2019
Contact name Wei Xie
Organization name Tsinghua University
Street address Zhongguancun north street
City Beijing
ZIP/Postal code 100084
Country China
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (78)
GSM2027204 RNA-Seq E3.5ICM rep1
GSM2027205 RNA-Seq E3.5ICM rep2
GSM2027206 RNA-Seq E3.5TE rep1
BioProject PRJNA307584
SRA SRP068043

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Supplementary file Size Download File type/resource
GSE76505_E6.5Epi_tetDKO_merge_mCG.txt.gz 90.5 Mb (ftp)(http) TXT
GSE76505_FPKM_IVC_D1-2.txt.gz 297.2 Kb (ftp)(http) TXT
GSE76505_FPKM_replicates.txt.gz 1.3 Mb (ftp)(http) TXT
GSE76505_Hi-C_processed_data_files.tar.gz 1.4 Gb (ftp)(http) TAR
GSE76505_RNA-FPKM_for_in_vitro_tissues.txt.gz 293.6 Kb (ftp)(http) TXT
GSE76505_RNA-FPKM_for_in_vivo_tissues.txt.gz 757.3 Kb (ftp)(http) TXT
GSE76505_STEM-seq_IVC_mCG.tar.gz 213.1 Mb (ftp)(http) TAR
GSE76505_STEM-seq_mESC_mCG.tar.gz 166.7 Mb (ftp)(http) TAR
GSE76505_STEM-seq_methylC_mCG.tar.gz 1.1 Gb (ftp)(http) TAR
GSE76505_STEM-seq_methylation_bedgraph_files.tar.gz 300.4 Mb (ftp)(http) TAR
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