GEO DataSets

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18480

51 Samples

Download data: BEDGRAPH

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18480

2 Samples

Download data: BEDGRAPH

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18480

32 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18480

17 Samples

Download data: BEDGRAPH

(Submitter supplied) Upon fertilization, drastic chromatin reorganization occurs during human preimplantation development. However, the global chromatin landscape and its molecular dynamics in this period remain largely unexplored. Deciphering such process is crucial for understanding both early human development and in vitro fertilization. Here, we investigated genome-wide chromatin accessibility in human preimplantation embryos by employing an improved ATAC-seq that uses as few as 20 cells. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL11154 GPL16791

55 Samples

Download data: BED, TXT, WIG

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL13112

646 Samples

Download data: BW

(Submitter supplied) In mammals, drastic epigenomic reprogramming occurs during preimplantation development. However, the functional associations between different epigenetic layers and transcriptional regulation remains unclear, and to what extent, the dynamic epigenomics contribute to the lineage segregation remains to be elucidated. Here, we developed a single cell multi-omics sequencing technology, and provided the first single cell multi-comics map of chromatin accessibility, DNA methylation and RNA transcription during mouse preimplantation development.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

27 Samples

Download data: BW

(Submitter supplied) In mammals, drastic epigenomic reprogramming occurs during preimplantation development. However, the functional associations between different epigenetic layers and transcriptional regulation remains unclear, and to what extent, the dynamic epigenomics contribute to the lineage segregation remains to be elucidated. Here, we developed a single cell multi-omics sequencing technology, and provided the first single cell multi-comics map of chromatin accessibility, DNA methylation and RNA transcription during mouse preimplantation development.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

218 Samples

Download data: BW

(Submitter supplied) In mammals, drastic epigenomic reprogramming occurs during preimplantation development. However, the functional associations between different epigenetic layers and transcriptional regulation remains unclear, and to what extent, the dynamic epigenomics contribute to the lineage segregation remains to be elucidated. Here, we developed a single cell multi-omics sequencing technology, and provided the first single cell multi-comics map of chromatin accessibility, DNA methylation and RNA transcription during mouse preimplantation development.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

401 Samples

Download data: XLSX

(Submitter supplied) Single-cell epigenome sequencing techniques have recently been developed. However, the combination of different layers of epigenome sequencing in an individual cell has not yet been achieved. Here, we developed a single-cell multi-omics sequencing technology (single-cell COOL-seq) that can analyze the chromatin state/nucleosome positioning, DNA methylation, copy number variation and ploidy simultaneously from the same individual mammalian cell. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL17021

329 Samples

Download data: BW, TXT

(Submitter supplied) Paternal and maternal epigenomes undergo dramatic changes after fertilization. How this relates to the 3D reorganisation of the parental genomes and their transcription patterns during early development remains unclear. Here we track structural dynamics during early mouse development using allele-specific single cell HiC integrated with transcriptome and chromatin changes, to combine parental features with early gene expression including during imprinted X-chromosome inactivation. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

1015 Samples

Download data: TXT

(Submitter supplied) Chromatin accessibility mapping is a powerful approach to identify potential regulatory elements. In the popular ATAC-seq method, Tn5 transposase inserts sequencing adapters into accessible DNA (‘tagmentation’). CUT&Tag is a tagmentation-based epigenomic profiling method in which antibody tethering of Tn5 to a chromatin epitope of interest profiles specific chromatin features in small samples and single cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

143 Samples

Download data: BED, BEDGRAPH, PDF

(Submitter supplied) In mammals, chromatin organization undergoes drastic reprogramming after fertilization. However, the three-dimensional structure of chromatin and its reprogramming in preimplantation development remain poorly understood. Here, by developing a low-input Hi-C (genomewide chromosome conformation capture) approach, we examined the reprogramming of chromatin organization during early development in mice. more...

Organism:

Mus musculus

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL21273 GPL18480 GPL17021

44 Samples

Download data: TXT

(Submitter supplied) There are two major developmental transitions that take place during the first four days of mouse embryogenesis. The first one is the maternal-to-zygotic transition in the zygote and 2-cell embryo, the second one is the first cell lineage commitment at the 32-cell stage. A number of transcription factors govern zygotic expression and the specification of pluripotent versus trophectoderm cells, while at the same time there are dynamic changes in DNA methylation and chromatin organization. more...

Organism:

Mus musculus

Type:

Expression profiling by RT-PCR

Platform:

GPL19459

189 Samples

Download data: TXT

(Submitter supplied) Zygotic genome activation (ZGA) marks the beginning of the embryonic program for a totipotent embryo, which gives rise to inner cell mass (ICM), where pluripotent epiblast arises, and extraembryonic trophectoderm. While much has been learned about pluripotency regulation, how ZGA is connected to the first lineage segregation in early embryos remains elusive. Here, we investigated the role of nuclear receptor transcription factors (NR TFs), whose motifs are highly enriched in accessible chromatin at the 2-cell (2C) to 8-cell (8C) stages after ZGA. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL21273

113 Samples

Download data: BW, TXT

(Submitter supplied) Histone acetylation H3K27ac is a well-established chromatin marker for active enhancers and promoters. However, reprogramming dynamics of H3K27ac during maternal-to-zygotic transition (MZT) in mammalian embryos has not been well studied. By profiling the allelic landscape of H3K27ac during mouse MZT, here we show that H3K27ac undergoes three waves of rapid global transitions from oocyte to 2-cell stages. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21626

32 Samples

Download data: BED, BIGWIG, TXT

(Submitter supplied) Zygotic genome activation (ZGA) is the first transcription event in life. However, it is unclear how RNA polymerase is engaged in initiating ZGA in mammals. Here, by developing small-scale Tn5-assisted chromatin cleavage with sequencing (Stacc–seq), we investigated the landscapes of RNA polymerase II (Pol II) binding in mouse embryos. We found that Pol II undergoes ‘loading’, ‘pre-configuration’, and ‘production’ during the transition from minor ZGA to major ZGA. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21273 GPL17021

116 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) ATAC sequencing of bovine oocytes and early embryos revealed a genome-wide map of accessible chromatin of bovine early embryo development, highlighting the critical features of chromatin landscape and epigenetic reprogramming during bovine preimplantation embryo development.

Organism:

Bos taurus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24230

56 Samples

Download data: TXT

(Submitter supplied) Histone modifications regulate gene expression and development. To address how they are reprogrammed in human early development, we investigated key histone marks in human oocytes and early embryos. Unlike that in mouse, the permissive mark H3K4me3 largely exhibits canonical patterns at promoters in human oocytes. After fertilization, pre-zygotic genome activation (ZGA) embryos acquire permissive chromatin and widespread H3K4me3 in CpG-rich regulatory regions. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL17021

42 Samples

Download data: BEDGRAPH, BROADPEAK, NARROWPEAK, TXT

(Submitter supplied) Histone modifications play critical roles in regulating developmental genes expression during embryo development in mammals1,2. However, genome-wide analysis of histone modifications in pre-implantation embryos has been impeded by technical difficulties and the scarcity of required materials. Here, by using a small-scale chromatin immunoprecipitation sequencing (ChIP-seq) method3, for the first time, we mapped the genome-wide profile of histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 trimethylation (H3K27me3), associated with gene activation and repression respectively, in mouse pre-implantation embryos. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

67 Samples

Download data: BW