GEO DataSets

(Submitter supplied) Somatic cell nuclear transfer (SCNT) can reprogram a somatic nucleus to a totipotent state. However, the re-organization of three-dimensional chromatin structure in this process remains poorly understood. Using low-input Hi-C, we revealed that during SCNT, the transferred nucleus first enters a mitotic-like state (premature chromatin condensation). Unlike fertilized embryos, SCNT embryos show stronger TADs at the 1-cell stage. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL17021 GPL24247 GPL21273

75 Samples

Download data: TSV, TXT

(Submitter supplied) The oocyte cytoplasm can reprogram somatic cell nucleus into a totipotent state but with low efficiency. The spatiotemporal chromatin organization of somatic cell nuclear transfer (SCNT) embryos remains elusive. Here, we examined higher-order chromatin structures of mouse SCNT embryos using an optimized low-input Hi-C approach. We found that the donor cell chromatin transformed to metaphase state rapidly after injection along with the dissolution of typical 3D chromatin structures. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL21273 GPL24247 GPL17021

51 Samples

Download data: BW, TXT

(Submitter supplied) Conservation and species specificity are both unveiled in the reprogramming process of epigenetic modifications in early embryos. Pig is important agricultural livestock that closely related to human life and understanding the mechanisms of epigenetic reprogramming in porcine embryos could be assistive to the pig breeding industry and also informative to human embryo research. Nevertheless, current knowledge of epigenetic reprogramming in porcine embryos is elusive. more...

Organism:

Sus scrofa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22918

30 Samples

Download data: BROADPEAK, BW

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

Organism:

Sus scrofa

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22918

28 Samples

Download data: NARROWPEAK, TXT

(Submitter supplied) Pigs are important animals for agricultural and biomedical research, and its assisted reproductive technologies are urgently needed to be improved. Determining the underlying mechanism of epigenetic reprogramming in the early stage of preimplantation embryos derived from in vitro fertilization (IVF), parthenogenesis (PA) and androgenesis (AG), will not only contribute to assisted reproduction technologies of pigs but also will shed light into early human development. more...

Organism:

Sus scrofa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22918

8 Samples

Download data: NARROWPEAK

(Submitter supplied) Pigs are important animals for agricultural and biomedical research, and its assisted reproductive technologies are urgently needed to be improved. Determining the underlying mechanism of epigenetic reprogramming in the early stage of preimplantation embryos derived from in vitro fertilization (IVF), parthenogenesis (PA) and androgenesis (AG), will not only contribute to assisted reproduction technologies of pigs but also will shed light into early human development. more...

Organism:

Sus scrofa

Type:

Other

Platform:

GPL22918

20 Samples

Download data: TXT

(Submitter supplied) Somatic cell nuclear transfer (SCNT) can be used to reprogram differentiated somatic cells to a totipotent state but has poor efficiency in supporting full-term development. H3K9me3 is considered to be an epigenetic barrier to zygotic genomic activation in 2-cell SCNT embryos. However, the mechanism underlying the failure of H3K9me3 reprogramming during SCNT embryo development remains elusive. Here, we perform genome-wide profiling of H3K9me3 in cumulus cell-derived SCNT embryos. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL24247

146 Samples

Download data: BW, EXP

(Submitter supplied) Somatic cell nuclear transfer (SCNT) can be used to reprogram differentiated somatic cells to a totipotent state but has poor efficiency in supporting full-term development. H3K9me3 is considered to be an epigenetic barrier to zygotic genomic activation in 2-cell SCNT embryos. However, the mechanism underlying the failure of H3K9me3 reprogramming during SCNT embryo development remains elusive. Here, we perform genome-wide profiling of H3K9me3 in cumulus cell-derived SCNT embryos. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

68 Samples

Download data: BW, EXP

(Submitter supplied) Somatic cell nuclear transfer (SCNT) can be used to reprogram differentiated somatic cells to a totipotent state but has poor efficiency in supporting full-term development. H3K9me3 is considered to be an epigenetic barrier to zygotic genomic activation in 2-cell SCNT embryos. However, the mechanism underlying the failure of H3K9me3 reprogramming during SCNT embryo development remains elusive. Here, we perform genome-wide profiling of H3K9me3 in cumulus cell-derived SCNT embryos. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

74 Samples

Download data: BROADPEAK, BW

(Submitter supplied) Somatic cell nuclear transfer (SCNT) can be used to reprogram differentiated somatic cells to a totipotent state but has poor efficiency in supporting full-term development. H3K9me3 is considered to be an epigenetic barrier to zygotic genomic activation in 2-cell SCNT embryos. However, the mechanism underlying the failure of H3K9me3 reprogramming during SCNT embryo development remains elusive. Here, we perform genome-wide profiling of H3K9me3 in cumulus cell-derived SCNT embryos. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

4 Samples

Download data: BW

(Submitter supplied) Fertilization triggers assembly of higher-order chromatin structure from a nucleosomal state to generate a totipotent embryo. Chromatin loops and domains are detected in mouse zygotes by single-nucleus Hi-C (snHi-C) but not bulk Hi-C; both are absent in Drosophila embryos. We investigated whether zygotic chromatin structures are generated by cohesin-dependent loop extrusion. Using snHi-C of mouse knockout embryos, we demonstrate the zygotic genome folds into loops and domains that critically depend on Scc1-cohesin and are regulated in size by Wapl. more...

Organism:

Mus musculus

Type:

Other

Platforms:

GPL21626 GPL17021

144 Samples

Download data: COOL

(Submitter supplied) Mammalian oocytes can reprogram somatic cells into totipotent state, which allows animal cloning through somatic cell nuclear transfer (SCNT). However, the great majority of SCNT embryos fail to develop to term due to poorly defined reprogramming defects. Here we demonstrate that histone H3 lysine 9 trimethylation (H3K9me3) in donor nuclei is a major epigenetic barrier that prevents efficient nuclear reprogramming in mouse oocytes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

14 Samples

Download data: TXT

(Submitter supplied) Here we analyze the genome-wide accessability during zebrafish embryogenesis before zygotice genome activation 2.5 hours post fertilization

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20828

2 Samples

Download data: BED

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

Organism:

Danio rerio

Type:

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

Platforms:

GPL20828 GPL18413 GPL14875

61 Samples

Download data: BED

(Submitter supplied) Methods: Triplicate RNA samples from morphologically stage-matched embryos were sequenced to compare expression profiles over time. Strand-specific libraries were prepared using the TruSeq stranded total RNA-ribozero kit (Illumina) and 100-bp paired-end sequencing was performed to depth of 10 million reads per library on an Illumina HiSeq 2000. Methods: On average, 19 million 100 bp paired-end reads per library were generated. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

45 Samples

Download data: TXT, XLS

(Submitter supplied) The formation of a transcriptional competent zygote is a not fully understood process potentially involving changes in chromatin structure. Cohesin and CTCF are important nuclear architectural proteins that contribute to chromatin structure and gene regulation. Here we analyze the genome-wide location of Rad21 binding during zebrafish embryogenesis and show increased Rad21 binding over developmental time (2.5 hpf, 4.5 hpf , 10 hpf).

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18413 GPL14875

14 Samples

Download data: BED

(Submitter supplied) Zygotic genome activation (ZGA) after fertilization is a conserved transcriptional activation process that enables the maternal-to-zygotic transition. However, the global view of ZGA, particularly at the initiation, is not yet completely understood. Here, we develop a method to capture and sequence newly synthesized RNA in the early mouse embryos, which provides a view of transcriptional reprogramming events during ZGA. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL24247 GPL21273

88 Samples

Download data: BW, TXT

(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) Coordinated gene expression is fundamental for cell identity, development and differentiation, and relies on a highly organized genome. Our central goal is to determine when and how higher-order 3D chromatin architecture is first established in early vertebrate embryos, its resemblance to paternal/sperm architecture, its impact on transcription, and its role in developmental transitions. We exploited the natural transition in zebrafish embryogenesis, where the zygotic genome remains transcriptionally silent until the onset of zygotic genome activation (ZGA) to assess the establishment of higher order 3D chromatin architecture by obtaining dense genome-wide Hi-C maps.  Through this approach, we defined higher-order architecture by combining advanced low-cell in-situ HiC methods with a Drosophila HiC spike-in control.  We have demonstrated the histone packed zebrafish sperm lack topological associated domains, but instead displays unique “hinge-like” domains. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18413

2 Samples

Download data: BW, NARROWPEAK

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

Organism:

Danio rerio

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24995 GPL18413

15 Samples

Download data: BW, NARROWPEAK, TXT