GEO DataSets

(Submitter supplied) We analyze the difference between ETX-side1 cells and ETX-side2 cells. Side1 cells are associated with the anterior domain of the natural embryo, side2 cells are associated with the posterior domain of natural embryo.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT

(Submitter supplied) We performed 3 single-cell RNAseq experiments to identify the mechanisms of definitive endoderm formation during gastrulation. To enrich for the rare endoderm and endoderm progenitor populations we used the FVF reporter mouse line. 103 homozygous FVF embryos were isloated at two consecutive days: 40 early to mid streak stage embryos at day 1, 39 early to mid streak embryos at day 2 , 24 mid streak to late streak embryos at day 2 . more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

8 Samples

Download data: TAR

(Submitter supplied) It is generally accepted that epiblast cells ingress into the primitive streak by epithelial-to-mesenchymal transition (EMT) to give rise to the mesoderm; however, it is less clear how the endoderm acquires an epithelial fate. Here, we used embryonic stem cell and mouse embryo knock‐in reporter systems to combine time-resolved lineage labelling with high-resolution single-cell transcriptomics. This allowed us to resolve the morphogenetic programs that segregate the mesoderm from the endoderm germ layer. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

16 Samples

Download data: CEL

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL17021 GPL18480

94 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Pioneer transcription factors (PTF) can recognize their binding sites on nucleosomal DNA and trigger chromatin opening for recruitment of other non-pioneer transcription factors. However, critical properties of PTFs are still poorly understood, such as how can these transcription factors selectively recognize cell type-specific binding sites and under which conditions can they initiate chromatin remodelling. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL18480

7 Samples

Download data: BIGWIG

(Submitter supplied) Pioneer transcription factors (PTF) can recognize their binding sites on nucleosomal DNA and trigger chromatin opening for recruitment of other non-pioneer transcription factors. However, critical properties of PTFs are still poorly understood, such as how can these transcription factors selectively recognize cell type-specific binding sites and under which conditions can they initiate chromatin remodelling. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18480

14 Samples

Download data: TXT

(Submitter supplied) Pioneer transcription factors (PTF) can recognize their binding sites on nucleosomal DNA and trigger chromatin opening for recruitment of other non-pioneer transcription factors. However, critical properties of PTFs are still poorly understood, such as how can these transcription factors selectively recognize cell type-specific binding sites and under which conditions can they initiate chromatin remodelling. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT

(Submitter supplied) Pioneer transcription factors (PTF) can recognize their binding sites on nucleosomal DNA and trigger chromatin opening for recruitment of other non-pioneer transcription factors. However, critical properties of PTFs are still poorly understood, such as how can these transcription factors selectively recognize cell type-specific binding sites and under which conditions can they initiate chromatin remodelling. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18480

17 Samples

Download data: BIGWIG

(Submitter supplied) Pioneer transcription factors (PTF) can recognize their binding sites on nucleosomal DNA and trigger chromatin opening for recruitment of other non-pioneer transcription factors. However, critical properties of PTFs are still poorly understood, such as how can these transcription factors selectively recognize cell type-specific binding sites and under which conditions can they initiate chromatin remodelling. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL18480

32 Samples

Download data: BIGWIG

(Submitter supplied) Pioneer transcription factors (PTF) can recognize their binding sites on nucleosomal DNA and trigger chromatin opening for recruitment of other non-pioneer transcription factors. However, critical properties of PTFs are still poorly understood, such as how can these transcription factors selectively recognize cell type-specific binding sites and under which conditions can they initiate chromatin remodelling. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18480

18 Samples

Download data: BIGWIG

(Submitter supplied) We report the analysis by inDrop single cell sequencing of mouse embryos at embryonic day E5.5 and E6.5 as well as the analysis of stem cell derived synthetic embryos at day 4 of development generated with the standard protocol (Sozen et al., 2018) and the new protocol reported in this study. We find that the visceral endoderm-like layer of the synthetic embryos generated with the new protocol is much more similar to the visceral endoderm of mouse embryos than the layer of the synthetic embryos generated with the standard protocol, and this new and improved visceral endoderm-like layer endows these novel synthetic embryos with broader developmental potential

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

6 Samples

Download data: CSV, H5AD

(Submitter supplied) To test the efficacy of stem cell lines to generate 'stem-cell-derived-synthetic blastocysts', we dissociated ES- (built by conventional embryonic stem cells and trophoblast stem cells) or EPS-blastoids (built by extended potential pluripotent stem cells and trophoblast stem cells) into single cells following 96h of culture for single-cell transcriptome analysis.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

1 Sample

Download data: MTX, TSV, TXT

(Submitter supplied) The bilaminar disc of early pig embryos closely mirrors that of humans making it a powerful model for studying gastrulation. Given the difficulties obtaining embryos in non-rodents, early cell-fate decisions during mammalian gastrulation remain ill-understood. Here we present a single-cell transcriptomic atlas of pig gastrulation and early organogenesis. We uncover the dynamics of cell fate emergence during pig peri-gastrulation and reveal conserved and species-specific transcriptional programs across different mammals. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20983

24 Samples

Download data: CSV, TAR

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

65 Samples

Download data

(Submitter supplied) Different types of in vitro expanded stem cells can contribute to embryonic or extra-embryonic compartments after microinjection into blastocysts. However, whether stem cells could give rise to advanced gastrulating whole embryo-like structures with both embryonic and extra-embryonic compartments, without relying on a micro-injected host embryo, remains to be achieved. Thus far, in vitro aggregated stem cells have failed to generate post-gastrulation embryos ex utero or in utero, which partially resulted from the lack of methods for prolonged expansion of embryos until advanced developmental stages ex utero. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

11 Samples

Download data: CSV, TXT

(Submitter supplied) Different types of in vitro expanded stem cells can contribute to embryonic or extra-embryonic compartments after microinjection into blastocysts. However, whether stem cells could give rise to advanced gastrulating whole embryo-like structures with both embryonic and extra-embryonic compartments, without relying on a micro-injected host embryo, remains to be achieved. Thus far, in vitro aggregated stem cells have failed to generate post-gastrulation embryos ex utero or in utero, which partially resulted from the lack of methods for prolonged expansion of embryos until advanced developmental stages ex utero. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

54 Samples

Download data: TXT

(Submitter supplied) We analyzed 1,205 cells from the epiblast and nascent mesoderm of gastrulating mouse embryos by single cell RNA-seq, representing the first transcriptome-wide in vivo view of mammalian gastrulation. Based on the distribution of key marker genes and their spatiotemporal expression patterns within the embryo, we identified 10 cell clusters corresponding to the epiblast and developing mesodermal populations. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

2 Samples

Download data: BED, BW

(Submitter supplied) Our ability to study early human post-implantation development remains highly limited due to the ethical and technical challenges associated with intrauterine development of the human embryo after implantation. Despite the great progress made on human blastoids or gastruloids, such elegant models do not constitute an integrated synthetic stem cell-derived embryoid models (SEMs) that includes all the key extra-embryonic tissues of the early pre-gastrulating implanted human conceptus (e.g. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data

(Submitter supplied) Our ability to study early human post-implantation development remains highly limited due to the ethical and technical challenges associated with intrauterine development of the human embryo after implantation. Despite the great progress made on human blastoids or gastruloids, such elegant models do not constitute an integrated synthetic stem cell-derived embryoid models (SEMs) that includes all the key extra-embryonic tissues of the early pre-gastrulating implanted human conceptus (e.g. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: RDS

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL24676

13 Samples

Download data