GEO DataSets

(Submitter supplied) Anterior mesoderm (AM) and definitive endoderm (DE) progenitors represent the earliest embryonic cell types that are specified during germ layer formation at the primitive streak (PS) of the mouse embryo. Genetic experiments indicate that both lineages segregate from Eomes expressing progenitors in response to different NODAL signaling levels. However, the precise spatiotemporal pattern of the emergence of these cell types and molecular details of lineage segregation remain unexplored. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

18 Samples

Download data: CSV, TXT

(Submitter supplied) The Tbx factors Eomesodermin (Eomes) and Brachyury instruct endoderm and mesoderm specification. Both Tbx factors have common large overlap in chromatin binding sites, however their embryonic phenotypes of mutants largely differ. In this study, we delineate the distinct binding patterns and gene target sets of Eomes and Brachyury providing a molecular model of distinct fate specification programs.

Organism:

Mus musculus

Type:

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

Platforms:

GPL24247 GPL19057

20 Samples

Download data: BED, BIGWIG, 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) Lineage segregation in the mouse embryo is a finely controlled process dependent upon coordination of signalling pathways and transcriptional responses. We employed conditional deletion of Oct4 to investigate consequences of interference with embryonic patterning and lineage specification. Nanog becomes upregulated in the first epiblast cells to lose Oct4, leading to an expanded Nanog-positive domain. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

5 Samples

Download data: TXT

(Submitter supplied) We applied BMP4 to circular micropattern cultures to differentiate human embryonic stem cells (H1 hESCs) into microcolonies termed ‘gastruloids’, comprising germ layer and extraembryonic cells. Time-course single cell RNA-sequencing was performed at 0h (immediately before BMP4 treatment), 12h, and 24h after BMP4 treatment. Combining these 0h, 12h, and 24h datasets with previously generated 44h datasets, we report transcriptomic dynamics over the course of BMP4-driven differentiation in micropatterned cultures.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: CSV, TSV

(Submitter supplied) We used circular micropattern cultures to differentiate human embryonic stem cells (H1 hESCs) into microcolonies termed ‘gastruloids’, comprising germ layer and extraembryonic cells. Differentiated gastruloids were dissociated and reseeded onto micropatterns in single cells solution to study cell sorting behaviors. We applied single-cell RNA sequencing to examine transcriptomes of gastruloids and reseeded cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

3 Samples

Download data: MTX, TSV

(Submitter supplied) Single cell analysis of 3 developmental stages to study the progenitors of axis formation

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19787

1 Sample

Download data: TSV, TXT

(Submitter supplied) The segmental organization of the vertebral column is established early in embryogenesis when pairs of somites are rhythmically produced by the presomitic mesoderm (PSM). The tempo of somite formation is controlled by a molecular oscillator known as the segmentation clock. While this oscillator has been well-characterized in model organisms, whether a similar oscillator exists in humans remains unknown. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL18573

11 Samples

Download data: CSV, TXT

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

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL19057

30 Samples

Download data: BW

(Submitter supplied) Precisely co-ordinated activation of lineage specific transcription factors direct cell fate decisions during mouse early development. The T-box transcription factor Eomes is dynamically expressed during mouse gastrulation and is a key regulator of the anterior visceral endoderm (AVE), cardiac mesoderm and definitive endoderm (DE) lineages. The cis-acting regulatory elements that direct spatiotemporally restricted Eomes expression domains have yet to be elucidated. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: BW

(Submitter supplied) Precisely co-ordinated activation of lineage specific transcription factors direct cell fate decisions during mouse early development. The T-box transcription factor Eomes is dynamically expressed during mouse gastrulation and is a key regulator of the anterior visceral endoderm (AVE), cardiac mesoderm and definitive endoderm (DE) lineages. The cis-acting regulatory elements that direct spatiotemporally restricted Eomes expression domains have yet to be elucidated. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

18 Samples

Download data: TXT

(Submitter supplied) Precisely co-ordinated activation of lineage specific transcription factors direct cell fate decisions during mouse early development. The T-box transcription factor Eomes is dynamically expressed during mouse gastrulation and is a key regulator of the anterior visceral endoderm (AVE), cardiac mesoderm and definitive endoderm (DE) lineages. The cis-acting regulatory elements that direct spatiotemporally restricted Eomes expression domains have yet to be elucidated. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: BW

(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