GEO DataSets

(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) 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) 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) 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) 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) 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) Genome-wide analysis of miRNA expression was performed in Activin A and Wnt3a-treated mouse ESCs during the different stages of DE differentiation to identify candidate miRNAs likely to be involved in Wnt3a and Activin A induced DE formation. Our analysis exhibited a distinct miRNA expression finger print. Furthermore, we found that forced expression of a subset of synergistically regulated miRNAs could partially mimic the roles of Wnt3a and Activin A. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL13493

39 Samples

Download data: TXT

(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 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) Current knowledge about the role of epigenetic modifiers in pancreas development has been exponentially increased. However, the precise function of TET dioxygenases in pancreas specification remains poorly understood. Using a stepwise human embryonic stem cell (hESC) differentiation system, TET1/TET2/TET3 triple-knockout (TKO) cells displayed severe defects in pancreatic differentiation. Whole-genome analysis revealed TET depletion led to aberrant DNA methylation and chromatin remodeling. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL16791 GPL23227 GPL18573

65 Samples

Download data: BW

(Submitter supplied) Transcriptional profiling of the preingression epiblast versus lateral epiblast, of preingression epiblast from control embryos treated with the DMSO carrier vehicle (0.5%) versus embryos treated with SU5402, U0126 or LY294002. Embryos were stages 5-6 at time of tissue isolation. The preingression epiblast (E2 region) is the region of epiblast just lateral to the primitive streak. Lateral epiblast is the E3 region. more...

Organism:

Gallus gallus

Type:

Expression profiling by array

Platform:

GPL13191

4 Samples

Download data: TXT

(Submitter supplied) The emergence of distinct cell types during embryonic development relies on the ability of progenitor cells to properly interpret environmental cues; yet how this developmental competence is established is unknown. Here we show that epigenetic priming of enhancers signifies developmental competence. Chromatin mapping during endodermal lineage diversification of human pluripotent stem cells revealed en masse acquisition of a poised chromatin state at enhancers for multiple descendant lineages in developmental intermediates. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL16791

53 Samples

Download data: BW

(Submitter supplied) Although histone-modifying enzymes are assumed to function in a manner dependent on their enzymatic activities, this assumption remains untested for many factors. Here we show the Tip60 (Kat5) lysine acetyltransferase (KAT), which is essential for embryonic stem cell (ESC) self-renewal and pre-implantation development, performs these functions independently of its KAT activity. Unlike ESCs depleted of Tip60, KAT–deficient ESCs exhibited minimal alterations in gene expression, chromatin accessibility at Tip60 binding sites, and self-renewal, thus demonstrating a critical KAT–independent role of Tip60 in ESC maintenance. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL13112 GPL21493 GPL19057

48 Samples

Download data: BEDGRAPH