GEO DataSets

(Submitter supplied) Single cell technologies hold promise for resolving complex early developmental phenotypes. Here we define a novel Hedgehog (Hh)-Fibroblast Growth Factor (FGF) signaling axis for the formation of anterior mesoderm lineages during gastrulation. Single-cell transcriptome analysis of Hh-deficient mesoderm revealed selective deficits in anterior mesoderm populations—culminating in defects to anterior embryonic structures including the pharyngeal arches, heart, and anterior somites. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

5 Samples

Download data: TSV, 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) To determine the in vivo cellular identity of BMP-treated human embryonic stem cells (hESCs), we performed bulk RNA sequencing data of hESCs under pluripotency and BMP-treated conditions. Our analyses show that BMP-treated hESCs resemble human trophoblast cells in vivo.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: XLSX

(Submitter supplied) The mesodermal precursor populations for different internal organ systems are specified during gastrulation by the combined activity of extracellular signaling systems such as BMP, Wnt, Nodal, and FGF. The BMP, Wnt and Nodal signaling requirements for the differentiation of specific mesoderm subtypes in mammals have been mapped in detail, but which mesodermal cell types depend on FGF signaling is not precisely known. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

5 Samples

Download data: MTX, TSV

(Submitter supplied) Single-cell technology was used to investigate dynamic transcriptional changes in the blastula and gastrula of Drosophila embryos. Cells from embryo of stages 5 to 9 were isolated and subjected to library construction. Mesoderm cells were labeled with mCD8-GFP utilizing the GAL/UAS system. PCA identified 12 unique cell clusters that represent the blastoderm, mesoderm, endoderm and ectoderm anlage, primordia, and a sampling of differentiating cell types. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21306 GPL25244

3 Samples

Download data: H5

(Submitter supplied) Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan. Recent studies employing single cell RNA-sequencing have identified major transcriptional changes associated with germ layer specification. Global epigenetic reprogramming accompanies these changes, but the role of the epigenome in regulating early cell fate choice remains unresolved, and the coordination between different epigenetic layers is unclear. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

2213 Samples

Download data: TSV

(Submitter supplied) Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan. Recent studies employing single cell RNA-sequencing have identified major transcriptional changes associated with germ layer specification. Global epigenetic reprogramming accompanies these changes, but the role of the epigenome in regulating early cell fate choice remains unresolved, and the coordination between different epigenetic layers is unclear. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

960 Samples

Download data: TSV

(Submitter supplied) Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan. Recent studies employing single cell RNA-sequencing have identified major transcriptional changes associated with germ layer specification. Global epigenetic reprogramming accompanies these changes, but the role of the epigenome in regulating early cell fate choice remains unresolved, and the coordination between different epigenetic layers is unclear. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by SNP array

Platform:

GPL19057

382 Samples

Download data: TSV

(Submitter supplied) Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan. Recent studies employing single cell RNA-sequencing have identified major transcriptional changes associated with germ layer specification. Global epigenetic reprogramming accompanies these changes, but the role of the epigenome in regulating early cell fate choice remains unresolved, and the coordination between different epigenetic layers is unclear. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing; Methylation profiling by SNP array

Platform:

GPL19057

192 Samples

Download data: TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. Useful links: Parsed data: (ftp://ftp.ebi.ac.uk/pub/databases/scnmt_gastrulation) Github repository: (https://github.com/rargelaguet/scnmt_gastrulation)

Organism:

Mus musculus

Type:

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

Platform:

GPL19057

5263 Samples

Download data: TSV

(Submitter supplied) Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan. Recent studies employing single cell RNA-sequencing have identified major transcriptional changes associated with germ layer specification. Global epigenetic reprogramming accompanies these changes, but the role of the epigenome in regulating early cell fate choice remains unresolved, and the coordination between different epigenetic layers is unclear. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL19057

758 Samples

Download data: TSV

(Submitter supplied) Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan. Recent studies employing single cell RNA-sequencing have identified major transcriptional changes associated with germ layer specification. Global epigenetic reprogramming accompanies these changes, but the role of the epigenome in regulating early cell fate choice remains unresolved, and the coordination between different epigenetic layers is unclear. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

758 Samples

Download data: TSV

(Submitter supplied) The blueprint of lineage segregation of early mouse embryo is established during gastrulation in which progenitors of various cell fates are regionalized and patterned in specific embryo locations. Despite the central importance of this period of mammalian development, we currently lack a comprehensive understanding of the underlying developmental trajectories and molecular processes, principally because research efforts either employed in vitro systems, focused on small numbers of genes, or limited the number of developmental stages or cell types that were studied. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL24247

1293 Samples

Download data: CSV, TXT

(Submitter supplied) To isolate cell-autonomous effects of TET loss during gastrulation, we utilized a chimeric embryo platform in which fluorescently tagged Tet-deficient and control mouse embryonic stem cells (mESCs) were either injected into tetraploid (4N) or diploid (2N) blastocysts, and allowed to develop in utero. In 4N complemented embryos, the resulting embryonic compartment is solely comprised of the injected mESCs derivatives (hereinafter denoted as whole-embryo chimera), whereas in chimeras obtained using 2N host blastocysts, the embryonic compartment contains both wild-type (WT) and injected cell derivatives (hereinafter denoted as mixed chimera). more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL19057 GPL24247

222 Samples

Download data: TSV, TXT

(Submitter supplied) Development of a multicellular organism uses the same genetic code to generate a broad diversity of cell types, which is instructed by extracellular cues and orchestrated by transcriptional activators and repressors. While transcription factors establish cell identities according to the central dogma, a number of enzymes, which index and regulate chromatin, appear to perform essential functions as well. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL24247 GPL21103

54 Samples

Download data: BW, MTX, TSV

(Submitter supplied) We performed scRNAseq on embryonic and extra-embryonic mesoderm cells from mouse embryo at Mid/Late Streak stage (Embryonic day 7.25) as well as on Late Bud stage (Embryonic day 7.75) microdissected amnion, chorion and allantois. We used transgenic embryos (Brachyury-Cre; mTmG) in which all mesoderm cells are converted to membrane-GFP upon Cre-mediated recombination and the rest express membrane Tomato. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

5 Samples

Download data: CSV, FA, TAR

(Submitter supplied) Our understanding of human early development is severely hampered by limited access to embryonic tissues. Due to their close evolutionary relationship with humans, non-human primates (NHPs) are often used as surrogates to understand human development but currently suffer from a lack of in vivo datasets, especially from gastrulation to early organogenesis during which the major embryonic cell types are dynamically specified. more...

Organism:

Macaca fascicularis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23096

7 Samples

Download data

(Submitter supplied) Mouse embryonic development is a canonical model system for studying mammalian cell fate acquisition. Recently, single-cell atlases comprehensively charted embryonic transcriptional landscapes, yet inference of the coordinated dynamics of cells over such atlases remains challenging. Here we introduce a temporal model for mouse gastrulation, consisting of data from 153 individually sampled embryos spanning 36 hours of molecular diversification. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL19057

154 Samples

Download data: TXT

(Submitter supplied) The house mouse, Mus musculus, is an exceptional model system, combining genetic tractability with close homology to human biology. Gestation in mouse development lasts just under three weeks, a period during which its genome orchestrates the astonishing transformation of a single cell zygote into a free-living pup composed of >500 million cells. Towards a global framework for exploring mammalian development, we applied single cell combinatorial indexing (sci-*) to profile the transcriptional states of 12.4 million nuclei from 83 precisely staged embryos spanning late gastrulation (embryonic day 8 or E8) to birth (postnatal day 0 or P0), with 2-hr temporal resolution during somitogenesis, 6-hr resolution through to birth, and 20-min resolution during the immediately postpartum period. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30172 GPL24247

9024 Samples

Download data: CSV, MTX

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

1225 Samples

Download data