GEO DataSets

(Submitter supplied) Single cell measurements of gene expression are providing new insights into lineage commitment, yet the regulatory changes underlying individual cell trajectories remain elusive. Here, we profiled chromatin accessibility in over 20,000 single nuclei across multiple stages of Drosophila embryogenesis. Our data reveal heterogeneity in the regulatory landscape prior to gastrulation that reflects anatomical position, a feature that aligns with future cell fate. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19132 GPL13304

4 Samples

Download data: BW, TXT

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

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL25244 GPL19132

2016 Samples

Download data

(Submitter supplied) Drosophila melanogaster is a powerful, long-standing model for metazoan development and gene regulation. We profiled chromatin accessibility in almost one million, and gene expression in half a million, nuclei from eleven tightly staged, overlapping windows of its embryogenesis. Leveraging the asynchronicity of embryos within each collection, we developed a statistical model to more precisely estimate the age of each nucleus, resulting in continuous views of molecular and cellular transitions throughout the majority of embryonic development. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

1908 Samples

Download data: MTX, TXT

(Submitter supplied) Drosophila melanogaster is a powerful, long-standing model for metazoan development and gene regulation. We profiled chromatin accessibility in almost one million, and gene expression in half a million, nuclei from eleven tightly staged, overlapping windows of its embryogenesis. Leveraging the asynchronicity of embryos within each collection, we developed a statistical model to more precisely estimate the age of each nucleus, resulting in continuous views of molecular and cellular transitions throughout the majority of embryonic development. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25244

108 Samples

Download data: MTX, TXT

(Submitter supplied) Cell fate transitions involve integration of genomic information encoded by regulatory elements, such as enhancers, with the cellular environment. However, identification of the genomic sequences that control the earliest steps of human embryonic development represents a formidable challenge. Here we show that in human embryonic stem cells (hESCs) unique chromatin signatures identify two distinct classes of genomic elements, both of which are marked by the presence of chromatin regulators p300 and BRG1, and monomethylation of histone H3 at lysine 4 (H3K4me1). more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL9052

16 Samples

Download data: BED, TXT

(Submitter supplied) Zebrafish is a popular model for studies of embryonic development. Recent surveys of zebrafish embryogenesis with single-cell transcriptomics have uncovered hundreds of cell types, but the dynamic accessible regions of the genome that determine regulatory programs responsible for the unique identity and function of each cell type during embryogenesis lack detailed study. Here, we present SPATAC-seq: a split-pool ligation-based high-throughput single-cell assay for transposase-accessible chromatin using sequencing. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30277 GPL30560 GPL24995

535 Samples

Download data: BED, BW, XLSX

(Submitter supplied) To establish an ultra-high-throughput single cell chromatin accessibility profiling method that is cost-effective and widely accessible, we built on sci-ATAC-seq (Cusanovich, D. A. et al. Science. 2015; Amini, S. et al. Nature Genetics. 2014) and SPLIT-seq (Rosenberg, A. B. et al. Science. 2018) to design SPATAC-seq, which in situ label chromatin fragment in the same single cell through combinatorial barcoding. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL26363 GPL25526

8 Samples

Download data: CSV, TSV

(Submitter supplied) Gonad development includes sex determination and divergent maturation of the testes and ovaries. Recent advances in measuring gene expression in single cells are providing new insights into this complex process. However, the underlying epigenetic regulatory mechanisms remain unclear. Here, we profiled chromatin accessibility in mouse gonadal cells of both sexes from embryonic day 11.5 to 14.5 using single-cell assay for transposase accessible chromatin by sequencing (scATAC-seq). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: TSV

(Submitter supplied) Establishment of spatial coordinates during early Drosophila embryogenesis relies on differential activity of axis patterning enhancers. Concentration gradients along the embryonic axes of activator and repressor transcription factors (TFs) provide positional information to each enhancer, which in turn promotes transcription of a target gene in a specific spatial pattern. In order to receive the TF input, an enhancer must be accessible. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19951

23 Samples

Download data: BW, GFF3

(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 used the assay for transposon-accessible chromatin using sequencing (ATAC-seq) on FACS-purified cells to profile chromatin accessibility during early cardiopharyngeal fate choices in Ciona. We obtained ~500 million unique reads from samples comprising cardiopharyngeal mesoderm and mesenchymal cells, as well as whole Ciona embryos and genomic DNA control. We combined ATAC-seq peaks from all the replicates to generate an atlas of 56,090 unique and non-overlapping accessible regions (accessome) covering 9.25% of the C. more...

Organism:

Ciona robusta

Type:

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

Platform:

GPL23563

58 Samples

Download data: BW, 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