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Links from GEO DataSets

Items: 20

1.

The emergent landscape of the mouse gut endoderm at single-cell resolution

(Submitter supplied) To comprehensively delineate the ontogeny of an organ system, we generated 112,217 single- cell transcriptomes representing all endoderm populations within the mouse embryo until midgestation. We employed graph-based approaches to model differentiating cells for spatio- temporal characterization of developmental trajectories. Our analysis reveals the detailed architecture of the emergence of the first (primitive or extra-embryonic) endodermal population and pluripotent epiblast. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
29 Samples
Download data: CSV
Series
Accession:
GSE123046
ID:
200123046
2.

The emergent landscape of the mouse gut endoderm at single-cell resolution

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL21103 GPL24247
45 Samples
Download data: CSV
Series
Accession:
GSE123135
ID:
200123135
3.

The emergent landscape of the mouse gut endoderm at single-cell resolution

(Submitter supplied) To comprehensively delineate the ontogeny of an organ system, we generated 112,217 single- cell transcriptomes representing all endoderm populations within the mouse embryo until midgestation. We employed graph-based approaches to model differentiating cells for spatio- temporal characterization of developmental trajectories. Our analysis reveals the detailed architecture of the emergence of the first (primitive or extra-embryonic) endodermal population and pluripotent epiblast. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21103
16 Samples
Download data: CSV
Series
Accession:
GSE123124
ID:
200123124
4.

Comparative Analysis of Extraembryonic Endoderm Cells with Cardiac Inducing Ability

(Submitter supplied) Comparative analysis of Endodermal-like cell lines with demonstrated ability to support myocardial differentiation
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6887
9 Samples
Download data: TXT
Series
Accession:
GSE19564
ID:
200019564
5.

Single Cell RNA-seq analysis of gene expression patterns of cells from stem-cell-derived-synthetic-blastocysts, called as 'ES-' or 'EPS-blastoids'.

(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
Series
Accession:
GSE134240
ID:
200134240
6.

Conversion of mES to cXEN cells

(Submitter supplied) The inner cell mass of the mouse pre-implantation blastocyst is comprised of epiblast progenitor and primitive endoderm cells of which cognate embryonic (mESCs) or extra-embryonic (XEN) stem cell lines can be derived. Importantly, each stem cell type retains the defining properties and lineage restriction of their in vivo tissue of origin. Recently, we demonstrated that XEN-like cells arise within mESC cultures. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6887
8 Samples
Download data: TXT
Series
Accession:
GSE38477
ID:
200038477
7.

Oct4 regulates the embryonic axis and coordinates exit from pluripotency and germ layer specification in the mouse embryo

(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
Series
Accession:
GSE103403
ID:
200103403
8.

Functional Heterogeneity of Embryonic Stem Cells Revealed Through Translational Amplification of an Early Endodermal Transcript

(Submitter supplied) Identification of transcripts in different subpopulations of the HIV mouse ES cell line growing under self-renewing conditions (+Lif, +10FCS, GMEM media and plated on gelatin coated dishes). Subpopulations were identified and isolated based on the expression of the cell surface marker, SSEA 1 (a marker of murine ES cells) and expression of the venus protein, the cDNA of which was knocked into the Hex locus (Hhex). more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6867
8 Samples
Download data: TXT
Series
Accession:
GSE13472
ID:
200013472
9.

Dynamic developmental signaling logic underlying lineage bifurcations during human endoderm induction and patterning from pluripotent stem cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL11154 GPL570
60 Samples
Download data: BEDGRAPH, CEL, TXT
Series
Accession:
GSE52658
ID:
200052658
10.

Dynamic developmental signaling logic underlying lineage bifurcations during human endoderm induction and patterning from pluripotent stem cells [Endoderm RNA-seq and ChIP-seq data sets]

(Submitter supplied) Unraveling complex signaling programs animating developmental lineage-decisions is pivotal to differentiate human pluripotent stem cells (hPSC) into pure populations of desired lineages for regenerative medicine. Developmental signals are strikingly temporally dynamic: BMP and Wnt initially specify primitive streak (progenitor to endoderm) yet 24 hours later suppress endoderm and induce mesoderm. At lineage bifurcations we show mutually-exclusive embryonic lineages are segregated through cross-repressive signals: TGFβ and BMP/MAPK duel to respectively specify pancreas versus liver from endoderm. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL11154
36 Samples
Download data: BEDGRAPH, TXT
11.

Dynamic developmental signaling logic underlying lineage bifurcations during human endoderm induction and patterning from pluripotent stem cells [Expression data set]

(Submitter supplied) The definitive endoderm germ layer is the provenance of multiple internal organs, including the lungs, liver, pancreas and intestines. Molecular events driving initial endoderm germ layer specification and subsequent anterior-posterior patterning of endoderm into distinct organ primordia remain largely cryptic. Through microarray analyses, we captured genome-wide transcriptional dynamics driving successive stages of endoderm development with the intent of identifying novel regulatory genes or diagnostic markers that respectively drive or mark endoderm committment.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
24 Samples
Download data: CEL
Series
Accession:
GSE52158
ID:
200052158
12.

Spatiotemporal sequence of mesoderm and endoderm lineage segregation during mouse gastrulation

(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
Series
Accession:
GSE151824
ID:
200151824
13.

Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis

(Submitter supplied) Background: Organogenesis is crucial for proper organ formation during mammalian embryonic development. However, the similarities and shared features between different organs and the cellular heterogeneity during this process at single-cell resolution remain elusive. Results: We perform single-cell RNA sequencing analysis of 1,916 individual cells from eight organs and tissues of E9.5 to E11.5 mouse embryos, namely, the forebrain, hindbrain, skin, heart, somite, lung, liver, and intestine. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21103
32 Samples
Download data: TXT, XLSX
Series
Accession:
GSE87038
ID:
200087038
14.

Single-cell RNA-seq of mouse embryos E6.5 and E7.5. Second batch.

(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
Series
Accession:
GSE133725
ID:
200133725
15.

Single-cell RNA-seq of mouse embryoid body cells, day 3 to day 7. Includes wild type and Tet TKO.

(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
Series
Accession:
GSE133689
ID:
200133689
16.

Single-cell methylation and accessibility of mouse embryos E6.5 and E7.5. Second batch.

(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
Series
Accession:
GSE133688
ID:
200133688
17.

Single-cell methylation and accessibility of mouse embryoid body cells, day 3 to day 7. Includes wild type and Tet TKO.

(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
Series
Accession:
GSE133687
ID:
200133687
18.

Multi-omics profiling of mouse gastrulation at single cell resolution

(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
Series
Accession:
GSE121708
ID:
200121708
19.

Single-cell methylation and accessibility of mouse embryos E4.5 to E7.5. First batch.

(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
Series
Accession:
GSE121690
ID:
200121690
20.

Single-cell RNA-seq of mouse embryos E4.5 to E7.5. First batch.

(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
Series
Accession:
GSE121650
ID:
200121650
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