GEO DataSets

(Submitter supplied) Recently, a new wave of synthetic embryo systems (SESs) have been established from cultured cells toward efficient and ethical embryonic development research. We recently reported our epiblast stem cell (EPISC) reprogramming SES that generates numerous blastocyst (BC)-like hemispheres (BCLH) with pluripotent and extraembryonic cell features detected microscopically. Here, we further explored the system over key time points with unprecedented single-cell RNA sequencing (scRNA-seq) analysis and revealed broad induction of the 2C-like reporter MERVL and RNA velocity diverging three major population regions with genetic expression resembling pluripotent epiblast (EPI), primitive endoderm (PE), and trophectoderm (TE). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

4 Samples

Download data: GTF, RDS, TSV

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL20795

112 Samples

Download data: BW, NARROWPEAK, TXT

(Submitter supplied) Supplemented with splicing inhibitor PlaB, we realize in vitro culturing of human totipotent stem cells comparable to 2-4-cell blastomeres Assay for transposase accessible chromatin with high-throughput sequencing in hESC sand hTBLCs

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20795

2 Samples

Download data: NARROWPEAK

(Submitter supplied) Supplemented with splicing inhibitor PlaB, we realize in vitro culturing of human totipotent stem cells comparable to 2-4-cell blastomeres

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

14 Samples

Download data: TXT

(Submitter supplied) Supplemented with splicing inhibitor PlaB, we realize in vitro culturing of human totipotent stem cells comparable to 2-4-cell blastomeres Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for h3k4me3 and h3k27me3 in hESC sand hTBLCs

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20795

4 Samples

Download data: BW

(Submitter supplied) Supplemented with splicing inhibitor PlaB, we realize in vitro culturing of human totipotent stem cells comparable to 2-4-cellb blastomeres Poly(A) RNA-seq is performed on hESCs cultured in MYCP medium

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

92 Samples

Download data: CSV

(Submitter supplied) Blastocyst-derived stem cell lines were shown to self-organize into embryo-like structures in 3D cell culture environments. Here, we provide evidence that embryo-like structures can be generated solely based on transcription factor-mediated reprogramming of embryonic stem cells in a simple 3D co-culture system. Embryonic stem cells in these cultures self-organize into elongated, compartmentalized embryo-like structures reflecting aspects of the inner regions of the early post-implantation embryo. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

1931 Samples

Download data: TXT

(Submitter supplied) Blimp1 (Prdm1), the key determinant of primordial germ cells (PGC), plays a combinatorial role with Prdm14 during PGC specification from postimplantation epiblast cells. They together initiate epigenetic reprogramming in early germ cells towards an underlying pluripotent state, which is equivalent to embryonic stem cells (ESC). Whereas Prdm14 alone can promote reprogramming and is important for the propagation of the pluripotent state, it is not known if Blimp1 is similarly involved. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

23 Samples

Download data: TXT

(Submitter supplied) ATAC-seq, RNA-seq and ChIP-seq in induced TSC and PSC 72 hours past Doxycyclin induction

Organism:

Mus musculus

Type:

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

Platform:

GPL19057

63 Samples

Download data: BED, BIGBED, BIGWIG, TXT

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

Organism:

Mus musculus; Homo sapiens

Type:

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

4 related Platforms

71 Samples

Download data: BED, CEL, TXT

(Submitter supplied) Mouse embryonic stem (ES) cells are isolated from the inner cell mass of blastocysts, and can be preserved in vitro in a naive inner-cell-mass-like configuration by providing exogenous stimulation with leukaemia inhibitory factor (LIF) and small molecule inhibition of ERK1/ERK2 and GSK3b signalling (termed 2i/LIF conditions). Hallmarks of naive pluripotency include driving Oct4 (also known as Pou5f1) transcription by its distal enhancer, retaining a pre-inactivation X chromosome state, global reduction in DNA methylation and in H3K27me3 repressive chromatin mark deposition on developmental regulatory gene promoters.Upon withdrawal of 2i/LIF, naïve mouse ES cells can drift towards a primed pluripotent state resembling that of the post-implantation epiblast. more...

Organism:

Homo sapiens; Mus musculus

Type:

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

Platforms:

GPL11154 GPL16791 GPL17021

59 Samples

Download data: BED, TXT

(Submitter supplied) Mouse embryonic stem (ES) cells are isolated from the inner cell mass of blastocysts, and can be preserved in vitro in a naive inner-cell-mass-like configuration by providing exogenous stimulation with leukaemia inhibitory factor (LIF) and small molecule inhibition of ERK1/ERK2 and GSK3b signalling (termed 2i/LIF conditions). Hallmarks of naive pluripotency include driving Oct4 (also known as Pou5f1) transcription by its distal enhancer, retaining a pre-inactivation X chromosome state, global reduction in DNA methylation and in H3K27me3 repressive chromatin mark deposition on developmental regulatory gene promoters.Upon withdrawal of 2i/LIF, naïve mouse ES cells can drift towards a primed pluripotent state resembling that of the post-implantation epiblast. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

12 Samples

Download data: CEL

(Submitter supplied) While the reprogramming factors OCT4, SOX2, KLF4, and MYC (OSKM) can reactivate the pluripotency network in terminally differentiated cells, they also regulate expression of non-pluripotency genes in other contexts, such as the mouse primitive endoderm. The primitive endoderm is an extraembryonic lineage established alongside the pluripotent epiblast in the blastocyst, and is the progenitor pool for extraembryonic endoderm stem (XEN) cells. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

17 Samples

Download data: TXT

(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) Transcriptomic analysis confirms the trophoblast identity of the naïve pluripotent stem cell derived TSC cultures by comparing to the placenta derived TSC culture.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

14 Samples

Download data: TXT

(Submitter supplied) Classical mouse embryology has established a paradigm of early development drivenby sequential lineage bifurcations. Accordingly, mouse embryonic stem cells derivedfrom early epiblast have lost the potency to produce extraembryonic trophectoderm.We show in contrast that human naive epiblast cells readily make trophectoderm.Inhibition of ERK signalling, instrumental in naive stem cell propagation, unexpectedlypotentiates trophectoderm formation, an effect enhanced by Nodal inhibition.Transcriptome analyses authenticate conversion into trophectoderm with subsequentproduction of syncitiotrophoblast, cytotrophoblast and trophoblast stem cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

20 Samples

Download data: TXT

(Submitter supplied) Classical mouse embryology has established a paradigm of early development drivenby sequential lineage bifurcations. Accordingly, mouse embryonic stem cells derivedfrom early epiblast have lost the potency to produce extraembryonic trophectoderm.We show in contrast that human naive epiblast cells readily make trophectoderm.Inhibition of ERK signalling, instrumental in naive stem cell propagation, unexpectedlypotentiates trophectoderm formation, an effect enhanced by Nodal inhibition.Transcriptome analyses authenticate conversion into trophectoderm with subsequentproduction of syncitiotrophoblast, cytotrophoblast and trophoblast stem cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

64 Samples

Download data: TXT

(Submitter supplied) Expression profiling of stem cell lines derived from the early embryo representing the trophoblast, primitive endoderm, early epiblast (inner cell mass E3.5) and late post-implantation epiblast (E5.5).

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL6246 GPL11533

4 Samples

Download data: CEL, CHP

(Submitter supplied) A novel strategy to generate bipotent primitive endoderm cultures from murine embryonic stem cells in vitro.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10787

29 Samples

Download data: TXT

(Submitter supplied) Epiblast stem cells (EpiSCs) were derived from the epiblast or the ectoderm (epi/ect) of pre-gastrula stage to late-bud stage mouse embryos. To identify if the EpiSCs retain any original stage specific characteristics or which developmental stage of epi/ect they most closely related to, we performed microarray analysis to compare the gene expression profile of multiple EpiSC lines with that of epi/ect of 7 different stages.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

112 Samples

Download data: TXT