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Links from GEO DataSets

Items: 20

1.

scRNA-seq experiments on primed mouse epiblast stem cells, blastocyst-like cell reprogramming and mouse embryonic stem cells.

(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
Series
Accession:
GSE166066
ID:
200166066
2.

Capturing totipotency in human cells through spliceosomal repression

(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
Series
Accession:
GSE226231
ID:
200226231
3.

Capturing totipotency in human cells through spliceosomal repression [ATAC-seq]

(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
Series
Accession:
GSE226229
ID:
200226229
4.

Capturing totipotency in human cells through spliceosomal repression [scRNA-seq]

(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
Series
Accession:
GSE226228
ID:
200226228
5.

Capturing totipotency in human cells through spliceosomal repression [ChIP-seq]

(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
Series
Accession:
GSE226227
ID:
200226227
6.

Capturing totipotency in human cells through spliceosomal repression [RNA-Seq]

(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
Series
Accession:
GSE224794
ID:
200224794
7.

Induction of Rosette-to-Lumen stage embryoids using reprogramming paradigms in ESCs

(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
Series
Accession:
GSE188394
ID:
200188394
8.

Investigations on the role of Blimp1 in pluripotency and reprogramming

(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
Series
Accession:
GSE35983
ID:
200035983
9.

Direct Induction of the Three Pre-Implantation Blastocyst Cell Types from Fibroblasts

(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
Series
Accession:
GSE98124
ID:
200098124
10.

Derivation of novel human ground state naïve pluripotent stem cells.

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens; Mus musculus
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
Series
Accession:
GSE52824
ID:
200052824
11.

Derivation of novel human ground state naïve pluripotent stem cells [ChIP-seq; RRBS-seq]

(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:
GPL16791 GPL11154 GPL17021
59 Samples
Download data: BED, TXT
Series
Accession:
GSE52617
ID:
200052617
12.

Derivation of novel human ground state naïve pluripotent stem cells [gene expression array]

(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
Series
Accession:
GSE46872
ID:
200046872
13.

OSKM induce extraembryonic endoderm stem (iXEN) cells in parallel to iPS cells

(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
Series
Accession:
GSE77550
ID:
200077550
14.

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
15.

Human Naïve Epiblast Cells Possess Unrestricted Lineage Potential II

(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
16.

Human Naïve Epiblast Cells Possess Unrestricted Lineage Potential

(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
Series
Accession:
GSE166422
ID:
200166422
17.

Human Naïve Epiblast Cells Possess Unrestricted Lineage Potential

(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
18.

Stem cell lines of the early mouse embryo

(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
Series
Accession:
GSE34799
ID:
200034799
19.

Converting self-renewal in naïve pluripotency to naïve endoderm [I]

(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
Series
Accession:
GSE77783
ID:
200077783
20.

Developmental equivalence of epiblast stem cells (EpiSCs)

(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
Series
Accession:
GSE46227
ID:
200046227
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