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Links from GEO DataSets

Items: 20

1.

Single cell RNA-sequencing reveals the existence of naïve and primed pluripotency in pre-implantation rhesus monkey embryos

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Macaca mulatta
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL19129 GPL24522
256 Samples
Download data
Series
Accession:
GSE117219
ID:
200117219
2.

Single cell RNA-sequencing reveals the existence of naïve and primed pluripotency in pre-implantation rhesus monkey embryos [161 cells]

(Submitter supplied) To explore the dynamic change of transcriptome in pre-implantation of rhesus monkey, we collected single cells for RNA-sequencing.
Organism:
Macaca mulatta
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24522
161 Samples
Download data: TXT
Series
Accession:
GSE117218
ID:
200117218
3.

Single cell RNA-sequencing reveals the existence of naïve and primed pluripotency in pre-implantation rhesus monkey embryos [95 cells]

(Submitter supplied) To explore the dynamic change of transcriptome in pre-implantation of rhesus monkey, we collected single cells for RNA-sequencing.
Organism:
Macaca mulatta
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19129
95 Samples
Download data: TXT
Series
Accession:
GSE106481
ID:
200106481
4.

Transcriptional landscape changes during human embryonic stem cell derivation

(Submitter supplied) Currently, there is only minimal information elucidating the transcriptional changes occurring during the in vitro transition of the inner cell mass (ICM) towards the human embryonic stem cell (hESC) stage and the role played by the post inner cell mass intermediate (PICMI). In this study, we perform in-depth analysis of the transcriptional heterogeneity between these three stages of hESC derivation in order to correlate their downstream effects on pluripotency states and differentiation. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
9 Samples
Download data: CSV
Series
Accession:
GSE119378
ID:
200119378
5.

Single-Cell RNA-seq Defines the Three Cell Lineages of the Human Blastocyst

(Submitter supplied) Here we provide fundamental insights into early human development by single-cell RNA-sequencing of human and mouse preimplantation embryos. We elucidate conserved transcriptional programs along with those that are human-specific. Importantly, we validate our RNA-sequencing findings at the protein level, which further reveals differences in human and mouse embryo gene expression. For example, we identify several genes exclusively expressed in the human pluripotent epiblast including the transcription factor KLF17. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
30 Samples
Download data: TXT
Series
Accession:
GSE66507
ID:
200066507
6.

Single-cell analysis of gene networks in trophoectoderm and inner cell mass during human, monkey and mouse preimplantation development

(Submitter supplied) Mammalian preimplantation development involves highly conserved genetic programs across species. However, temporal differences in gene network activation and membership differences in gene modules are also observed. In this study, we focus on understanding the activation of crucial gene networks in trophoectoderm (TE) and inner cell mass across species using human, monkey, and mouse models. By single cell RNA sequencing analysis in cynomolgus monkey early embryos, we find relatively late major embryonic genome activation occurring at early morula stages. more...
Organism:
Homo sapiens; Macaca fascicularis; Mus musculus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL11154 GPL18648 GPL13112
195 Samples
Download data: TXT
Series
Accession:
GSE75764
ID:
200075764
7.

Single-cell RNA-seq reveals cellular heterogeneity of pluripotency transition and X-chromosome dynamics during early mouse development

(Submitter supplied) Here, we present a comprehensive transcriptome roadmap of the critical developmental time window prior to gastrulation by sequencing and analysis of 1724 individual cells from 28 pregastrula mouse embryos. Our analyses reveal the cellular substructure in EPI through clustering cells into anterior, transition and posterior states. The induction of the primitive streak (PS) is achieved via a transition state of a high cellular variability and up-regulation of the PS signature genes. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
1745 Samples
Download data: TXT
Series
Accession:
GSE109071
ID:
200109071
8.

The Long Terminal Repeats of ERV6 Are Activated in Pre-Implantation Embryos of Cynomolgus Monkey

(Submitter supplied) Precise temporal development is an important event during embryo development. However, transcriptional changes in the temporal development of early epiblast cells (EPI), primitive endoderm (PrE) and trophectoderm (TrB) cells remain unclear. Long terminal repeat elements (LTRs) of ERVs (Endogenous retroviruses) are dynamically expressed in blastocysts of mammalian embryos. However, the expression of LTRs in monkey blastocyst is still unknown. more...
Organism:
Macaca fascicularis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23096
166 Samples
Download data: RDS
Series
Accession:
GSE182061
ID:
200182061
9.

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
10.

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
11.

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
12.

A developmental coordinate of the spectrum of pluripotency among mice, monkeys, and humans

(Submitter supplied) The epiblast (EPI) is the origin of all somatic and germ cells in mammals, and of the spectrum of pluripotent stem cells (PSCs) in vitro. To explore the ontogeny of human/primate pluripotency, we performed comprehensive single-cell RNA sequencing for pre- and post-implantation EPI development in cynomolgus monkeys. Here we show that after specification in the blastocysts [embryonic day (E)7], cyEPI undergoes major transcriptome changes upon implantation. more...
Organism:
Macaca fascicularis; Mus musculus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL19944 GPL15907
492 Samples
Download data: TXT
Series
Accession:
GSE74767
ID:
200074767
13.

Generation of Naïve Induced Pluripotent Stem Cells from Rhesus Monkey Fibroblasts

(Submitter supplied) Conventional embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs) derived from primates resemble mouse epiblast stem cells, raising an intriguing question regarding whether the naïve pluripotent state resembling mouse embryonic stem cells (mESCs) exists in primates and how to capture it in vitro. Here we identified several specific signaling modulators that are sufficient to generate rhesus monkey fibroblast-derived iPSCs with the features of naïve pluripotency in terms of growth properties, gene expression profiles, self-renewal signaling, X-reactivation and the potential to generate cross-species chimeric embryos. more...
Organism:
Macaca mulatta
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19129
6 Samples
Download data: TXT
Series
Accession:
GSE61420
ID:
200061420
14.

A Molecular Roadmap of the Phased Progression of Pluripotency

(Submitter supplied) Pluripotency is highly dynamic and progresses through a continuum of pluripotent stem cell states. The two states that bookend the pluripotency continuum, naïve and primed, are well characterized, but our understanding of the intermediate states and the transitions between them remain incomplete. To address this gap in knowledge, using a previously validated system to induce naive mouse embryonic stem cells (ESCs) to post-implantation pre-grastrulating epiblast-like cells (EpiLCs), we generated comprehensive high-temporal-resolution maps of the proteome, phosphoproteome, transcriptome, and epigenome of ESCs transitioning from naïve to primed pluripotency. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17021
72 Samples
Download data: BW
Series
Accession:
GSE117896
ID:
200117896
15.

In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. SubSeries GSE105762 contains bulk RNA-Seq data, while SubSeries GSE145726 contains single-cell RNA-Seq data.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL17021 GPL19057
23 Samples
Download data: TXT
Series
Accession:
GSE145727
ID:
200145727
16.

In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states (II, single-cell RNA-Seq data)

(Submitter supplied) Naive pluripotent cells in the implanting mouse blastocyst generate a rosette structure before undergoing lumenogenesis to form the egg cylinder. Simultaneously, they acquire primed pluripotency, the ability to differentiate into the primary germ layers. The existence of discrete intermediate pluripotent states during this transition has not been demonstrated. We identify here a distinct rosette pluripotent state, defined by co-expression of naive factors with transcription factor OTX2. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
6 Samples
Download data: TXT
Series
Accession:
GSE145726
ID:
200145726
17.

In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states

(Submitter supplied) Upon implantation, the naive pluripotent epiblast of the mouse blastocyst generates a rosette, undergoes lumenogenesis and forms the primed pluripotent egg cylinder, able to generate the embryonic tissues. How pluripotency progression and morphogenesis are linked, and whether intermediate pluripotent states exist remain controversial. We identify here a rosette pluripotent state, defined by co-expression of naive factors with transcription factor OTX2. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
4 Samples
Download data: BED, BW
Series
Accession:
GSE112234
ID:
200112234
18.

In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states (I, bulk RNA-Seq data)

(Submitter supplied) Naive pluripotent cells in the implanting mouse blastocyst generate a rosette structure before undergoing lumenogenesis to form the egg cylinder. Simultaneously, they acquire primed pluripotency, the ability to differentiate into the primary germ layers. The existence of discrete intermediate pluripotent states during this transition has not been demonstrated. We identify here a distinct rosette pluripotent state, defined by co-expression of naive factors with transcription factor OTX2. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
17 Samples
Download data: TXT, XLSX
Series
Accession:
GSE105762
ID:
200105762
19.

Human Stem Cells from Single Blastomeres Reveal Pathways of Embryonic or Trophoblast Fate Specification.

(Submitter supplied) Mechanisms of initial cell fate decisions differ among species. To gain insights into lineage allocation in humans, we derived ten human embryonic stem cell lines from single blastomeres of four 8-cell embryos and one 12-cell embryo from a single couple (UCSFB1-10). Versus numerous conventional lines from blastocysts, they had unique gene expression and DNA methylation patterns, in part, indicative of trophoblast competence. more...
Organism:
Homo sapiens
Type:
Expression profiling by array; Methylation profiling by genome tiling array
Platforms:
GPL6947 GPL10558 GPL13534
383 Samples
Download data: TXT
Series
Accession:
GSE72923
ID:
200072923
20.

Distinct classes of genes behave as either drivers or dependents of replication timing switches.

(Submitter supplied) Duplication of the genome in mammalian cells occurs in a defined temporal order referred as its replication-timing program (RT). RT is regulated in units of 400-800 Kb referred as replication domains (RDs) and changes dynamically during development. Changes in RT are generally coordinated with transcriptional competence and changes in sub-nuclear position. We generated genome-wide RT profiles for 29 distinct human cell types including embryonic stem cell (hESC)-derived, primary cells and established cell lines representing intermediate stages of endoderm, mesoderm, ectoderm and neural crest (NC) development. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10558
64 Samples
Download data: TXT
Series
Accession:
GSE63592
ID:
200063592
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