Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells [scRNA_seq_timecourse_naiveTSC]

ABSTRACT: Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells [scRNA_seq_timecourse_naiveTSC]

PROVIDER: PRJNA842268 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR19395049.fastq.gz	Fastqsanger.gz
	SRR19395050.fastq.gz	Fastqsanger.gz
	SRR19395051.fastq.gz	Fastqsanger.gz
	SRR19395052.fastq.gz	Fastqsanger.gz
	SRR19395053.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells

Project description:Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells

| PRJNA790842 | ENA

Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells [scRNA_seq_RACL_NACL]

Project description:Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells [scRNA_seq_RACL_NACL]

| PRJNA842388 | ENA

Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells [scATAC-seq]

Project description:Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells [scATAC-seq]

| PRJNA790848 | ENA

Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells [scRNA-seq]

Project description:Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells [scRNA-seq]

| PRJNA790847 | ENA

Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells [scRNA_seq_timecourse_naiveTSC]

Project description:time course scRNAseq of naïve to trophoblast stem cells and extraembryonic mesoderm conversion and D70 sorted extraembryonic mesoderm. Samples were collected at day 0, 1, 2, 4, 8, 13 and 18.

2022-08-01 | GSE204779 | GEO

Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells.

Project description:A hallmark of primate postimplantation embryogenesis is the specification of extraembryonic mesoderm (EXM) before gastrulation, in contrast to rodents where this tissue is formed only after gastrulation. Here, we discover that naive human pluripotent stem cells (hPSCs) are competent to differentiate into EXM cells (EXMCs). EXMCs are specified by inhibition of Nodal signaling and GSK3B, are maintained by mTOR and BMP4 signaling activity, and their transcriptome and epigenome closely resemble that of human and monkey embryo EXM. EXMCs are mesenchymal, can arise from an epiblast intermediate, and are capable of self-renewal. Thus, EXMCs arising via primate-specific specification between implantation and gastrulation can be modeled in vitro. We also find that most of the rare off-target cells within human blastoids formed by triple inhibition (Kagawa et al., 2021) correspond to EXMCs. Our study impacts our ability to model and study the molecular mechanisms of early human embryogenesis and related defects.

| S-EPMC9438972 | biostudies-literature

Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells [scRNA-seq]

Project description:scRNAseq of day 30 of trophoblast conversion together with naïve and primed hPSCs. Cells were mixed using the following ratio (H9 primed: Sigma primed: H9 naive: Sigma naive: day 30 ASECRiAV conversion = 1:1:1:1:2)

2022-08-01 | GSE191285 | GEO

RNA-seq of H9 cell line during differentiation from naïve extraembryonic endoderm to extraembryonic mesoderm.

Project description:Extraembryonic mesoderm (ExM) is one of the first cell types that emerges during embryogenesis and constitutes essential supportive tissues for the pregnancy. Primate ExM is known to form prior to gastrulation, unlike its murine counterpart which is derived from the primitive streak. Based on the embryonic morphology and the proximity of ExM to the extraembryonic endoderm (hypoblast), we hypothesised that ExM can be derived in vitro from the naïve extraembryonic endoderm (nEnd) cell line. We applied a mesoderm differentiation protocol, which has been reported to induce ExM from mouse epiblast stem cells, on human nEnd and analysed the transcriptome on day 0, 1, 2, 8 and 15.

2023-06-29 | E-MTAB-12517 | biostudies-arrayexpress

CDX2 dose-dependently influences the GRN underlying vascularization in human extraembryonic mesoderm-like cells

Project description:Proper regulation of gene dosage is critical for the development of the early embryo and the extraembryonic tissues that support it. Specifically, loss of Cdx2 in vivo leads to stunted development of the allantois, an extraembryonic mesoderm-derived structure that is critical for nutrient delivery and waste removal in the early embryo. In this study, we investigate how CDX2 dose-dependently influences the gene regulatory network underlying extraembryonic mesoderm development. By generating an allelic series for CDX2 in human induced pluripotent stem cells consisting of WT, heterozygous, and null CDX2 genotypes, differentiating these cells in a 2D gastruloid model, and subjecting these cells to multiomic single nucleus RNA and ATAC sequencing, we identify several genes regulating cytoskeletal integrity, adhesiveness, and polarity of the extraembryonic mesoderm and in a dose-dependent manner, including CDH1 and WNT5B. Despite these dose-dependent gene expression patterns, snATAC-seq reveals that heterozygous CDX2 expression is capable of inducing a WT-like chromatin accessibility profile, suggesting accessibility is not sufficient to drive gene expression when the CDX2 dose is reduced. Finally, because the loss of CDX2 or TBXT phenocopy one another in vivo, we compare differentially expressed genes in our CDX2 knock-out model to those from TBXT knock-out hiPSCs differentiated in an analogous experiment. This comparison identifies several genes critical for cytoskeletal integrity and vasculogenesis, including ANK3 and ANGPT1. Taken together, these results inform how CDX2 dose-dependently regulates gene expression in the extraembryonic mesoderm and suggest these genes may underlie defects in vascular development and allantoic elongation seen in the absence or reduction of CDX2 in vivo.

2024-02-14 | GSE251813 | GEO

scRNA-seq of mouse EpiSCs (epiblast stem cells) differentiated to extraembryonic mesoderm in vitro, in a monolayer

Project description:EpiSCs derived from epiblast of a gastrulating embryo differentiated towards extraembryonic mesoderm to test the efficiency of the differentiation protocol and identity and homogeneity of the resulting cell population.

2022-11-30 | E-MTAB-12107 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data