Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

62 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Karin Farkas

PROVIDER: E-MTAB-12517 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Single-cell RNA-seq of H9 nEnd cells subjected to mesoderm differentiation.

Project description:The origin of human extraembryonic mesoderm (ExM) has been heavily debated. In order to address if ExM can be derived from primitive endoderm (PrE), we treated the human PrE cell line (also called na�ve extraembryonic endoderm (nEnd)) with a mesoderm induction protocol and sequenced the entire day 15 cell population.

2023-06-29 | E-MTAB-12562 | biostudies-arrayexpress

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

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

| PRJEB58990 | 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

Stk40 deletion enhances c-Jun protein stability and compromises mesoderm differentiation

Project description:Serine/threonine kinase 40 (Stk40) was previously identified as a direct target gene of pluripotency-associated transcription factor Oct4 and its overexpression could facilitate differentiation of mouse embryonic stem cells (mESCs) towards the extraembryonic endoderm. Stk40-/- mice are lethal at the perinatal stage, displaying multiple organ failures. However, the molecular mechanisms underlying the physiological functions of Stk40 remain elusive. Here, we report that Stk40 ablation compromises the mesoderm differentiation from mESCs in vitro and in embryos. Mechanistically, Stk40 interacts with both mammalian constitutive photomorphogenic protein 1 (Cop1) and c-Jun, promoting degradation of c-Jun. Consequently, Stk40 knockout leads to c-Jun protein accumulation, which, in turn, might suppress the Wnt signaling activity and impair the mesoderm differentiation process. Overall, this study reveals that Stk40, together with Cop1, represent a novel axis for modulating c-Jun protein levels within an appropriate range during mesoderm differentiation from mESCs. Our finding provides new insight into the molecular mechanism regulating c-Jun protein stability and may have potential for managing related cellular disorders.

2019-05-14 | PXD012579 | Pride

MicroRNA expression data from differentiation of human H9 ESCs into definitive endoderm on MEF feeder layers

Project description:Pluripotent hESCs can differentiate into the three primary embryonic lineages (endoderm, mesoderm, ectoderm) as well as extraembryonic tissues. Definitive endoderm (DE) is the first step into the pathway to endoderm dreived tissues (pancreas, liver, gut, lung). We used microarrays to detail the changes in microRNA expression during the transition from pluripotent hESCs into definitive endoderm.

2010-07-30 | GSE16689 | GEO

MicroRNA expression data from differentiation of human H9 ESCs into definitive endoderm on MEF feeder layers

2010-07-30 | E-GEOD-16689 | biostudies-arrayexpress

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

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

Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells

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

| PRJNA790842 | ENA

Genes induced in Xenopus foregut endoderm by mesoderm

Project description:Foregut organogenesis is regulated by inductive interactions between the endoderm and the adjacent mesoderm. We identified genes induced in the foregut progenitors by the adjacent mesoderm. We used microarrays to detail the global programme of early foregut endoderm gene expression resulting from mesoderm induction and identified distinct classes of up-regulated genes during this process. Xenopus foregut endoderm explants cultured from Stages 15 to 23 either intact with mesoderm or as endoderm alone. Total RNA was isolated from the endoderm of these two culture conditions in quadruplicate and were subjected to Affymetrix microarray analysis.

2012-06-11 | E-GEOD-38654 | 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