Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profile at single cell level of control gastruloids at 96hpa or treated with indicated chemicals

ABSTRACT: Metabolic pathways can influence cell fate decisions, but their regulative role during embryonic development remains poorly understood. Here, we demonstrate a crucial role of glycolytic activity in regulating signalling pathways involved in mesoderm and endoderm specification. Using an mESC-based in vitro model for gastrulation, we found that glycolysis inhibition increases ectodermal cell fates at the expense of mesodermal and endodermal lineages. We used single cell RNA sequencing (scRNA-seq) to analyze the mechanistic insight into the nutritional regulation of cell fate decision making.

ORGANISM(S): Mus musculus

PROVIDER: GSE282050 | GEO | 2025/03/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

AMPK governs lineage specification through Tfeb-dependent regulation of lysosomes

Project description:Faithful execution of developmental programs relies on the acquisition of unique cell identities from pluripotent progenitors, a process governed by combinatorial inputs from numerous signaling cascades that ultimately dictate lineage-specific transcriptional outputs. Despite growing evidence that metabolism is integrated with many molecular networks, how pathways that control energy homeostasis may affect cell fate decisions is largely unknown. Here, we show that AMPK, a central metabolic regulator, plays critical roles in lineage specification. Although AMPK-deficient embryonic stem cells (ESCs) were normal in the pluripotent state, these cells displayed profound defects upon differentiation, failing to generate chimeric embryos and preferentially adopting an ectodermal fate at the expense of the endoderm during embryoid body (EB) formation. AMPK-/- EBs exhibited reduced levels of Tfeb, a master transcriptional regulator of lysosomes, leading to diminished endolysosomal function. Remarkably, genetic loss of Tfeb also yielded endodermal defects, while AMPK-null ESCs over-expressing this transcription factor normalized their differential potential, revealing an intimate connection between Tfeb/lysosomes and germ layer specification. The compromised endolysosomal system resulting from AMPK or Tfeb inactivation blunted Wnt signaling, while up-regulating this pathway restored expression of endodermal markers. Collectively, these results uncover the AMPK pathway as a novel regulator of cell fate determination during differentiation. 2 WT and 2 AMPK DKO ESC lines were differentiated into embryoid bodies (EBs) for various lengths of time (2, 4, 8, and 12 days) in high and low glucose conditions. Both ESC and EB samples were profiled by mRNA-seq to examine how global gene expression changes associated with ESC differentiation are affected by AMPK deletion.

2016-03-09 | E-GEOD-77705 | biostudies-arrayexpress

AMPK governs lineage specification through Tfeb-dependent regulation of lysosomes

2016-03-09 | GSE77705 | GEO

Endoderm- vs ectoderm-specific expression of symbiosis genes in the snakelocks sea anemone

Project description:Transcriptional comparison between endodermal and ectodermal compartment in symbiotic sea anemones Anemonia viridis were analysed in several specimens. We generated an oligonucleotide microarray (2000 selected features), which is to date the only available oligonucleotide array for symbiotic cnidarians. We were able to identify a subset of genes clearly involved in symbiosis. RNA was extracted from ectodermal or endodermal samples were prepared from 4 symbiotic specimens. Hybridizations were performed against a single reference (VBl) in a dye-swap experiment.

2011-06-01 | E-GEOD-22361 | biostudies-arrayexpress

Comparative single cell RNA seq of gastruloids from mESCs grown in 3 distinct media conditions facilitating distinct pluripotent states at 3 different developmental time points

Project description:Comparative single cell transcriptomic study (using 10x Genomics v3.1 kits) of gastruloids, aggregates of mESCs, at different developmental timepoints. mESCs, corresponding to the 0h timepoint, were also sequenced. The source mESCs were grown in 2 distinct media conditions: DMEM-based Serum-LIF (SL), SL + 0.3uM PD03 (SL + 1i) and SL + 1.5uM CGP77 + 3uM CHIR99 (SL + a2i). The following sets of timepoints were compared: 0hpa (hours post-aggregation) SL, 0hpa SL + 1i, 0hpa SL + a2i (corresponding to the mESC timepoint; 48hpa SL, 48hpa SL + 1i, 72hpa SL + a2i (corresponding to the pre-CHIR99 timepoint); 72hpa SL, 72hpa SL + 1i, 96hpa SL + a2i (corresponding to the post-CHIR99 timepoint); 120hpa SL, 120hpa SL + 1i, 144hpa SL + a2i (corresponding to the maximum elongation timepoint). The aim of this study was to delineate whether mESC pluripotent state influences cell and tissue fate acquisition dynamics. Gastruloids used in this study were generated from a transgenic G4 mESC line (George et al., PNAS 2007) modified via CRISPR-Cas9 mediated heterozygous knock-in of a Bra/T reporter allele (p2a-H2B-eGFP) as well as a ubiquitous nuclear marker allele (CAG::H2B-mKO2).

2024-11-13 | E-MTAB-13643 | biostudies-arrayexpress

Bulk RNA-seq of mouse embryonic progenitor cells

Project description:Population RNA-Seq analysis shows distinct gene expression profiles in specification of Nkx2-1+ endodermal and ectodermal populations

2019-12-20 | GSE138903 | GEO

Genome-wide analysis of the transcriptomes of mouse embryonic stem cells (mESC) maintained in different indicated conditions.

Project description:Analysis of genes involved in the mESC maintainance between different conditions of growth. The hypothesis tested in the present study was that Myc can sustain mESC self renewal and pluripotency. Results provide important information on the mechanism by which Myc supports mESC self renewal, in comparison with the routinely used LIF+serum culture condition, such as a Myc-dependent specific transcriptional program, which involves induction of an alternative Core Regulatory Network, modulation of signallign pathways (Wnt/bcat) and repression of developmental genes. Total RNA obtained from mESC growth 3 days in the indicated condition compared to the routinely used LIF+serum culture condition. Total RNA obtained from EpiSC growth 3 days in standard condition were also used as control for primed stem cell state.

2016-03-31 | E-GEOD-58656 | biostudies-arrayexpress

E-GEOD-59037

Project description:Dissecting engineered cell types and enhancing cell fate conversion via CellNet

2015-08-04 | E-GEOD-59037 | ExpressionAtlas

YAP1 Drives Lineage Specification and Patterning in hESC-derived Gastruloids

Project description:The gastrulation process is controlled by the interplay between morphogenetic signals from BMP, WNT and NODAL pathways. Increasing evidences support an emerging role of the Hippo-YAP signaling in the cell-fate decisions that guide lineage specification in mouse and human Embryonic Stem Cells (hESCs). However, the contribution of YAP to the process of gastrulation in hESCs remains unknown. Here, we show that YAP1 regulates the specification, size and patterning of the three-germ layers. Using hESC-derived 2D-micropatterned gastruloids and directed differentiation approaches we show that YAP maintains a semi-active NODAL signaling during gastrulation essential to regulate the exit of pluripotency. In absence of YAP1, a hyperactive NODAL signaling retains SMAD2.3 in the nuclei, impeding the exit of pluripotency and the acquisition of the ectodermal gene program. Accordingly, the inhibition of NODAL signaling is sufficient to rescue the gastrulation-defective phenotype of the YAP1 KO hESCs. Our work revealed that Hippo-YAP1 signaling is an important component of the developmental network that coordinate hESC pluripotency and gastrulation.

2022-01-14 | GSE168377 | GEO

Tissue specific differential expression in response to a thermal stress in the snakelocks sea anemone.

Project description:Differential expression between endodermal (zooxanthellate) and ectodermal tissue layers in the endosymbiotic sea anemone Anemonia viridis has been analyzed for 3 specimens subjected to a thermal stress (+10°C) for a 2 days period. A symbiosis-dedicated oligonucleotide microarray (2000 selected features) was generated, representing to date the only available oligonucleotide array used for symbiotic cnidarians (GPL10546). We are describing here the preferential expression in ectoderm vs endoderm (also called epidermis and gastroderm, respectively) during the time course of this thermal stress. RNA was extracted from ectodermal or endodermal dissected tissues. 3 different symbiotic anemones were subjected to a thermal and UV stress (+10°C), sampled at T0, T12h and T36h. Tissue dissections were carried out from tentacles immediately after sampling. For each sample, dye-swap hybridizations compared T0 and later time points. For each time point, statistical analysis combines the 3 biological replicates.

2011-11-17 | E-GEOD-28576 | biostudies-arrayexpress

Analysis of gene expression in MyD88-Knockdown-Hydra vulgaris (AEP)

Project description:Analysis of MyD88 as a putative mediator in host-microbe-interactions MyD88-Hairpin was micro-injected in Hydra AEP embryos. The resulting Hatchling D3 showed a patchy distribution of the transgene observed by GFP. By asexual reproduction via budding and constant selection for the marker gene GFP the transgene could be driven into different cell ines. Therefore two different cultures were established. Polyps that showed no GFP-Signal anymore (control) and Polyps with both, endodermal and ectodermal transgenic cell-lines (knockdown).

2012-10-08 | E-GEOD-32383 | 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