Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome profiling at four stages of turbot development from phylotypic to post-metamorphic stages [RNA-seq]

ABSTRACT: Metamorphosis is a widely studied post-embryonic process in which many tissues undergo dramatic modifications to adapt to the new adult lifestyle. Flatfish represent a good example of metamorphosis in teleosts. During flatfish metamorphosis, organ regression and neo-formation occur, being the most remarkable change the migration of one of the eyes to the other side of the body. In order to create a useful and reliable tool to advance the molecular study of metamorphosis in flatfish, we generated a chromatin accessible atlas as well as gene expression profile during four developmental stages ranging from a phylotypic stage to a post-metamorphic stage. We identified 29,019 accessible regions of chromatin and 3,253 differentially expressed genes. We found stage-specific regulatory regions and gene expression profile, supporting the quality of the results. Our work provides strongly reproducible data for further studies to elucidate the regulatory elements that ensure successful metamorphosis.

ORGANISM(S): Scophthalmus maximus

PROVIDER: GSE215395 | GEO | 2023/02/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Chromatin accessibility at four key stages of turbot development, from phylotypic to post-metamorphic stages [ATAC-seq]

Project description:Metamorphosis is a widely studied post-embryonic process in which many tissues undergo dramatic modifications to adapt to the new adult lifestyle. Flatfish represent a good example of metamorphosis in teleosts. During flatfish metamorphosis, organ regression and neo-formation occur, being the most remarkable change the migration of one of the eyes to the other side of the body. In order to create a useful and reliable tool to advance the molecular study of metamorphosis in flatfish, we generated a chromatin accessible atlas as well as gene expression profile during four developmental stages ranging from a phylotypic stage to a post-metamorphic stage. We identified 29,019 accessible regions of chromatin and 3,253 differentially expressed genes. We found stage-specific regulatory regions and gene expression profile, supporting the quality of the results. Our work provides strongly reproducible data for further studies to elucidate the regulatory elements that ensure successful metamorphosis.

2023-02-16 | GSE215396 | GEO

Unraveling the Genetic Landscape of Eye Migration and Visual Adaptation during Flatfish Metamorphosis

Project description:Flatfish have evolved their visual system to meet the demands of their environment through a fascinating process of metamorphosis. This morphological transformation involves a significant change in lifestyle from pelagic to benthic, accompanied by changes in body structure to achieve an asymmetrical flat shape. However, the fundamental change lies in the migration of one eye from its original position to the opposite location on the body. Although the role of thyroid hormone in triggering flatfish metamorphosis is well established, the specific gene regulatory network responsible for this extraordinary eye migration is still unknown. Here we show a global view through the creation of a general map of gene expression during the metamorphic process, encompassing both migrant and non-migrant eyes. Our research uncovers significant differences between migrant and non-migrant eyes of turbot in the pre-metamorphic and climax phases, emphasizing genetic disparities crucial for benthic adaptation.

2024-02-06 | GSE245741 | GEO

Label-free quantitative proteomic analysis of insect larval and metamorphic molts

Project description:Molting is an essential biological process occurring characteristic times throughout the life cycle of holometabolous insects. However, it is not clear how insects determine whether the direction of molting is to remain status quo or to initiate metamorphosis. Here, we used liquid chromatography-mass spectrometry to identify the molecules involved in larval and metamorphic molting, and compare the differentially expressed proteins (DEPs) in the two processes, to explore the functional factors that determine the direction of molts. There were 322 and 1140 DEPs identified in larval and metamorphic molting process, respectively. Bioinformatics analyses show that the amino sugar pathway was up-regulated in both processes. The up-regulated protease contributed to the metamorphosis. In addition, several proteins with different expression patterns in larval-larval and larval-pupal transitions, including Endochitinase, GRIM-19 (Genes associated with retinoid-IFN-induced mortality-19), IDE (Insulin-degrading enzyme), Sorcin (Soluble resistance related calcium binding protein), OBP (Odorant-binding protein-2 precursor), TRAP1(Tumor necrosis factor receptor associated protein-1), etc., were further identified by parallel reaction monitoring, which may play diverse functions in the determination of molting properties. These results provide a proteomic insight into molecules involved in larval and metamorphic molts, and will likely improve the current understanding of determination of direction of molts.

2020-10-30 | PXD020414 | Pride

DNA methylation dynamics underlie metamorphic gene regulation programs in Xenopus tadpole brain [ChIP-seq]

Project description:Association of thyroid hormone receptors (TRs) in chromatin across the genome of neural cells in the preoptic area/hypothalamus/thalamus of metamorphic climax stage Xenopus tropicalis tadpoles, analyzed by chromatin-immunoprecipitation sequencing (ChIP-seq).

2022-10-05 | GSE214697 | GEO

Metabolic basis of metamorphic climax in the wood frog, Rana omeimontis

Project description:In this study, we compared the metabolic networks in the liver and tail between pro-metamorphic and climax metamorphic (natural and T3-driven) Rana omeimontis tadpoles by a combination of metabolomics and transcriptomics.

2020-10-01 | GSE147618 | GEO

Identify and characterize the circular RNAs expressed in in the half-smooth tongue sole (Cynoglossus semilaevis)

Project description:Half-smooth tongue sole (Cynoglossus semilaevis) is a commercially valuable flatfish, ranking among the most valuable fishes in the coastal areas of China. It has an asymmetric body shape with lateralization of the eyes to the same side during metamorphosis as same as the other flatfish species. However, little is known about the function and profile of circRNAs in the half-smooth tongue sole. In this study,a total of 2730 circRNAs were identified from in the fish by deep RNA-sequencing technique.

2017-09-27 | GSE103984 | GEO

Genome-wide identification and prediction of long non-coding RNAs in the half-smooth tongue sole (Cynoglossus semilaevis)

Project description:Half-smooth tongue sole (Cynoglossus semilaevis) is a commercially valuable flatfish, ranking among the most valuable fishes in the coastal areas of China. It has an asymmetric body shape with lateralization of the eyes to the same side during metamorphosis as same as the other flatfish species. However, little is known about the function and profile of lncRNAs in the half-smooth tongue sole. In this study, we carry out a genome-wide review of lncRNAs in the fish by using large-scale deep sequencing.

2017-09-27 | GSE98425 | GEO

Temporal and Spatial Transcriptomic Dynamics across Brain Development in Xenopus laevis tadpoles

Project description:We conducted differential gene expression analyses of the developing X. laevis tadpole midbrain between stages 44 and 61, and across brain regions at stage 46. We found that genes pertaining to positive regulation of neural progenitor cell proliferation as well as known progenitor cell markers were upregulated in the midbrain prior to metamorphic climax; concurrently, expression of cell cycle timing regulators decreased across this period. We also found that at the start of metamorphosis, neural progenitor populations appeared to be similar across the fore-, mid-, and hindbrain regions. Genes pertaining to negative regulation of differentiation were upregulated in the spinal cord compared to the rest of the brain. Finally, we found that regulation of biological processes like cell fate commitment and synaptic signaling follow similar trajectories in the brain across early tadpole metamorphosis and mid- to late-embryonic mouse development.

2022-02-22 | GSE183193 | GEO

Transcriptomic responses of hornyhead turbot (Pleuronichthys verticalis) to environmentally relevant doses of polybrominated diphenyl ethers or polychlorinated biphenyls

Project description:Hornyhead turbot (Pleuronichthys verticalis), a sentinel flatfish species, were intraperitoneally injected with environmentally relevant mixtures of polybrominated diphenyl ethers (PBDEs) or polychlorinated biphenyls (PCBs). After 96 h, fish were sacrificed and liver tissue was collected for gene expression analysis using a custom-designed microarray.

2020-10-01 | GSE151532 | GEO

DNA methylation dynamics underlie metamorphic gene regulation programs in Xenopus tadpole brain

Project description:Changes in DNA methylation in the preoptic area/hypothalamus/thalamus of Xenopus tropicalis tadpoles were analyzed using Methylated DNA Capture sequencing (MethlCap-seq) at four stages of metamorphosis.

2019-10-23 | GSE139267 | GEO

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