Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

TRANSCRIPTOME ANALYSIS DURING THE METAMORPHOSIS OF THE ASCIDIAN CIONA INTESTINALIS

ABSTRACT: Tunicates, including ascidians, are recognized as the true “sister group” of vertebrates and are emerging as models to study the development and degeneration of central nervous system (CNS). Ascidian larvae have the typical chordate body plan that includes a dorsal neural tube. During their metamorphosis, a deep tissue reorganization takes place, with some tissues that degenerate while others develop to become functional during the adult life. The larval CNS also degenerates and most neurons disappear, making room to the formation of adult CNS. The genome of the ascidian Ciona intestinalis has been sequenced and annotated, with several CNS specific genes that have been characterized, revealing specification mechanisms shared with humans. These features make ascidian metamorphosis a good model to study the mechanisms underlying physiological CNS degeneration and to compare them to the pathological condition typical of neurodegenerative diseases. In order to shed light on the molecular determinants of C. intestinalis metamorphosis and neurodegeneration, we analyzed its transcriptome at three stages of development: swimming larva (SwL, Hotta stage 28), settled larva (SetL, Hotta stage 32) and metamorphosing larva (MetL, Hotta stage 34). Supported by SoE-SEED-2020 Grant, University of Milan.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Ciona intestinalis

SUBMITTER: Cristina Battaglia

PROVIDER: E-MTAB-13385 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Identification of differentially expressed genes in the mutant tail regression failed (trf) in Ciona intestinalis.

Project description:Tunicate ascidians exhibit metamorphosis that converts tadpole, swimming larva into immotile adult. In ascidian Ciona intestinalis, the mutant tail regression failed (trf) which shows defects in the metamorphosis was previously reported (Nakayama-Ishimura et al., 2009). In the metamorphosis process, trf larvae settle normally with their adhesive papillae, but do not start tail regression, papillae retraction and sensory vesicle retraction, while development of adult organs proceed. To understand the molecular mechanism of the metamorphosis, microarray analysis of trf mutant was performed.

2020-06-30 | GSE124672 | GEO

Ciona intestinalis (ascidian): control vs. TBT exposed

Project description:Transcriptional profiling of Ciona intestinalis comparing ethanol exposed asidian (control) with TBT exposed ascidian.

2010-07-20 | GSE22995 | GEO

Ciona intestinalis (ascidian): control vs. TBT exposed

Project description:Transcriptional profiling of Ciona intestinalis comparing ethanol exposed asidian (control) with TBT exposed ascidian. Two conditions experiment comparing ethanol exposed asidian (control) with TBT exposed ascidian.

2010-07-20 | E-GEOD-22995 | biostudies-arrayexpress

TRANSCRIPTOME ANALYSIS DURING THE METAMORPHOSIS OF THE ASCIDIAN CIONA INTESTINALIS

Project description:TRANSCRIPTOME ANALYSIS DURING THE METAMORPHOSIS OF THE ASCIDIAN CIONA INTESTINALIS

| PRJEB66283 | ENA

Single-cell transcriptome profiling of the Ciona larval brain

Project description:The tadpole-type larva of Ciona has emerged as an intriguing model system for the study of neurodevelopment. The Ciona intestinalis connectome has been recently mapped, revealing the smallest central nervous system (CNS) known in any chordate, with only 177 neurons. This minimal CNS is highly reminiscent of larger CNS of vertebrates, sharing many conserved developmental processes, anatomical compartments, neuron subtypes, and even specific neural circuits. Thus, the Ciona tadpole offers a unique opportunity to understand the development and wiring of a chordate CNS at single-cell resolution. Here we report the use of single-cell RNAseq to profile the transcriptomes of single cells isolated by fluorescence-activated cell sorting (FACS) from the whole brain of Ciona robusta (formerly intestinalis Type A) larvae. We have also compared these profiles to bulk RNAseq data from specific subsets of brain cells isolated by FACS using cell type-specific reporter plasmid expression. Taken together, these datasets have begun to reveal the compartment- and cell-specific gene expression patterns that define the organization of the Ciona larval brain.

2018-10-26 | GSE121807 | GEO

Comparative analysis of gene expression profiles between Nodal-overexpressing embryos with control embryos

Project description:A comprehensive search for downstream genes is necessary for understanding of functions of Nodal signaling in embryos of the ascidian Ciona intestinalis. The level of mRNA expression in Nodal-overexpressing embryos was compared with that in normal embryos at the late gastrula stage by a microarray analysis. Overexpression of Ci-nodal elevated the level of expression of 115 genes more than two-fold. These candidate target genes include those encoding transcription factors, proteins involved in cell-cell communication, and extracellular matrix components. Many of these genes were expressed in the neural plate at the late gastrula stage. Overexpression of nodal also affected the expression of genes involved in the planar cell polarity pathway and Wnt/Ca2+ pathway (prickle, Rho-like2, and PLC2), and delta1-protocadherin-like. Keywords: ascidian, Ciona intestinalis, Nodal, embryogenesis, gene expression profile

2010-01-26 | GSE14567 | GEO

Comparative analysis of gene expression profiles between Nodal-overexpressing embryos with control embryos

2010-05-15 | E-GEOD-14567 | biostudies-arrayexpress

small RNA sequencing of two developmental stages of Ciona intestinalis

Project description:We report the comprehensive sequencing of small RNA libraries created from different developmental stages (larva and gastrula) of the basal chordate, Ciona intestinalis. These libraries were used for the identification of microRNAs in this organism. Sequencing of small RNA libraries from 2 stages of Ciona intestinalis.

2010-03-27 | E-GEOD-21078 | biostudies-arrayexpress

The hypothalamus predates the origin of vertebrates

Project description:The hypothalamus coordinates neuroendocrine functions in vertebrates, including circadian rhythm, metabolism, and appetite. To explore its evolutionary origin, we attempt to create integrated transcription/connectome brain maps for swimming tadpoles of the ascidian, Ciona intestinalis, which serves as an approximation of the ancestral proto-vertebrate. This map features several cell types related to different regions of the vertebrate hypothalamus, including coronet cells, magnocellular neurons and the arcuate nucleus. Coronet cells express melanopsin and share additional properties with the saccus vasculosus, a specialized region of the hypothalamus that mediates photoperiodism in non-tropical fishes such as salmon. Comparative transcriptome analyses identified orthologous cell types for mechanosensory switch neurons, and VP+ and VPR+ relay neurons in different regions of the mouse hypothalamus. These observations provide evidence that the hypothalamus predates the evolution of the vertebrate brain. We discuss the possibility that switch neurons, coronet cells, and FoxP+/VPR relay neurons comprise a behavioral circuit that helps trigger metamorphosis of Ciona larvae in response to twilight.

2021-04-28 | GSE166235 | GEO

High-throughput sequencing of small RNA during metamorphosis in the Japanese flounder (Paralichthys olivaceus)

Project description:Many known miRNAs in fish come from zebrafish and fugu whose genome sequence data are available. The Japanese flounder undergoes typical metamorphosis which is characterized by major morphological, functional, and behavioral changes during growth due to this metamorphosis from larva to juvenile. Metamorphosis is a biological process by which an animal physically develops after birth or hatching, involving a conspicuous and relatively abrupt change in the animal's body structure through cell growth and differentiation. Here, the high-throughput sequencing was adopted to identify the miRNAs during metamorphosis in the Japanese flounder. We found abundant microRNAs during metamorphosis in the Japanese flounder. Small RNAs were sequenced from metamorphosis stages of Japanese flounder

2010-12-23 | E-GEOD-25995 | 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