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ABSTRACT: ascidian larval transcriptome

PROVIDER: PRJNA795827 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17518789_1.fastq.gz	Fastqsanger.gz
	SRR17518789_2.fastq.gz	Fastqsanger.gz
	SRR17518790_1.fastq.gz	Fastqsanger.gz
	SRR17518790_2.fastq.gz	Fastqsanger.gz
	SRR17518791_1.fastq.gz	Fastqsanger.gz

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TRANSCRIPTOME ANALYSIS DURING THE METAMORPHOSIS OF THE ASCIDIAN CIONA INTESTINALIS

Project description: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.

2024-08-31 | E-MTAB-13385 | biostudies-arrayexpress

ZicL ChIP-chip on Ciona intestinalis embryo (early gastrula)

Project description:A genomic overview of in vivo binding of a transcription factor ZicL in the ascidian gastrula embryo. ZicL is a key regulator of the early ascidian development, and so called 'master-regulatory genes' for mesodermal and neural tissues are under the control of ZicL. Keywords: ChIP-chip

2010-03-09 | GSE10803 | GEO

Comprehensive single cell transcriptome lineages of a proto-vertebrate

Project description:Studies of ascidian (sea squirt) embryos have highlighted the importance of cell lineages in animal development for over 100 years. As simple proto-vertebrates, they are also used to explore the evolutionary origins of novel cell types, such as cranial placodes and neural crest in vertebrates. To build upon these efforts we have determined comprehensive single cell transcriptomes of Ciona intestinalis throughout embryogenesis. More than 90,000 cells from 10 different developmental stages were examined, spanning the entirety of morphogenesis, from the onset of gastrulation at the 110-cell stage to the hatching of swimming tadpoles. This represents an average of over 12-fold coverage for every cell at every stage of development, owing to the small cell numbers that are a hallmark property of ascidian embryogenesis. Single cell transcriptome trajectories were used to construct “virtual” cell lineage maps, which confirm and extend those determined by conventional labeling methods. These datasets were also used to reconstruct regulatory cascades and provisional gene networks for a variety of cell types, including nearly 40 different neuronal subtypes comprising the larval nervous system. We summarize several applications of these datasets, including the identification of individual transcriptomes within the complete synaptome of swimming tadpoles, visualizing dynamic changes in gene expression during the birth, migration, and axogenesis of defined neurons, and the evolution of novel cell types such as the vertebrate telencephalon.

2019-07-08 | GSE131155 | GEO

Tbx6b ChIP-chip on Ciona intestinalis embryo (early gastrula)

Project description:A genomic overview of in vivo binding of a transcription factor Tbx6b in the ascidian early gastrula embryo.

2010-03-09 | GSE17694 | GEO

SoxC ChIP-chip on Ciona intestinalis embryo (early gastrula)

Project description:A genomic overview of in vivo binding of a transcription factor SoxC in the ascidian early gastrula embryo.

2010-03-09 | GSE17692 | GEO

Snail ChIP-chip on Ciona intestinalis embryo (early gastrula)

Project description:A genomic overview of in vivo binding of a transcription factor Snail in the ascidian early gastrula embryo.

2010-03-09 | GSE17691 | GEO

Otx ChIP-chip on Ciona intestinalis embryo (early gastrula)

Project description:A genomic overview of in vivo binding of a transcription factor Otx in the ascidian early gastrula embryo.

2010-03-09 | GSE17690 | GEO

Neurogenin ChIP-chip on Ciona intestinalis embryo (64-cell stage)

Project description:A genomic overview of in vivo binding of a transcription factor Neurogenin in the ascidian 64-cell stage embryo.

2010-03-09 | GSE17689 | GEO

FoxA-a ChIP-chip on Ciona intestinalis embryo (64-cell stage)

Project description:A genomic overview of in vivo binding of a transcription factor FoxA-a in the ascidian 64-cell stage embryo.

2010-03-09 | GSE17687 | GEO

FoxD-a/b ChIP-chip on Ciona intestinalis embryo (64-cell stage)

Project description:A genomic overview of in vivo binding of a transcription factor FoxD-a/b in the ascidian 64-cell stage embryo.

2010-03-09 | GSE17688 | GEO

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