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Oikopleura dioica

ABSTRACT: Genome sequencing of Japanese Oikoplaura dioica

PROVIDER: PRJDB9887 | ENA |

REPOSITORIES: ENA

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Dataset's files

Source:

			Action	DRS
	DRR228648_1.fastq.gz	Fastqsanger.gz
	DRR228648_2.fastq.gz	Fastqsanger.gz
	DRR228649_subreads.fastq.gz	Fastqsanger.gz
	DRR228650_subreads.fastq.gz	Fastqsanger.gz
	DRR228651_subreads.fastq.gz	Fastqsanger.gz

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Oikopleura dioica

Project description:Oikopleura dioica genome sequencing

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Spatio-temporal transcriptome maps in the early embryos of Oikopleura dioica

Project description:The larvacean, Oikopleura dioica, is a planktonic chordate and belongs to tunicate that is the closest relative to vertebrates. Its simple and transparent body, invariant embryonic cell lineages and short life cycle of five days make it a promising model organism for research in developmental biology. The genome browser, OikoBase, has been established in 2013 using Norwegian O. dioica. However, genome information of other populations is not available, despite that many researchers have used local populations. In the present study, we sequenced genome of O. dioica of a southwestern Japanese population using RNA-Seq data. These RNA-Seq data covers expressions in 8 cell and 12 hours post fertilization (HPF) embryos of Animal(A), Vegetal(V) and whole-embryo regions, as well as whole embryo of 13 stages, including OD_STAGE01 (unfertilized egg), OD_STAGE02 (fertilized egg), OD_STAGE03 (2-cell), OD_STAGE04 (4-cell), OD_STAGE05 (8-cell), OD_STAGE06 (16-cell), OD_STAGE07 (32-cell), OD_STAGE08 (1.5 hours post fertilization), OD_STAGE09 (2.5 hours post fertilization, tadpole larvae), OD_STAGE10 (3 hours post fertilization, hatched larvae), OD_STAGE11 (5 hours post fertilization, early organogenesis), OD_STAGE12 (8 hours post fertilization, late organogenesis), OD_STAGE13 (10 hours post fertilization, juvenile), Adult male and Adult female. These genome assembly, transcript assembly, and transcript models are incorporated into the ANISEED (https://www.aniseed.cnrs.fr/) for genome browsing and blast searches. The genome and transcriptome resources will be useful datasets for developmental biology, evolutionary biology and molecular ecology using this model organism.

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ChIP-seq in Oikopleura dioica

Project description:ChIP-seq was used to generate chromatin state maps, profile binding patterns of key architectural proteins and locate putative enhancer regions in the early development (TB stage) and developing gonads of the marine chrodate Oikopleura dioica.

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Project description:High-resolution genome-wide transcriptomics analysis of O. dioica development

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Project description:Developemtanl transcriptomes of an appendicularian, Oikopleura dioica.

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Project description:Oikopleura dioica (Japan) Transcriptome or Gene expression

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Genome-wide profiling of translation in Oikopleura dioica during growth arrest and recovery

Project description:Under crowded, nutrient-limiting conditions, growth in the marine chordate O. dioica arrests until favorable conditions return. We profiled translation genome-wide using ribosome profiling in O. dioica during growth arrest and growth arrest recovery. We found that initial recovery is independent of nutrient-responsive, trans-spliced genes, suggesting that animal density is the primary trigger for the resumption of development in this species.

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