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RNA_Seq analysis of localization along animal-vegetal axis of Danio rerio

ABSTRACT: RNA_Seq analysis of localization along animal-vegetal axis of Danio rerio

PROVIDER: PRJNA702290 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR13729821_1.fastq.gz	Fastqsanger.gz
	SRR13729821_2.fastq.gz	Fastqsanger.gz
	SRR13729822_1.fastq.gz	Fastqsanger.gz
	SRR13729822_2.fastq.gz	Fastqsanger.gz
	SRR13729823_1.fastq.gz	Fastqsanger.gz

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RNA_Seq analysis of localization along animal-vegetal axis of Danio rerio

Project description:Asymmetrical localization of biomolecules inside the egg, results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs, of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However, our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal-vegetal axis of mature eggs of four diverse models, Xenopus laevis, Danio rerio, Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO-Seq. Surprisingly, we revealed RNAs that code for many known important genes such as germ layer determinants, germ plasm factors and members of key signalling pathways, are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model.

2022-10-20 | GSE166917 | GEO

RNA_Seq analysis of localization along animal-vegetal axis of Acipenser ruthenus

Project description:We performed cryosectioning of oocytes along the animal-vegetal axis (first developmental axis, section A (first animal) to section E (last vegetal), followed by RNA-Seq to determine the localization profiles of coding and noncoding RNAs. The method allowed for a complete view on RNA localization. We found that nearly all RNAs are localized, but only a small percentage is actively transported during oogenesis.

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RNA_Seq analysis of localization along animal-vegetal axis of axolotl (Ambystoma mexicanum)

2022-10-20 | GSE166916 | GEO

RNA_Seq analysis of localization along animal-vegetal axis of Acipenser ruthenus

Project description:RNA_Seq analysis of localization along animal-vegetal axis of Acipenser ruthenus

| PRJNA517649 | ENA

RNA_Seq analysis of localization along animal-vegetal axis of axolotl (Ambystoma mexicanum)

Project description:RNA_Seq analysis of localization along animal-vegetal axis of axolotl (Ambystoma mexicanum)

| PRJNA702289 | ENA

RNA-Seq analysis of localization along animal-vegetal axis of Xenopus laevis

Project description:We combined cryosectining of oocytes along the animal-vegetal axis (first developmental axis) and RNA-Seq to determine localization profiles of coding and noncoding RNAs. It provides complete view on RNA localization. We found that nearly all RNAs are localized, but only small percentage is actively transported during oogenesis.

2018-05-31 | GSE104848 | GEO

RNA-Seq analysis of localization along animal-vegetal axis of Xenopus laevis

Project description:RNA-Seq analysis of localization along animal-vegetal axis of Xenopus laevis

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Comparison of animal-blastomeres' RNA content to vegetal-most half of vegetal blastomeres' RNA content at the 8-cell stage of Xenopus laevis embryos to identify animal-enriched transcripts

Project description:In Xenopus laevis, a number of studies identified vegetal factors that specify the germ line, endoderm and dorsal axis, but there are few studies demonstrating roles for animal-enriched maternal mRNAs. Therefore, we carried out a microarray analysis to identify novel maternal transcripts enriched in animal blastomeres. We sought to maximize differences between animal and vegetal samples. To that end, we dissected 8-cell embryos into animal blastomeres and vegetal blastomeres, and further dissected the vegetal blastomeres into vegetal-most halves (VP) and equatorial regions (discarded).

2013-12-21 | E-GEOD-48659 | biostudies-arrayexpress

The identification of differentially expressed genes between animal and vegetal blastomeres in Xenopus laevis

Project description:To identify asymmetrically localized maternal mRNAs along the animal-vegetal axis in cleavage Xenopus embryos, we isolated animal and vegetal blastomeres at 8-cell stage, extracted the maternal mRNA respectively and analyzed them by RNA-seq technology. We identified 43 maternal transcripts significantly enriched in the vegetal region (FDR<0.05) by R/Bioconductor package DESeq

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The identification of differentially expressed genes between animal and vegetal blastomeres in Xenopus laevis

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