RNA_Seq analysis of localization along animal-vegetal axis of Acipenser ruthenus
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ABSTRACT:
PROVIDER: PRJNA517649 | ENA |
REPOSITORIES: ENA
Similar Datasets
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.
2020-06-16 | GSE125819 | GEO
Project description:In this study we analyzed the spatial and temporal localization of maternal transcripts during oogenesis in Acipenser ruthenus. The occurrence of transcript asymmetry in A. ruthenus has been described at a global level only in matured eggs. However not much is known about the asymmetry during oogenesis. In this study we assessed the temporal establishment of the transcript localization at a global level for A. ruthenus. We were able to determine that there are many transcripts that show temporal variability in the establishment of their localization. We observed an early, predefined and also late pathways for both the vegetally and animally localized transcripts. Additionally, we showed that some maternal transcripts are dynamic during oogenesis with degradation and de novo production being observed. Our study showed that in additional to spatial orientation to the transcripts, there is a strong temporal factor. The discovery of these new temporal profiles should help to better understand the driving forces during embryogenesis.
2022-08-23 | GSE211412 | GEO
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
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 | GSE166916 | GEO
Project description:Acipenser ruthenus Genome sequencing and assembly
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Project description:Acipenser ruthenus (Sterlet ) Genome sequencing and assembly
| PRJNA561280 | ENA
Project description:Acipenser ruthenus x Huso huso Transcriptome or Gene expression
| PRJNA523995 | ENA
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
Project description:In this study we analyzed the spatial and temporal localization of maternal transcripts during oogenesis in Xenopus laevis. The occurrence of transcript asymmetry in X. laevis has been described at a global level only in matured eggs, while the establishment of the asymmetry during oogenesis has been described only for a few transcripts. In this model it was discerned that there exist three pathways (early, intermediate, late) for the establishment of the vegetal gradient, while for the animal gradient not much is known for its production. In this study we assessed the temporal establishment of the transcript localization at a global level for Xenopus laevis. We were able to determine that there are many transcripts that show temporal variability in the establishment of their localization. We observed the previously described early, intermediate (predefined) and also late pathways but found more member transcripts within these groups. We also described, perhaps for the first time, an early, intermediate (predefined) and late pathway for the animal genes as well. Additionally, we showed that some maternal transcripts are dynamic during oogenesis with degradation and de novo production being observed. Our study showed that in additional to spatial orientation to the transcripts, there is a strong temporal factor. The discovery of these new temporal profiles should help to better understand the driving forces during embryogenesis.
2022-08-23 | GSE211415 | GEO