Xenopus tropicalis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA242712 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss of synchronous cell divisions. Little is known about what triggers the activation of transcription or how newly expressed genes interact with each other. Here we use high-resolution expression profiling to identify three waves of gene activity: a post-fertilization wave involving polyadenylation of maternal transcripts; a broad wave of zygotic transcription detectable as early as the 7th cleavage and extending beyond the MBT at the 12th cleavage; and a shorter post-MBT wave of transcription that becomes apparent as development proceeds. Our studies have also allowed us to define a set of maternal genes whose mRNAs are deadenylated shortly after fertilization, and are likely to be degraded thereafter. Experimental analysis indicates that the polyadenylation of maternal transcripts is necessary for the establishment of proper levels of zygotic transcription at the MBT, and that genes activated in the second wave of expression, including Brachyury and Mixer, contribute to the regulation of genes expressed in the third. Together, our high-resolution time series and experimental studies have yielded a deeper understanding of the temporal organization of gene regulatory networks in the early Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization
2014-03-27 | E-GEOD-56242 | biostudies-arrayexpress
Project description:Nascent transcriptome of Xenopus laevis embryos at mid-blastula transition (MBT) stages
| PRJNA545469 | ENA
Project description:To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted total RNA were harvested across six developmental stages and subjected to high throughput sequencing. The maternally loaded transcriptome is highly diverse and consists of both polyadenylated and deadenylated transcripts. Many maternal genes show peak expression in the oocyte and include genes which are known to be the key regulators of events like oocyte maturation and fertilization. Of all the transcripts that increase in abundance between an early blastula and larval stages, about 30% of the embryonic genes are induced by fourfold or more by the late blastula stage and another 35% by late gastrulation. Using a gene model validation and discovery pipeline, we identified novel transcripts, the majority of which show hallmarks of being long non-coding RNAs both in terms of their coding potential and gene structure. Profiles of polyadenylated mRNA (6 stages) and ribosomal RNA-depleted total RNA (3 stages) through early Xenopus tropicalis development
2013-11-12 | E-GEOD-43652 | biostudies-arrayexpress
Project description:Single-base resolution methylomes of Xenopus laevis x Xenopus tropicalis embryos
| PRJNA356296 | ENA
Project description:The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss of synchronous cell divisions. Little is known about what triggers the activation of transcription or how newly expressed genes interact with each other. Here we use high-resolution expression profiling to identify three waves of gene activity: a post-fertilization wave involving polyadenylation of maternal transcripts; a broad wave of zygotic transcription detectable as early as the 7th cleavage and extending beyond the MBT at the 12th cleavage; and a shorter post-MBT wave of transcription that becomes apparent as development proceeds. Our studies have also allowed us to define a set of maternal genes whose mRNAs are deadenylated shortly after fertilization, and are likely to be degraded thereafter. Experimental analysis indicates that the polyadenylation of maternal transcripts is necessary for the establishment of proper levels of zygotic transcription at the MBT, and that genes activated in the second wave of expression, including Brachyury and Mixer, contribute to the regulation of genes expressed in the third. Together, our high-resolution time series and experimental studies have yielded a deeper understanding of the temporal organization of gene regulatory networks in the early
2014-03-27 | GSE56242 | GEO
Project description:High-throughput sequencing of small RNAs from Xenopus tropicalis
| PRJNA111817 | ENA
Project description:Global gene expression during early differentiation of Xenopus (Silurana) tropicalis gonad tissues.
| PRJNA253012 | ENA
Project description:A Genome-Wide Survey of Maternal and Embryonic Transcripts during Xenopus tropicalis Development
| PRJNA186932 | ENA