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| Status |
Public on Nov 12, 2013 |
| Title |
A Genome-Wide Survey of Maternal and Embryonic Transcripts during Xenopus tropicalis Development |
| Organism |
Xenopus tropicalis |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
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.
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| |
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| Overall design |
Profiles of polyadenylated mRNA (6 stages) and ribosomal RNA-depleted total RNA (3 stages) through early Xenopus tropicalis development
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| |
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| Contributor(s) |
Paranjpe S, Jacobi UG, van Heeringen SJ, Veenstra GC |
| Citation(s) |
24195446 |
| |
| Submission date |
Jan 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Gert Jan Veenstra |
| E-mail(s) |
g.veenstra@science.ru.nl
|
| Phone |
+31 24 3610541
|
| Organization name |
Radboud University
|
| Department |
Molecular Developmental Biology
|
| Street address |
Geert Grooteplein 28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
| |
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| Platforms (1) |
| GPL13741 |
Illumina Genome Analyzer IIx (Xenopus (Silurana) tropicalis) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA186932 |
| SRA |
SRP018091 |
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