Xenopus laevis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA91671 | ENA |
REPOSITORIES: ENA
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Project description:The development of massively parallel sequencing technologies has revolutionized transcriptome analysis. Sequencing of total cDNA (RNA-Seq) can determine the expression levels of known and novel transcripts with high sensitivity from various developmental stages or conditions. Here we report a robust method for RNA-Seq in Xenopus laevis and apply it to understanding how modulation of retinoic acid signaling alters the transcriptome in early Xenopus laevis development. Three biological conditions were tested: early blastula stage embryos were treated with 1. a retinoic acid receptor (RAR) agonist NRX204647 (4647) at a concentration that stimulated all 3 RAR subtypes (alpha, beta, and gamma); 2. The same agonist at an RAR[gamma] selective dose, and 3. vehicle control. Five single-clutch replicates were obtained for each chemical treatment group, and harvested at neurula stage. We found that single-clutch replicates reflect the stochastic variation of the general outbred population and contribute more statistical power to RNA-Seq experiments due to their feasibility of replication. Our RNA-Seq dataset identified 1590 up-regulated and 685 down-regulated unique genes differentially regulated by all RAR subtypes, and 160 up-regulated and 60 down-regulated genes likely to be regulated specifically by RAR[gamma]. Differential expression detected by RNA-Seq was validated for selected genes by QPCR, which demonstrated nearly 100% quantitative agreement with the deep sequencing data. We further validated RAR-responsive genes by comparison with two previous, published microarray datasets and found substantial agreement. Gene ontology analysis identified RAR targets which may underlie such developmental processes as axial elongation, neurogenesis/synaptogenesis, dorsoventral regulation of the retina, homeotic fate specification, and central nervous system development. We investigated RAR[gamma]-selective targets identified by RNA-Seq and inferred that transcriptional repression by unliganded RARs is of substantial importance to embryonic patterning events. Overall, this paper demonstrates the utility of RNA-Seq in Xenopus laevis, obviating the perceived requirement to use X. tropicalis for genomic analyses.
2019-12-31 | GSE77281 | GEO
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2015-09-05 | GSE40620 | GEO
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