Expression profiling of retinoic acid targets in lateral mesoderm from Xenopus laevis embryos
Ontology highlight
ABSTRACT:
ORGANISM(S): Xenopus laevis
PROVIDER: GSE205827 | GEO | 2022/06/13
REPOSITORIES: GEO
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Project description:We screened for differentially expressed genes in the developing notochord using the Affymetrix microarray system in Xenopus laevis. At late gastrula, we dissected four regions from the embryo, anterior mesoderm, posterior mesoderm, notochord and presomitic mesoderm. Three types of comparison were carried out to generate a list of predominantly notochord expressed genes: (1) Posterior mesoderm vs. anterior mesoderm; notochord genes are expected to be increased since the notochord is located in the posterior mesoderm. (2) Posterior mesoderm vs. whole embryos; notochord genes are expected to be increased. (3) Notochord vs. somite. This comparison sub-divided the group of posterior mesodermal genes identified in (1) and (2). All tissues are dissected using tungsten needles. We first dissected dorsal tissue above the archenteron from late gastrula to early neurula. To loosen tissue, we treated the dissected dorsal explant in a 1% cysteine solution (pH 7.4) and removed the neuroectodermal layer. Anterior mesoderm was dissected corresponding to about the anterior one-third of the archenteron roof, and the rest was collected as posterior mesoderm. The posterior mesodermal explant was dissected into notochord and somites, following a clearly visible border between the two tissues. The accuracy of all dissection was confirmed by RT-PCR of marker genes.
2006-12-31 | E-MEXP-717 | biostudies-arrayexpress
Project description:Retinoid signaling is important for patterning the vertebrate hindbrain and midaxial regions. We recently showed that signaling through retinoic acid receptors (RARs) is essential for anteroposterior patterning along the entire body axis. To further investigate the mechanisms through which RARs act, we employed microarray analysis to investigate the effects of modulating RAR activity on target gene expression. We identified 334 upregulated genes (92% of which were validated) including known RA responsive genes, known genes that have never been proposed as RA targets and many hypothetical and unidentified genes (n = 166). 67 validated downregulated genes were identified including known RA responsive genes and anterior marker genes. The expression patterns of selected upregulated genes (n = 45) were examined at neurula stages using whole mount in situ hybridization. We found that most of these genes were expressed in the neural tube and many were expressed in anterior tissues such as neural crest, brain, eye anlagen, and cement gland. Some were expressed in tissues such as notochord, somites, pronephros and blood islands, where retinoic acid (RA) plays established roles in organogenesis. Members of this set of newly identified RAR target genes are likely to play important roles in neural patterning and organogenesis under the control of RAR signaling pathways and their further characterization will expand our understanding of RA signaling during development. Keywords = retinoid Keywords = microarray Keywords = RAR Keywords = neurula Keywords = anteroposterior patterning Keywords = and organogenesis
2010-06-10 | E-GEOD-2295 | biostudies-arrayexpress
Project description:Retinoid signaling is important for patterning the vertebrate hindbrain and midaxial regions. We recently showed that signaling through retinoic acid receptors (RARs) is essential for anteroposterior patterning along the entire body axis. To further investigate the mechanisms through which RARs act, we employed microarray analysis to investigate the effects of modulating RAR activity on target gene expression. We identified 334 upregulated genes (92% of which were validated) including known RA responsive genes, known genes that have never been proposed as RA targets and many hypothetical and unidentified genes (n = 166). 67 validated downregulated genes were identified including known RA responsive genes and anterior marker genes. The expression patterns of selected upregulated genes (n = 45) were examined at neurula stages using whole mount in situ hybridization. We found that most of these genes were expressed in the neural tube and many were expressed in anterior tissues such as neural crest, brain, eye anlagen, and cement gland. Some were expressed in tissues such as notochord, somites, pronephros and blood islands, where retinoic acid (RA) plays established roles in organogenesis. Members of this set of newly identified RAR target genes are likely to play important roles in neural patterning and organogenesis under the control of RAR signaling pathways and their further characterization will expand our understanding of RA signaling during development. Keywords = retinoid Keywords = microarray Keywords = RAR Keywords = neurula Keywords = anteroposterior patterning Keywords = and organogenesis Keywords: repeat sample
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Project description:Expression profiling of retinoic acid targets in lateral mesoderm from Xenopus laevis embryos
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Project description:Foregut organogenesis is regulated by inductive interactions between the endoderm and the adjacent mesoderm. We identified genes induced in the foregut progenitors by the adjacent mesoderm. We used microarrays to detail the global programme of early foregut endoderm gene expression resulting from mesoderm induction and identified distinct classes of up-regulated genes during this process.
2012-06-12 | GSE38654 | GEO
Project description:Foregut organogenesis is regulated by inductive interactions between the endoderm and the adjacent mesoderm. We identified genes induced in the foregut progenitors by the adjacent mesoderm. We used microarrays to detail the global programme of early foregut endoderm gene expression resulting from mesoderm induction and identified distinct classes of up-regulated genes during this process. Xenopus foregut endoderm explants cultured from Stages 15 to 23 either intact with mesoderm or as endoderm alone. Total RNA was isolated from the endoderm of these two culture conditions in quadruplicate and were subjected to Affymetrix microarray analysis.
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