Xenopus cDNA microarray identification of genes with endodermal organ expression. Xenopus laevis

The endoderm is classically defined as the innermost layer of three Metazoan germ layers. During organogenesis, the endoderm gives rise to the digestive and respiratory tracts as well as associated organs such as the liver, pancreas, and lung. At present, however, how the endoderm forms the variety of cell types of digestive and respiratory tracts as well as the budding organs is not well understood. In order to investigate the molecular basis and mechanism of organogenesis and to identify the endodermal organ-related marker genes, we carried out microarray analysis using Xenopus cDNA chips. To achieve this goal, we isolated the Xenopus gut endoderm from three different stages of Xenopus organogenesis, and separated each stage of gut endoderm into anterior and posterior region. Competitive hybridization of cDNA between the anterior and posterior endoderm regions, to screen genes that specifically expressed in the major anterior organs, revealed 891 candidates. We then selected 104 clones for in situ hybridization analysis. Here, we report the identification and expression patterns of the 104 Xenopus endodermal genes, which would serve as useful markers for studying endodermal organ development. Keywords: Xenopus, endoderm, microarray, organogenesis Overall design: In order to isolate the endodermal organ-related genes, we carried out a microarray analysis using high-density Xenopus cDNA chip. To this aim, we isolated the Xenopus endoderm from three different stages (St. 30, 39, and 46) and manually dissected the each stage of endoderm to anterior and posterior region. The anterior endoderm will later become major organs such as the lung, oesophagus, duodenum, stomach, pancreas, liver, and gallbladder, and the posterior endoderm will become the intestine. Duplicate sets of three individual microarray experiments were performed using anterior endoderm cDNAs of each stage, labeled by Cy5, and the posterior endoderm cDNAs of each stage, labeled by Cy3. The normalization strategy involves condensing the duplicate array data for each of the three developmental stages, thus giving rise to three GEO Samples.