Xenopus laevis cDNA microarray

We are excited to announce the preparation and hybridization of what we believe to be the first Xenopus laevis cDNA microarray. The current array contains 900 clones which includes 800 random clones from a gastrula expression library and ~50 tissue specific markers in duplicate. The microarray was probed with samples obtained from Stage 6 and Stage 11 whole embryos. As you can see, many clones are represented in about equal amounts (yellow signal) while a few are differentially expressed (either red or green).

We are currently in the process of obtaining and organizing as many known Xenopus genes as we can. A search of the database reveals that there are approximately 3000 Xenopus genes. While there are a number of duplicate entries, we expect that up to 2000 of these genes would be important to include on any Xenopus microarray. In addition to known genes, we are in the process of preparing ~10,000 random clones to be included on the array for gene discovery purposes.

While we are in the process of optimizing the conditions for the preparation of the samples, which are hybridized to the array, our early experiments indicate that 15 ug of total RNA is sufficient for each sample. This makes this experimental approach feasible for a variety of standard Xenopus approaches including animal cap assays. We expect optimized conditions to improve the signal to noise ratio and the sensitivity of the assay up to 100 fold which will allow the identification of genes with low levels of expression.

Our intention is to make Xenopus chips available to the Xenopus community, free of charge (demand permitting). We believe that the application of microarray technology to the Xenopus system will be an extremely valuable tool. We will also maintain a database of results obtained with the microarrays and make this freely available to everyone via the web. Investigators who would like to collaborate or who have suggestions are welcome.

We want to make this technology available to all Xenopus labs as quickly as possible. We believe that this will ensure that Xenopus remains the pre-eminent system for the study of early vertebrate development and accelerates our progress in understanding the molecular basis of development.

We look forward to any suggestions, comments or assistance from the community.

Ali Hemmati-Brivanlou, Associate Professor, Head of Laboratory, The Rockefeller University, Laboratory of Molecular Vertebrate Embryology, 1230 York Avenue, New York, NY 10021, 212-327-8656

Curtis R. Altmann, Ph.D., The Rockefeller University, Laboratory of Molecular Vertebrate Embryology, 1230 York Avenue, New York, NY 10021, 212-327-8684