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XB-ART-8720
Dev Biol. August 1, 2001; 236 (1): 64-75.

Microarray-based analysis of early development in Xenopus laevis.

Altmann CR , Bell E , Sczyrba A , Pun J , Bekiranov S , Gaasterland T , Brivanlou AH .


Abstract
In order to examine transcriptional regulation globally, during early vertebrate embryonic development, we have prepared Xenopus laevis cDNA microarrays. These prototype embryonic arrays contain 864 sequenced gastrula cDNA. In order to analyze and store array data, a microarray analysis pipeline was developed and integrated with sequence analysis and annotation tools. In three independent experimental settings, we demonstrate the power of these global approaches and provide optimized protocols for their application to molecular embryology. In the first set, by comparing maternal versus zygotic transcription, we document groups of genes that are temporally regulated. This analytical approach resulted in the discovery of novel temporally regulated genes. In the second, we examine changes in gene expression spatially during development by comparing dorsal and ventral mesoderm dissected from early gastrula embryos. We have discovered novel genes with spatial enrichment from these experiments. Finally, we use the prototype microarray to examine transcriptional responses from embryonic explants treated with activin. We selected genes (two of which are novel) regulated by activin for further characterization. All results obtained by the arrays were independently tested by RT-PCR or by in situ hybridization to provide a direct assessment of the accuracy and reproducibility of these approaches in the context of molecular embryology.

PubMed ID: 11456444
Article link: Dev Biol.
Grant support: EY 12370 NEI NIH HHS , HD32105 NICHD NIH HHS

Genes referenced: cirbp eif3a eif4g1 gata4 gmnn gpd1 gpd1l gypc hnrnpa2b1 hnrnpl hnrnpu hsp90ab1 loc100498440 mapk1 nop56 orc6 pttg1ip.1 rbmx ssr2 trmt5 ttc30a washc2a



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