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Background: Zebrafish (Danio rerio) is an important model for the study of earlyvertebrate development. The transition from fertilized egg to embryo is accompaniedby a multitude of changes in gene expression and the transcriptional events thatunderlie these processes have not been fully characterized. In this study we useRNA_Seq to characterize and compare the transcriptome of four early developmentalstages in zebrafish on a global scale.Results: An average of 79M total reads were detected from the different stages. Outof the total number of reads 65% - 73% reads were successfully mapped to thezebrafish genome and 36% - 44% out of those were uniquely mapped. The totalnumber of detected unique gene transcripts was 11187 of which 10096 of these werealready present at 1-cell stage. The largest number of common transcripts wasobserved between 1-cell stage and 16-cell stage. An enrichment of gene transcriptswith molecular functions of DNA binding, protein folding and processing as well asmetal ion binding was observed with progression of development. To confirm ourRNA-Seq results, and to further investigate the developmental expression of specificgenes, the transcript levels of a subset of genes were analyzed using TaqMan® arraymicro fluidic card (TLDA).Conclusion: Clustering analysis of the detected transcripts show a majority of genetranscripts being present at steady levels, with a minority of the gene transcriptsclustering as increasing or decreasing in expression during development.Developmental stages pre-MBT were similar when comparing highly expressedgenes, whereas 50% epiboly stage differed from the earlier three stages in highlyexpressed genes, number of uniquely expressed genes and enrichment of GOmolecular functions. |