Biological variation between zebrafish development series

Transcriptome analysis during embryogenesis usually requires pooling of embryos to obtain sufficient RNA. Hence, the measured levels of gene-expression represent the average mRNA levels of pooled samples and the biological variation among individuals is lost for inclusion into statistical models used to analyze transcriptome data. This can irreversibly reduce the robustness, resolution and expressiveness of the experiment. Therefore, we developed a robust method to isolate abundant high-quality RNA from individual embryos to perform single embryo transcriptome analyses using the zebrafish as a model. RNA from 8 individual embryos (16-cell, 128-cell, sphere, dome, germ ring, shield, 75%-epiboly & 8-somite stage) was isolated and hybridized against a common reference (pool of these 8 samples).