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GEO Series: GSE65785
Summary
Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack a comprehensive understanding of transcript kinetics, which limits quantitative biology. This is an acute challenge in embryonic development where rapid changes in gene expression dictate cell fate decisions. By ultra-high frequency sampling of Xenopus embryos and absolute normalization of sequence reads, we present smooth gene expression trajectories in absolute transcript numbers. During a developmental period approximating the first 8 weeks of human gestation, transcript kinetics vary by 8 orders of magnitude. Ordering genes by expression dynamics, we find temporal synexpression predicts common gene function. Remarkably, a single parameter, the characteristic timescale, can classify transcript kinetics globally and distinguish genes regulating development from those involved in cellular metabolism. Overall, our analysis provides unprecedented insight into the reorganization of maternal and embryonic transcripts and redefines our ability to perform quantitative biology.
Gene expression profiles may be visualized at http://genomics.crick.ac.uk/apps/profiles/
Contributors: Mike Gilchrist, Nick Owens, Ira Blitz, Maura Lane, Ilya Patrushev, John Overton, Michael Gilchrist, Ken Cho, Mustafa Khokha
Experiment Type: High Resolution Time series covering the first 66 hours of development of Xenopus tropicalis with PolyA+ and ribosomal depletion sequencing.
Article:
XB-ART-51804,
PubMed
Source: NCBI GEO,
Xenbase Download
Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
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