Vertebrate embryogenesis is a highly complex and stereotypic process. Key to a successful progression from a fertilized oocyte to a patterned embryo is the regulation of gene activity. The mechanisms that control when and where each gene becomes active are still poorly understood. Using zebrafish (Danio rerio) as a model organism, we employ high-throughput sequencing technologies to identify and study chromatin- and RNA-based gene regulatory mechanisms that control embryogenesis.
This website is meant to facilitate easy access to our published data sets. Data can be directly downloaded or conveniently viewed (View / Download data) in the Integrative Genomics Viewer (IGV) or in the UCSC genome browser (http://genome.ucsc.edu). Data sets are described in more detail in accompanying publications that can also be accessed from this website.
This website will be updated as more data becomes published.
Pauli et al., Genome Research 2012:
In our most recent ‘genomics’ publication, we analysed the zebrafish embryonic coding and non-coding transcriptome in unprecedented depth: Assembly of >2 billion strand-specific RNA-Seq reads from eight embryonic stages (from 2-4 cell to 5 days post fertilization) resulted in a ‘high-confidence’ embryonic transcriptome of ~56,000 transcripts, corresponding to ~28,000 loci. A stringent filtering pipeline aimed at distinguishing protein-coding from non-coding transcripts identified 1,133 multiexonic, embryonically expressed long non-coding RNAs (intergenic, intronic overlapping as well as antisense overlapping). Similar to their mammalian counterparts, zebrafish lncRNA loci carry common chromatin marks (H3K4me3 and H3K27me3), are expressed at ~10-fold lower levels than protein-coding genes and are less conserved than protein-coding genes. In addition to their highly restricted expression patterns, our developmental time-series revealed high temporal specificity as a novel characteristic of embryonic lncRNAs.