DiatOmicBase is a genome portal to perform research on Phaeodactylum tricornutum, Thalassiosira pseudonana and Pseudo-nitzschia multistriata, gathering comprehensive omic resources to ease the exploration of dispersed public datasets.
Here you will find:
The steering committee consists of Chris Bowler (ENS France), Angela Falciatore (IBPC France), Klaas Vandepoele (VIB-UGent, PLAZA), Michele Fabris (University of Southern Denmark; DiatomCyc).
The project is managed by Emilie Villar and developed by Nathanael Zweig.
We thanks Mariella Ferrante, Svenja Mager, and Anna Santin for helping us to add Pseudo-nitzschia multistriata.
Here you will find:
- Genes pages: each genes model page displays cDNA and protein sequences, a genome browser, comparisons of gene expression in public RNA-Seq datasets, co-expression networks as well as several domains annotation. Gene pages can be accessed through the general search bar in the header, or through specific search (e.g. domaines, annotation) or blast.
- A genome browser with the latest annotation updates: Genes models, ecotype variants, histone marks, non-coding RNAs, domains.
- A transcriptomic module where you can re-analyse published RNA-Seq datasets, and your own data through an iDEP instance.
- A resource page to download the latest omic resources available.
Note about RNA-Seq analysis:
We precomputed Differential Expression for a hundred pairwise comparisons corresponding to 30 already published BioProjects, using the nf-core rnaseq pipeline and DESeq2 R package (see Methods). Results are displayed by gene (for all the comparisons) on gene pages, and by experiment (for all the genes) on the resource page. Read densities are shown on the genome browser of gene pages only for significant comparisons. If you want to compare other conditions, please use the transcriptomic module and choose the subsets to compare.If you use this web service, please cite: DiatOmicBase, "https://www.diatomicsbase.bio.ens.psl.eu/"
Acknowledgement:
DiatOmicBase is funded by the Gordon and Betty Moore Foundation.The steering committee consists of Chris Bowler (ENS France), Angela Falciatore (IBPC France), Klaas Vandepoele (VIB-UGent, PLAZA), Michele Fabris (University of Southern Denmark; DiatomCyc).
The project is managed by Emilie Villar and developed by Nathanael Zweig.
We thanks Mariella Ferrante, Svenja Mager, and Anna Santin for helping us to add Pseudo-nitzschia multistriata.
Picture credit: Diatom mandala, Taken by Falciatore.A and Bowler.C, IBPC, Sorbonne Université and Departement de Biologie, Ecole Normale Superieure, Paris, France