NvERTx - An embryogenesis & regeneration gene expression plotter
Understanding the relationship between embryogenesis and regeneration is a long standing question in regenerative biology as both developmental strategies lead to fully functional organisms. Modern sequencing techniques have allowed us to re-examine this question at the systems level. This site provides a set of tools to analyze gene expression in both embryogenesis and regeneration of the starlet sea anemone Nematostella vectensis (Anthozoa, Cnidaria). Here you will find tools to mine RNAseq datasets for embryonic development and oral regeneration of Nematostella vectensis. The data can be accessed by searching for your gene of interest using a gene name, NvERTx.4 ID, or JGI Nemve1 accession number. If you have a sequence you can use the BLAST function to retrieve corresponding NvERTx transcripts. You can also explore a list of genes corresponding to a given embryonic or regeneration co-expression cluster.
References for regeneration and novel embryonic datasets: Warner et al(a), 2017, Warner et al(b), 2017. Re-analyzed embryonic datasets: Fischer et al. 2014,Tulin et al. 2013,and Helm et al. 2013
More About Nematostella
Frequently Asked Questions
How can i credit the images/ data I use?
The plots and sequences on this site are distributed under a creative commons attribution license. We ask that in publications, all four original data papers are cited: Warner et al(a), 2017, Warner et al(b), 2017. Re-analyzed embryonic datasets: Fischer et al. 2014,Tulin et al. 2013,and Helm et al. 2013
Why are there multiple NvERTx.4 IDs per 'gene'?
This transcriptome includes multiple transcripts per gene. These transcripts can include isoforms and SNPs. Therefore when searching for a gene name you will notice several NvERTx.4 matches that have equivalent annotations. Each match is a different transcript but if the best hit to Nemve1 is the same we consider them the same gene (and quantify them equally).
Certain NvERTx.4 IDs have the exact same profile/ count
Given the multiple transcripts per gene described above, we quantified all genes that have the same top hit to Nemve1 equivalently.
Certain NvERTx.4 IDs have the same Nemve1 hit but different or no hits to nr/uniprot
The transcript with a hit to Nemve1 but no hit to nr is likely a transcript containing a large untranslated region. This has to do with how the transcripts were annotated. The NvERTx trancsripts were compared to Nemve1 using blastn, but only the coding regions of each transcript were compared to nr or uniprot using blastp.
My gene has a regeneration expression profile but no embryonic expression or vice versa
During quantification we employed a modest expression cutoff to remove lowly expressed genes. Therefore genes may be found in one dataset but not another in which it is lowly expressed.
Data Availability
Datasets are publicly available. The NvERTx.4 trinity assembly is available for download using this direct download link. Raw sequencing reads from Fischer et al. 2014 (0-19Hpf hourly) and Tulin et al. 2013 (0,6,12,18,24Hpf) are available on the Woods Hole Open Access Server here and here. Raw sequencing reads from Helm et al. 2013 (2,7,12,24,120,240 Hpf) are available on the NCBI sequence read archive project number PRJNA189768
About this site
This site was developed using the Django framework and coded by Vincent Guerlais and Jake Warner. To report bugs or request data, send us an email at: eric.rottinger\at/unice.fr
Funding
Funding for the project, this site and it's developers was graciously provided by an ATIP-Avenir award (CNRS/INSERM via Plan Cancer, C13992AS), a Marie-Curie Career Integration Grant (CIG—FP7 European Commission, 631665), the Association pour la Recherche sur le Cancer (ARC, PJA 2014120186), the Fondation pour la Recherche Médicale (FRM, ), the French Ministry of Higher Education and Science, the “Ligue contre le Cancer”, the University Côte d’Azur as well as the Institute for Research on Cancer and Aging, Nice (IRCAN).
