This repository consolidates omic data from the coral Montipora digitata and aims at provided a central place where to store resources to facilitate the study of this coral.
By using these data you agree to cite this repository and the papers describing how the dataset here stored were generated and analyzed.
The data is organized in folders that correspond to the studies/papers that generated different omic resources available in this repo.
Please note that this repository will be constantly updated for a while (as we generate more data) and that, probably, some files are going to change with time (e.g. scripts). Because of this, we strongly recommend that you clone or fork the repository and avoid downloading it. This way you can always have an updated version of the repository (if you pull every now and then. Once the contents of the repository are stable, we will produce a release of the repository and mint a DOI for it. In general releases will be done after publication of new data.
If you have comments or concerns about the data or scripts, please use the Issues tab provided by Github. We are not going to answer to comments or concerns about the repository unless they are documented in as an Issues. This is so to increase the transparency of the repository and of changes done in response to individual requests. Please remember that, although we are happy to fix/correct errors raised through the Issues tab of the repo, this may take a while. We will try our best to keep the repo in a nice state and correct errors as soon as possible.
Below you can find a list and an explanation of the structure in each of the folders.
Raúl A. González-Pech, Sergio Vargas, Warren R. Francis & Gert Wörheide
This is the companion site for González-Pech et al. submitted. and contains the transcriptome of Montipora digitata, the transcriptome annotations and the count matrix used in the manuscripts to assess the effect of ocean acidification on gene expression in this coral system.
This part of the repository is organized in an easy-to-follow manner. The count matrices used in the analyses of gene expression can be found in the folder Counts, the annotated transcriptome for the coral and its symbionts can be found the folder Annotated_transcriptome and the script used to analyze the data in R with DESeq2 can be found in the folder Scripts.