Data & Code
Open access research is one of the best ways to maintain scientific consistency and reproducibility, and to encourage constant improvement of lab methods, molecular pipelines, and statistical analyses. We aim to encourage this practice with our research by making all of our code and datasets publicly available.
GITHUB PIPELINES
Protocols, code, and example datasets for our analysis pipelines including RNA-Seq, transcriptome annotation, microsatellite analysis, corallite morphometrics, 3D modeling, and benthic community analysis are available on GitHub. Files and methods may change over time, so make sure to redownload the most updated versions before replicating analyses.
github.com/mstudiva
Protocols, code, and example datasets for our analysis pipelines including RNA-Seq, transcriptome annotation, microsatellite analysis, corallite morphometrics, 3D modeling, and benthic community analysis are available on GitHub. Files and methods may change over time, so make sure to redownload the most updated versions before replicating analyses.
github.com/mstudiva
DATASET REPOSITORIES
thermal stress/estuarine discharge Montastraea cavernosa and Cladocopium spp. transcriptomic analyses
Montastraea cavernosa and Cladocopium spp. transcriptome sequences
Please cite: Studivan MS, Shatters A, Dodge DL, Beal JL, Voss JD (2021) Synergistic effects of thermal stress and estuarine discharge on transcriptomic variation of Montastraea cavernosa corals in southeast Florida. Frontiers in Marine Science 8:662220
mesophotic Montastraea cavernosa and Cladocopium spp. transcriptomic analyses
Montastraea cavernosa and Cladocopium spp. transcriptome sequences
Please cite: Studivan MS, Voss JD (2020) Transcriptomic plasticity of mesophotic corals among natural populations and transplants of Montastraea cavernosa in the Gulf of Mexico and Belize. Molecular Ecology 29:2399–2415
Montastraea cavernosa corallite morphometrics
Please cite: Studivan MS, Milstein G, Voss JD (2019) Montastraea cavernosa corallite structure demonstrates distinct morphotypes across shallow and mesophotic depth zones in the Gulf of Mexico. PLoS ONE 14:e0203732
Gulf of Mexico Montastraea cavernosa genotypes
Please cite: Studivan MS, Voss JD (2018) Population connectivity among shallow and mesophotic Montastraea cavernosa corals in the Gulf of Mexico identifies potential for population refugia. Coral Reefs 37:1183–1196
Northwest Gulf of Mexico Montastraea cavernosa genotypes
Please cite: Studivan MS, Voss JD (2018) Assessment of mesophotic coral ecosystem connectivity for proposed expansion of a marine sanctuary in the northwest Gulf of Mexico: population genetics. Frontiers in Marine Science 5:152
thermal stress/estuarine discharge Montastraea cavernosa and Cladocopium spp. transcriptomic analyses
Montastraea cavernosa and Cladocopium spp. transcriptome sequences
Please cite: Studivan MS, Shatters A, Dodge DL, Beal JL, Voss JD (2021) Synergistic effects of thermal stress and estuarine discharge on transcriptomic variation of Montastraea cavernosa corals in southeast Florida. Frontiers in Marine Science 8:662220
mesophotic Montastraea cavernosa and Cladocopium spp. transcriptomic analyses
Montastraea cavernosa and Cladocopium spp. transcriptome sequences
Please cite: Studivan MS, Voss JD (2020) Transcriptomic plasticity of mesophotic corals among natural populations and transplants of Montastraea cavernosa in the Gulf of Mexico and Belize. Molecular Ecology 29:2399–2415
Montastraea cavernosa corallite morphometrics
Please cite: Studivan MS, Milstein G, Voss JD (2019) Montastraea cavernosa corallite structure demonstrates distinct morphotypes across shallow and mesophotic depth zones in the Gulf of Mexico. PLoS ONE 14:e0203732
Gulf of Mexico Montastraea cavernosa genotypes
Please cite: Studivan MS, Voss JD (2018) Population connectivity among shallow and mesophotic Montastraea cavernosa corals in the Gulf of Mexico identifies potential for population refugia. Coral Reefs 37:1183–1196
Northwest Gulf of Mexico Montastraea cavernosa genotypes
Please cite: Studivan MS, Voss JD (2018) Assessment of mesophotic coral ecosystem connectivity for proposed expansion of a marine sanctuary in the northwest Gulf of Mexico: population genetics. Frontiers in Marine Science 5:152