Data
Iron physiology and metabolism of model phytoplankton taxa in the South Atlantic Bight
Growth and physiology culture data, bioinformatic bash scripts, R analysis scripts, and jupyter notebooks are available on GitHub (https://github.com/CohenLabUGA/SAB_isolates).
Microeukaryote metabolism across the western North Atlantic Ocean revealed through autonomous underwater profiling. Preprint: biorxiv.org/content/10.1101/2023.11.20.567900v1.full
AE1913 CTD data and processed trace metal, and macronutrient concentrations are available on BCO-DMO (https://www.bco-dmo.org/project/765945). Raw sequences have been deposited to the NCBI SRA database under BioProject ID PRJNA903389 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA903389). Metatranscriptomic assembly, annotations and count data are available through Zenodo (https://zenodo.org/record/8287779). Metaproteomic mass spectrometry data is available on ProteomeXchange through PRIDE accession PXD045395 (https://www.ebi.ac.uk/pride/archive/projects/PXD045395). Analysis notebooks are available on GitHub (https://github.com/cnatalie/BATS).
Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean (2021) Nature Microbiology 6:173–186 https://www.nature.com/articles/s41564-020-00814-7
Environmental metadata from the 2011 METZYME expedition including macronutrients, pigments and physiochemical data is available through BCO-DMO project 2236. Mass spec proteomics data and assembled fasta can be found on ProteomeXchange under identifier PXD014230. Raw reads are available through NCBI under Bioproject number PRJNA555787. R code used to create heatmaps, ordination plots, 18S rRNA and WCGNA analyses are located on GitHub.
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Transcriptomic and proteomic responses of the oceanic diatom Pseudo-nitzschia granii to iron limitation (2018) Environmental Microbiology 20(8): 3109–3126 doi:10.1111/1462-2920.14386
For assembled contigs, KEGG annotations and raw read counts please visit the Marchetti Lab page. Raw sequences are located on NCBI under Bioproject number PRJNA432444. Mass spec proteomics data is available via ProteomeXchange under identifier PXD009698
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Diatom transcriptional and physiological responses to changes in iron bioavailability across ocean provinces (2017) Frontiers in Marine Science 4:360. doi:10.3389/fmars.2017.00360
For assembled contigs, taxonomic and functional annotations, and raw read count information please visit the Marchetti Lab page. Raw sequences for California Upwelling and Northeast Pacific incubations can be found on NCBI under Bioproject numbers PRJNA320398 and PRJNA388329, respectively.
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Iron and vitamin interactions in marine diatom isolates and natural assemblages of the Northeast Pacific Ocean (2017) Limnology and Oceanography 62: 2076-2096. doi:10.1002/lno.10552
For assembled contigs, annotations, and normalized counts, please visit the Marchetti Lab page. Raw sequences are located on NCBI under Bioproject PRJNA320386.