Dataset: Phytoplankton MicroTOOLs microarray-based metatranscriptomes collected from a nutrient amendment experiment conducted during R/V New Horizon Cruise NH1417 in the California Current System from 2014-08-23 to 2014-08-26

Release Date:2020-04-15Final no updates expectedVersion 1 (2019-07-18)Dataset Type:Unknown

Principal Investigator: Jonathan P. Zehr (University of California-Santa Cruz)

Contact: Dr Irina Shilova (University of California-Santa Cruz)

BCO-DMO Data Manager: Amber D. York (Woods Hole Oceanographic Institution)

Program: Dimensions of Biodiversity (Dimensions of Biodiversity)

Project: Oligotrophic phytoplankton community response to changes in N substrates and the resulting impact on genetic, taxonomic and functional diversity (PhytoNsubResponse)

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Transcription changes by surface microbial communities from the California Current System in response to added nitrogen and/or iron substrates were assessed using MicroTOOLs microarrays. Samples were collected during the R/V New Horizon Cruise NH1417 in 2014.

These data are available at The National Center for Biotechnology Information (NCBI) under NCBI Gene Expression Omnibus (GEO) accession number GSE130464 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE130464. BioProject https://www.ncbi.nlm.nih.gov/bioproject/PRJNA540297.

The manuscript "Phytoplankton transcriptomic and physiological responses to fixed nitrogen in the California Current System" by Shilova and Magasin et al. (2020) describes the experiment, metatranscriptomic data, and results. The previously published manuscript details other measurements obtained from the same experiment and includes phytoplankton cell counts, Fast Repetition Rate Fluorometry measurements, nutrients and Chlorophyll a concentrations, and 16S rRNA gene sequences (Shilova et al., 2017).

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Results
Shilova IN, Magasin JD, Mills MM, Robidart JC, Turk-Kubo KA, et al. (2020) Phytoplankton transcriptomic and physiological responses to fixed nitrogen in the California current system. PLOS ONE 15(4): e0231771. doi: 10.1371/journal.pone.0231771
Results
Shilova, I. N., Mills, M. M., Robidart, J. C., Turk-Kubo, K. A., Björkman, K. M., Kolber, Z., … Zehr, J. P. (2017). Differential effects of nitrate, ammonium, and urea as N sources for microbial communities in the North Pacific Ocean. Limnology and Oceanography, 62(6), 2550–2574. doi:10.1002/lno.10590
Methods
Alhamdoosh, M., Ng, M., Wilson, N. J., Sheridan, J. M., Huynh, H., Wilson, M. J., & Ritchie, M. E. (2016). Combining multiple tools outperforms individual methods in gene set enrichment analyses. Bioinformatics, btw623. doi:10.1093/bioinformatics/btw623
Methods
Langfelder, P., & Horvath, S. (2008). WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics, 9(1). doi:10.1186/1471-2105-9-559
Methods
Shilova, I. N., Robidart, J. C., James Tripp, H., Turk-Kubo, K., Wawrik, B., Post, A. F., … Zehr, J. P. (2014). A microarray for assessing transcription from pelagic marine microbial taxa. The ISME Journal, 8(7), 1476–1491. doi:10.1038/ismej.2014.1

Zehr, J. P., Shilova, I. (2019) Phytoplankton MicroTOOLs microarray-based metatranscriptomes collected from a nutrient amendment experiment conducted during R/V New Horizon Cruise NH1417 in the California Current System from 2014-08-23 to 2014-08-26. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2019-07-18 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/773486 [access date]

Terms of Use

This dataset is licensed under Creative Commons Attribution 4.0.


If you wish to use this dataset, it is highly recommended that you contact the original principal investigators (PI). Should the relevant PI be unavailable, please contact BCO-DMO (info@bco-dmo.org) for additional guidance. For general guidance please see the BCO-DMO Terms of Use document.

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Funded by the U.S. National Science Foundation