Dataset: Assembled metagenomes collected in the Eastern Tropical North Pacific Oxygen Deficient Zone in April 2012 from R/V Thomas G. Thompson cruise TN278

Final no updates expectedDOI: 10.26008/1912/bco-dmo.733748.1Version 1 (2018-04-19)Dataset Type:Cruise Results

Principal Investigator, Contact: Gabrielle Rocap (University of Washington)

Contact: Clara Fuchsman (University of Washington)

BCO-DMO Data Manager: Shannon Rauch (Woods Hole Oceanographic Institution)

Project: EAGER: Harnessing the power of short-read technology to investigate unexplored microbial communities in the deep euphotic zone (EAGER Deep Prochlorococcus)

Abstract

This dataset describes assembled metagenomes collected in the Eastern Tropical North Pacific Oxygen Deficient Zone in April 2012 from R/V Thomas G. Thompson cruise TN278.

Cite Dataset

XXX

Views

XX

Downloads

X

Citations

Assembled metagenomes collected in the Eastern Tropical North Pacific Oxygen Deficient Zone in April 2012 on cruise TN278.

These data were published in (Fuchsman et al., 2017)

Related Datasets

IsRelatedTo
Dataset: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA350692
University of Washington. marine metagenome Eastern Tropical North Pacific 2012. 2018/01. In: BioProject [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; 2011-. Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA350692. NCBI:BioProject: PRJNA350692.

Related Publications

Results
Fuchsman, C. A., Devol, A. H., Saunders, J. K., McKay, C., & Rocap, G. (2017). Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone. Frontiers in Microbiology, 8. doi:10.3389/fmicb.2017.02384
Methods
Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114–2120. doi:10.1093/bioinformatics/btu170
Methods
Brown, C. T., Howe, A., Zhang, Q., Pyrkosz, A. B., and Brom, T. H. (2012). A reference-free algorithm for computational normalization of shotgun sequencing data. arXiv:1203.4802v2.
Methods
Crusoe, M. R., Alameldin, H. F., Awad, S., Boucher, E., Caldwell, A., Cartwright, R., Charbonneau, A., Constantinides, B., Edvenson, G., Fay, S., Fenton, J., Fenzl, T., Fish, J., Garcia-Gutierrez, L., Garland, P., Gluck, J., González, I., Guermond, S., Guo, J., … Brown, C. T. (2015). The khmer software package: enabling efficient nucleotide sequence analysis. F1000Research, 4, 900. https://doi.org/10.12688/f1000research.6924.1
Methods
Magoc, T., & Salzberg, S. L. (2011). FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics, 27(21), 2957–2963. https://doi.org/10.1093/bioinformatics/btr507

Rocap, G. (2022) Assembled metagenomes collected in the Eastern Tropical North Pacific Oxygen Deficient Zone in April 2012 from R/V Thomas G. Thompson cruise TN278. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-04-19 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.733748.1 [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.

NSF Logo©2020 Biological and Chemical Oceanography Data Management Office.
Funded by the U.S. National Science Foundation