Dataset: NCBI accession metadata for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014

ValidatedFinal no updates expectedDOI: 10.1575/1912/bco-dmo.745527.1Version 1 (2018-09-04)Dataset Type:Other Field Results

Principal Investigator: David Caron (University of Southern California)

Co-Principal Investigator, Contact: Sarah K. Hu (University of Southern California)

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

Project: Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series (SPOT)

Abstract

Raw DNA and RNA V4 tag sequences include spatially and temporally distinct samples from coastal California. Samples were collected in Niskin bottles with a CTD rosette at the San Pedro Ocean Time-series (SPOT) between April of 2013 and January of 2014. This dataset contains sequence data accession numbers and metadata for the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (SRA Study ID: SRP070577, BioProject: PRJNA311248).

Cite Dataset

These data were published in Hu et al., 2016.
Sequence data can be found in the NCBI SRA database under accession number SRP070577 with the associated BioProject PRJNA311248.

Related Datasets

References
Dataset: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA311248
University of Southern California (2016). marine metagenome, DNA and RNA based tag sequences raw sequence reads. 2016/02. 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/PRJNA311248. NCBI:BioProject: PRJNA311248.

Related Publications

Results
Hu, S. K., Campbell, V., Connell, P., Gellene, A. G., Liu, Z., Terrado, R., & Caron, D. A. (2016). Protistan diversity and activity inferred from RNA and DNA at a coastal ocean site in the eastern North Pacific. FEMS Microbiology Ecology, fiw050. doi:10.1093/femsec/fiw050
Methods
Hu, S. (2017). RNA (and optional DNA) extraction from environmental samples (filters) v2 (protocols.io.hk3b4yn). Protocols.io. doi:10.17504/protocols.io.hk3b4yn
Methods
Hu, S. (2017). Sample collection from the field for downstream molecular analysis - microbial eukaryote-focused v1. Protocols.io. doi:10.17504/protocols.io.hisb4ee
Methods
Mesrop, L., & Hu, S. (2017). 18S V4 tag sequencing PCR amplification and library prep (Illumina) v1. Protocols.io. doi:10.17504/protocols.io.hdmb246
Software
Hu, S. (2018). 18S rRNA gene tag-sequencing code - V4 hypervariable region (Version v2) [Software]. GitHub. Retrieved September 16, 2018, from https://github.com/BCODMO/V4_tagsequencing_18Sdiversity_q1/tree/v2

Caron, D., Hu, S. (2018) NCBI accession metadata for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-09-04 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.745527.1 [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.

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Funded by the U.S. National Science Foundation