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

Name: NCBI accession metadata for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014
Published: 2018-09-04
Keywords: microbial ecology, microbial eukaryotes, protistan diversity, 18S rRNA gene sequencing, cDNA sequencing, DNA/RNA comparison, oceans

Final 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

Spatial Extent: N:33.71 E:-118.26 S:33.45 W:-118.48
Temporal Extent: 2013-04-24 - 2014-01-15

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Citations

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

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

Final 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

Cite Dataset

Spatial Extent: N:33.71 E:-118.26 S:33.45 W:-118.48
Temporal Extent: 2013-04-24 - 2014-01-15

XXX

Views

XX

Downloads

X

Citations

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

Related Publications

Results

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

File(s)	Type	Description	Action
SRA_metadata.csv (27.82 KB)	Comma Separated Values (.csv)	Primary data file for dataset ID 745527	Download What is ERDDAP? SUBSET DATA VIEW TABLE CSV TSV GeoJSON MATLAB netCDF

Supplemental File(s)	Type	Description	Action
V4_tagsequencing_18Sdiversity_q1-v2.zip (813.68 KB)	ZIP Archive (ZIP)	Zip file containing release https://github.com/BCODMO/V4_tagsequencing_18Sdiversity_q1/tree/v2	Download

File(s)	Type	Description	Action
SRA_metadata.csv (27.82 KB)	Comma Separated Values (.csv)	Primary data file for dataset ID 745527	Download What is ERDDAP? SUBSET DATA VIEW TABLE CSV TSV GeoJSON MATLAB netCDF

Supplemental File(s)	Type	Description	Action
V4_tagsequencing_18Sdiversity_q1-v2.zip (813.68 KB)	ZIP Archive (ZIP)	Zip file containing release https://github.com/BCODMO/V4_tagsequencing_18Sdiversity_q1/tree/v2	Download

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

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

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Files

Supplemental Files

Related Datasets

Related Publications

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

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

XXX

XX

X

Files

Supplemental Files

Related Datasets

Related Publications

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

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

Metadata

XXX

XX

X

Files

Supplemental Files

Related Datasets

Related Publications

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

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

Metadata

XXX

XX

X

Files

Supplemental Files

Related Datasets

Related Publications