CalCOFI Microbial/Plankton Community Genomics (16S and 18S rDNA) NCOG- JCVI & SIO, UCSD
jcvi_ncog-metabarcodingJCVIexternal
Not yet in the integrated database. CalCOFI holds or tracks this dataset; it has no release tables, no ERDDAP service and no parquet yet. What is below is the record as it stands, and where the data live today.
Overview
CalCOFI Microbial/Plankton Community Genomics (16S and 18S rDNA) contains ribosomal RNA (rRNA) gene metabarcoding sequence data, collected as part of the NOAA CalCOFI Genomics Program (NCOG) to characterize microbial and plankton community composition in the California Current. The dataset covers CalCOFI and California Current Ecosystem Long-Term Ecological Research (CCE-LTER) stations off Southern and Central California and spans 2014 to 2019, archived across two NCBI BioProject deposits (PRJNA555783 for 2014-2016 and PRJNA665326 for 2017-2019, which also includes some 2014-2016 samples and extends metatranscriptomics data through 2020). Whole water samples were filtered onto 0.2 micrometer filters to capture DNA and RNA at four depths, 10 meters, the subsurface chlorophyll maximum layer, 170 meters, and 515 meters, then sequenced using 16S V4 metabarcoding to identify bacteria and archaea, and 18S V4 and V9 metabarcoding to identify eukaryotic plankton such as protists and small zooplankton. The same archived deposits also include total mRNA sequencing (metatranscriptomics) data from these samples. This dataset supports research identifying amplicon sequence variants (ASVs), a method for distinguishing microbial and plankton taxa at high resolution, and characterizing community structure and diversity, and is intended for researchers studying plankton and microbial ecology in the California Current.
Access
This dataset is not in the integrated database, so nothing below comes from a CalCOFI release. Here is where it lives today.
Where it lives today
CalCOFI has not ingested this dataset, so there is no release table, no parquet and no ERDDAP service for it. This is where it is now.
https://www.ncbi.nlm.nih.gov/bioproject/555783
Status
Where this sits in the ingest queue, and what it is waiting on.
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Cite
The provider has not confirmed a citation for this dataset yet. Cite the release below, and name the dataset by its key.
CalCOFI Microbial/Plankton Community Genomics (16S and 18S rDNA) NCOG- JCVI & SIO, UCSD [dataset].BibTeX
@misc{jcvi_ncog-metabarcoding,
title = {CalCOFI Microbial/Plankton Community Genomics (16S and 18S rDNA) NCOG- JCVI & SIO, UCSD}
}