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5 results for “16S 18S rRNA”
Catalog of GenBank sequence read archive (SRA) entries of 16S and 18S rRNA genes from bacterial and protistan planktonic communities along the Eastern Beaufort Sea coast, North Slope, Alaska, 2011-2013
Microbial communities in the coastal Arctic Ocean experience extreme variability in organic matter and inorganic nutrients driven by seasonal shifts in sea ice extent and freshwater inputs. Lagoons border more than half of the Beaufort Sea coast and provide important habitats for migratory fish and seabirds; yet, little is known about the planktonic food webs supporting these higher trophic levels. To investigate seasonal changes in bacterial and protistan planktonic communities, amplicon sequences of 16S and 18S rRNA genes were generated from samples collected during periods of ice-cover (April), ice break-up (June), and open water (August) from shallow lagoons along the eastern Alaska Beaufort Sea coast from 2011 through 2013. This data package catalogs sequence read archive (SRA) entries available through GenBank BioProject PRJNA530074 at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA530074. This data package is associated with the following publication: Kellogg CTE, McClelland JW, Dunton KH and Crump BC (2019) Strong Seasonality in Arctic Estuarine Microbial Food Webs. Front. Microbiol. 10:2628. doi: 10.3389/fmicb.2019.02628 Environmental variables (physiochemical data from YSI and HOBO data loggers, as well as organic matter analysis and stable isotope data from discrete water samples) associated with this genomic dataset are available from the Arctic Data Center: Kenneth Dunton, Byron Crump, and James McClelland. Physical, chemical, and biological data from lagoons and open coastal waters in the nearshore environment of the eastern Alaska Beaufort Sea, 2011-2013. Arctic Data Center. doi:10.18739/A2DG13. To join the two datasets together, please use the provided site codes (column "site_name" here) and collection dates (column "collection_date" here) in each dataset. Note that the site codes in this package are without hyphens (e.g. JAA) while site codes in the above environmental data package have hyphens (e.g. JA-A). Instead of citing this package which is jus
Inventory of High-resolution phylogenetic profiles of the planktonic microbial communities (via 16S and 18S rRNA gene amplicons) from Shark River Slough and Taylor Slough, Everglades National Park (FCE LTER), Florida, USA, 2017 - ongoing
Planktonic microbial communities mediate many vital biogeochemical processes in wetland ecosystems, yet compared to other aquatic ecosystems, like oceans, lakes, rivers, or estuaries, they remain relatively underexplored. Our study site, the Florida Everglades (USA)—a vast iconic wetland consisting of a slow-moving system of shallow rivers connecting freshwater marshes with coastal mangrove forests and seagrass meadows—is a highly threatened model ecosystem for studying salinity and nutrient gradients, as well as the effects of sea level rise and saltwater intrusion. This dataset provides the first high-resolution phylogenetic profiles of planktonic bacterial and eukaryotic microbial communities (using 16S and 18S rRNA gene amplicons) from these environments. The dataset contains 16S and 18S rRNA data from 2017, and contains 16S rRNA data for monthly (2019) and quarterly water samples (2020-ongoing). The 2017 data are published in Laas et al. 2022. A detailed list of sequence data and their accession numbers in GenBank is provided and will be updated as more data are published. This data package is an inventory of sequence read archive (SRA) entries available through GenBank BioProject PRJNA525456 (at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA525456) and BioProject PRJNA1018945 (at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1018945). This data package is associated with the following publication: Laas, P., Ugarelli, K., Travieso, R., Stumpf, S., Gaiser, E. E., Kominoski, J. S., & Stingl, U. (2022). Water column microbial communities vary along salinity gradients in the Florida Coastal Everglades wetlands. Microorganisms, 10(2), 215. https://doi.org/10.3390/microorganisms10020215 Instead of citing this package, which is an inventory, please cite the original GenBank data or journal article, as appropriate. Citation guidance for the journal article is available on the respective publisher's website.
Modena E. coli (16S and 23S) and S. cerevisiae (18S and 25S) rRNA test dataset samples 1 to 5
<p>Samples 1 to 5 of the rRNA test dataset accompanying the article "<em>Nanopore based computational method for detecting a wide range of epigenetic/epitranscriptomic modifications".</em></p> <p>Each sample comprises seven subsamples with coverage depths ranging from 10 to 2000.</p> <p>If you have any questions about the content of this dataset, feel free to contact Siniša Biđin at sinisa@heuristika.hr.</p>
Modena E. coli (16S and 23S) and S. cerevisiae (18S and 25S) rRNA test dataset samples 6 to 10
<p>Samples 6 to 10 of the rRNA test dataset accompanying the article "<em>Nanopore based computational method for detecting a wide range of epigenetic/epitranscriptomic modifications".</em></p> <p>Each sample comprises seven subsamples with coverage depths ranging from 10 to 2000.</p> <p>If you have any questions about the content of this dataset, feel free to contact Siniša Biđin at sinisa@heuristika.hr.</p>
Supplementary material 1 from: Sogawa S, Tsuchiya K, Nagai S, Shimode S, Kuwahara VS (2022) Annual dynamics of eukaryotic and bacterial communities revealed by 18S and 16S rRNA metabarcoding in the coastal ecosystem of Sagami Bay, Japan. Metabarcoding and Metagenomics 6: e78181. https://doi.org/10.3897/mbmg.6.78181
Figures S1–S8
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