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OAS accession Detail for 0277250
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| accessions_id: | 0277250 | archive |
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| Title: | Operational taxonomic unit (OTU) table for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014 (NCEI Accession 0277250) |
| Abstract: | This dataset contains biological data collected on R/V Yellowfin during cruise SPOT_Yellowfin_Cruises from 2013-04-24 to 2014-01-15. These data include taxon and taxon_code. The instruments used to collect these data include Automated DNA Sequencer, CTD Sea-Bird SBE 911plus, and Niskin bottle. These data were collected by David Caron and Sarah K Hu of University of Southern California as part of the "Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series (SPOT)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2023-01-23. The following is the text of the dataset description provided by BCO-DMO: Dataset Description: This dataset is a raw output operational taxonomic unit (OTU) table generated by processing and clustering raw 18S rRNA gene tag sequences from extracted DNA and RNA. Columns represent samples, including month sampled, material (either extracted RNA or DNA), and depth (in meters); thus values in each column represent the number of sequences in that sample that belong to a given OTU (OTUs by row). Each row represents a single OTU. The last column lists the taxonomic identifier assigned to each OTU. The raw sequence data can be found in the NCBI SRA database under accession number SRP070577 with the associated BioProject PRJNA311248. Metadata for these sequences can be found in the dataset: ”18S rRNA gene tag sequences from DNA and RNA": https://www.bco-dmo.org/dataset/745527 |
| Date received: | 20230123 |
| Start date: | 20130424 |
| End date: | 20140115 |
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| West boundary: | -118.475167 |
| East boundary: | -118.259167 |
| North boundary: | 33.7125 |
| South boundary: | 33.452833 |
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| Submitting institution: | Biological and Chemical Oceanography Data Management Office |
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| Supplementary information: | Acquisition Description: These data were published in Hu et al., 2016. This dataset is a raw output operational taxonomic unit (OTU) table generated by processing and clustering raw 18S rRNA gene tag sequences from DNA and RNA. The numbers in each column represent the number of sequences from that sample belonging to a given OTU (row), with the last column listing the taxonomic ID assigned to each OTU. The raw sequence data can be found in the NCBI SRA database under accession number with the associated BioProject . Metadata for these sequences can be found in the dataset: ”18S rRNA gene tag sequences from DNA and RNA": https://www.bco-dmo.org/dataset/745527 Nucleotide bases with a Q score lower than 20 for the last 30 bp of each sequence were trimmed. Paired-end sequences were merged using FLASh (Magoc and Salzberg 2011) with a minimum of 10 bp and maximum of 150 bp overlap between each sequence pair. Sequences shorter than 350 bp, longer than 460 bp, or which had an average quality score lower than 25 were discarded using QIIME v1.8 (Caporaso et al . 2010). Chimeric sequences were identified and removed, by either de novo or reference-based chimera checking (identify chimeric seqs.py in QIIME, intersection method). The code release v2 associated with this version of the dataset can be downloaded as a .zip file from the Supplemental Documents section of this page. Future code updates will be accessible from the GitHub repository . |
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| Metadata version: | 1 |
| Keydate: | 2023-03-30 14:49:16+00 |
| Editdate: | 2023-03-30 14:49:34+00 |