| nice_raw {ulrb} | R Documentation |
V4-V5 16S rRNA gene amplicons, raw OTU table (N-ICE, 2015)
Description
This is the "raw" data for the N-ICE dataset.
Usage
nice_raw
Format
nice_raw
A data frame with 524 rows and 17 columns:
- ERR2044662, ERR2044663, ERR2044664, ERR2044665, ERR2044666, ERR2044667, ERR2044668, ERR2044669 and ERR2044670
Sample ID
- OTU
OTU ID
- Domain
Domain level classification of OTU
- Phylum
Phylum level classification of OTU
- Class
Class level classification of OTU
- Order
Order level classification of OTU
- Family
Family level classification of OTU
- Genus
Genus level classification of OTU
- Species
Species level classification of OTU
...
Details
The original sequencing results are available at European Nucleotide Archive (accession number: PRJEB15043). Those reads were processed into OTUs by MGnify platform (Study: MGYS00001922). The later study accession provides the table used in here.
This table contains the taxonomy and an abundance score for each taxonomic lineage, which we will refer to as "OTU" (Operational OTU) for simplicity sake.
For details on the sampling campaign in the Arctic ocean, sequencing protocols and bioinformatic processing, please see ref (de Sousa et al., 2019).
Source
https://www.ebi.ac.uk/metagenomics/studies/MGYS00001922#analysis
References
de Sousa, A. G. G., Tomasino, M. P., Duarte, P., Fernández-Méndez, M., Assmy, P., Ribeiro, H., Surkont, J., Leite, R. B., Pereira-Leal, J. B., Torgo, L., & Magalhães, C. (2019). Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime. Microbial Ecology, 78(2), 388–408. https://doi.org/10.1007/s00248-018-01314-2