nice_raw: 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

Arguments

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).

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