TARAoceans {mixKernel}

TARA ocean microbiome data

Description

The TARA Oceans expedition facilitated the study of plankton communities by providing oceans metagenomic data combined with environmental measures to the scientific community. This dataset focuses on 139 prokaryotic-enriched samples collected from 68 stations and spread across three depth layers: the surface (SRF), the deep chlorophyll maximum (DCM) layer and the mesopelagic (MES) zones. Samples were located in height different oceans or seas: Indian Ocean (IO), Mediterranean Sea (MS), North Atlantic Ocean (NAO), North Pacific Ocean (NPO), Red Sea (RS), South Atlantic Ocean (SAO), South Pacific Ocean (SPO) and South Ocean (SO). Here, only a subset of the original data is provided (1% of the 35,650 prokaryotic operational taxonomic units (OTUs) and of the 39,246 bacterial genes (NOGs) (selected at random).

Usage

data(TARAoceans)

Format

A list containing the following components:

phychem

data matrix with 139 rows and 22 columns. Each row represents a sample and each column an environmental variable.

pro.phylo

data matrix with 139 rows (samples) and 356 columns (prokaryotic OTUs).

taxonomy

data matrix with 356 rows (prokaryotic OTUs) and 6 columns indicating the taxonomy of each OTU.

phylogenetic.tree

a phylo object (see package 'ape') representing the prokaryotic OTUs phylogenetic tree.

pro.NOGs

data matrix with 139 rows (samples) and 638 columns (NOGs).

sample

a list containing three following entries (all three are character vectors): name (sample name), ocean (oceanic region of the sample) and depth (sample depth).

Source

The raw data were downloaded from http://ocean-microbiome.embl.de/companion.html.

References

Sunagawa S., Coelho L.P., Chaffron S., Kultima J.R., Labadie K., Salazar F., Djahanschiri B., Zeller G., Mende D.R., Alberti A., Cornejo-Castillo F., Costea P.I., Cruaud C., d'Oviedo F., Engelen S., Ferrera I., Gasol J., Guidi L., Hildebrand F., Kokoszka F., Lepoivre C., Lima-Mendez G., Poulain J., Poulos B., Royo-Llonch M., Sarmento H., Vieira-Silva S., Dimier C., Picheral M., Searson S., Kandels-Lewis S., Tara Oceans coordinators, Bowler C., de Vargas C., Gorsky G., Grimsley N., Hingamp P., Iudicone D., Jaillon O., Not F., Ogata H., Pesant S., Speich S., Stemmann L., Sullivan M., Weissenbach J., Wincker P., Karsenti E., Raes J., Acinas S. and Bork P. (2015). Structure and function of the global ocean microbiome. Science, 348, 6237.