Jan 09, 2020
Handling of genomics samples
- Adriana Alberti1,
- Julie Poulain2,
- Stefan Engelen2,
- Karine Labadie2,
- Sarah Romac3,4,
- Isabel Ferrera5,
- Guillaume Albini2,
- Jean-Marc Aury2,
- Caroline Belser2,
- Alexis Bertrand2,
- Corinne Cruaud2,
- Corinne Da Silva2,
- Carole Dossat2,
- Frédéric Gavory2,
- Shahinaz Gas2,
- Julie Guy2,
- Maud Haquelle2,
- E'krame Jacoby2,
- Olivier Jaillon2,6,7,
- Arnaud Lemainque2,
- Eric Pelletier2,
- Gaëlle Samson2,
- Marc Wessner2,
- Genoscope Technical Team2,
- Silvia G. Acinas5,
- Marta Royo-Llonch5,
- Francisco M. Cornejo-Castillo5,
- Ramiro Logares5,
- Beatriz Fernández-Gómez5,8,9,
- Chris Bowler10,
- Guy Cochrane11,
- Clara Amid11,
- Petra Ten Hoopen11,
- Colomban De Vargas3,4,
- Nigel Grimsley12,13,
- Elodie Desgranges12,13,
- Stefanie Kandels-Lewis14,15,
- Hiroyuki Ogata16,
- Nicole Poulton17,
- Michael E. Sieracki17,18,
- Ramunas Stepanauskas17,
- Matthew B. Sullivan19,20,
- Jennifer R. Brum20,21,
- Melissa B. Duhaime22,
- Bonnie T. Poulos23,
- Bonnie L. Hurwitz24,
- Stéphane Pesant25,26,
- Eric Karsenti10,14,27,
- Patrick Wincker2,6,7
- 1CEA, Institut de Biologie Intégrative de la Cellule;
- 2CEA - Institut de Biologie François Jacob, Genoscope, Evry, France;
- 3CNRS, UMR 7144, Station Biologique de Roscoff, France;
- 4Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, France;
- 5Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain;
- 6CNRS, UMR 8030, Evry , France;
- 7Université d'Evry, UMR 8030, Evry, France;
- 8FONDAP Center for Genome Regulation, Santiago, Chile;
- 9Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Libano Macul, Santiago, Chile;
- 10Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l’Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, Paris, France;
- 11European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge , UK;
- 12CNRS UMR 7232, BIOM, Banyuls-sur-Mer, France;
- 13Sorbonne Universités Paris 06, OOB UPMC, Banyuls-sur-Mer , France;
- 14Directors’ Research European Molecular Biology Laboratory, Heidelberg, Germany;
- 15Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany;
- 16Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan;
- 17Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA;
- 18National Science Foundation, Arlington, Virginia, USA;
- 19Departments of Microbiology and Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, Ohio, USA;
- 20Department of Microbiology, The Ohio State University, Columbus, Ohio, USA;
- 21Present address: Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, Louisiana, USA;
- 22Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA;
- 23University of Arizona, Tucson, Arizona, USA;
- 24Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, Arizona, USA;
- 25MARUM, Center for Marine Environmental Sciences, University of Bremen, Germany;
- 26PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Germany;
- 27Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d’oceanographie de Villefranche (LOV), Observatoire Océanologique, Villefranche-sur-mer, France
- Tara Oceans
External link: https://www.nature.com/articles/sdata201793#methods
Protocol Citation: Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Marc Wessner, Genoscope Technical Team, Silvia G. Acinas, Marta Royo-Llonch, Francisco M. Cornejo-Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Chris Bowler, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Stefanie Kandels-Lewis, Hiroyuki Ogata, Nicole Poulton, Michael E. Sieracki, Ramunas Stepanauskas, Matthew B. Sullivan, Jennifer R. Brum, Melissa B. Duhaime, Bonnie T. Poulos, Bonnie L. Hurwitz, Stéphane Pesant, Eric Karsenti, Patrick Wincker 2020. Handling of genomics samples. protocols.io https://dx.doi.org/10.17504/protocols.io.qwfdxbn
Manuscript citation:
Alberti, A. (2017). Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Scientific Data 4, 170093 (2017)
doi: 10.1038/sdata.2017.93
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: June 11, 2018
Last Modified: January 09, 2020
Protocol Integer ID: 12967
Abstract
This protocol describes the handling of genomics samples for the Tara Oceans expedition and is part of Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.
Figure 1: Overview of -omics analysis strategy applied on Tara Oceans samples.
Attachments
Guidelines
Genomics samples were transferred on average every 6 weeks from a port of call to the European Molecular Biology Laboratory (EMBL, Heidelberg) in Germany. Transportation was organized by experts from World Courier (www.worldcourier.com) who ensured that the chain of cold was never broken. At EMBL, samples were sorted, repackaged according to their final destination, and transported again by World Courier to the different laboratories responsible for their analysis (Table 1).
Table 1: Summary of libraries generated from Tara Oceans DNA and RNA samples and sequencing experiments performed on each type of library.
*Number of libraries with available readsets in public databases at the date of publication of the paper
In the respective laboratories, samples were immediately identified by scanning/reading their barcode label and were stored in cryo boxes or in −80 °C freezers. During all these steps, samples were manipulated on dry ice. Each laboratory used its own sample management system to record the storage location and to monitor sample usage.