The ReproGenomics Viewer: A multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community

Thomas A. Darde; Estelle Lecluze; Aurélie Lardenois; Isabelle Stévant; Nathan Alary; Frank Tüttelmann; Olivier Collin; Serge Nef; Bernard Jégou; Antoine D. Rolland; Frédéric Chalmel

doi:10.1093/bioinformatics/btz047

The ReproGenomics Viewer: A multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community

Thomas A. Darde, Estelle Lecluze, Aurélie Lardenois, Isabelle Stévant, Nathan Alary, Frank Tüttelmann, Olivier Collin, Serge Nef, Bernard Jégou, Antoine D. Rolland, Frédéric Chalmel

Research output: Contribution to journal › Article › peer-review

39 Scopus citations

Abstract

Motivation: Recent advances in transcriptomics have enabled unprecedented insight into gene expression analysis at a single-cell resolution. While it is anticipated that the number of publications based on such technologies will increase in the next decade, there is currently no public resource to centralize and enable scientists to explore single-cell datasets published in the field of reproductive biology. Results: Here, we present a major update of the ReproGenomics Viewer, a cross-species and cross-technology web-based resource of manually-curated sequencing datasets related to reproduction. The redesign of the ReproGenomics Viewer's architecture is accompanied by significant growth of the database content including several landmark single-cell RNA-sequencing datasets. The implementation of additional tools enables users to visualize and browse the complex, high-dimensional data now being generated in the reproductive field.

Original language	English
Pages (from-to)	3133-3139
Number of pages	7
Journal	Bioinformatics
Volume	35
Issue number	17
DOIs	https://doi.org/10.1093/bioinformatics/btz047
State	Published - 1 Sep 2019
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2019 The Author(s).

Funding

This work was supported by the French agency for food and safety [ANSES n° EST-13-081, n° EST-17-256 to F.C.]; the French National Research Agency [ANR n° 16-CE14-0017-02, n°18-CE14-0038-02 to F.C.]; the Fondation pour la recherche médicale [FRM n° DBI20131228558 to F.C.]; the Swiss National Science Foundation [SNF n° CRS115_171007 to B.J.]; the DFG Clinical Research Unit ‘Male Germ Cells: from Genes to Function’ [CRU 326 to F.T.]; the French National Institute of Health and Medical Research (Inserm); the University of Rennes 1; and the French School of Public Health (EHESP).

Funders	Funder number
French National Institute of Health and Medical Research
French School of Public Health
French agency for food and safety	EST-13-081, EST-17-256
Deutsche Forschungsgemeinschaft	CRU 326
Agence Nationale de la Recherche	16-CE14-0017-02, 18-CE14-0038-02
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung	CRS115_171007
Fondation pour la Recherche Médicale	DBI20131228558
École des hautes études en santé publique

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10.1093/bioinformatics/btz047

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Darde, T. A., Lecluze, E., Lardenois, A., Stévant, I., Alary, N., Tüttelmann, F., Collin, O., Nef, S., Jégou, B., Rolland, A. D., & Chalmel, F. (2019). The ReproGenomics Viewer: A multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community. Bioinformatics, 35(17), 3133-3139. https://doi.org/10.1093/bioinformatics/btz047

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abstract = "Motivation: Recent advances in transcriptomics have enabled unprecedented insight into gene expression analysis at a single-cell resolution. While it is anticipated that the number of publications based on such technologies will increase in the next decade, there is currently no public resource to centralize and enable scientists to explore single-cell datasets published in the field of reproductive biology. Results: Here, we present a major update of the ReproGenomics Viewer, a cross-species and cross-technology web-based resource of manually-curated sequencing datasets related to reproduction. The redesign of the ReproGenomics Viewer's architecture is accompanied by significant growth of the database content including several landmark single-cell RNA-sequencing datasets. The implementation of additional tools enables users to visualize and browse the complex, high-dimensional data now being generated in the reproductive field.",

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Darde, TA, Lecluze, E, Lardenois, A, Stévant, I, Alary, N, Tüttelmann, F, Collin, O, Nef, S, Jégou, B, Rolland, AD & Chalmel, F 2019, 'The ReproGenomics Viewer: A multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community', Bioinformatics, vol. 35, no. 17, pp. 3133-3139. https://doi.org/10.1093/bioinformatics/btz047

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AU - Lecluze, Estelle

AU - Lardenois, Aurélie

AU - Stévant, Isabelle

AU - Alary, Nathan

AU - Tüttelmann, Frank

AU - Collin, Olivier

AU - Nef, Serge

AU - Jégou, Bernard

AU - Rolland, Antoine D.

AU - Chalmel, Frédéric

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The ReproGenomics Viewer: A multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community

Abstract

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