P. Calvel, A. D. Rolland, B. Jegou, and C. Pineau, Testicular postgenomics: targeting the regulation of spermatogenesis, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.5, issue.9, pp.1481-1500, 2010.
DOI : 10.1021/pr0600733
URL : https://hal.archives-ouvertes.fr/inserm-00518191

A. D. Rolland, B. Jegou, and C. Pineau, Testicular Development and Spermatogenesis: Harvesting the Postgenomics Bounty, Adv. Exp. Med. Biol, vol.636, pp.16-41, 2008.
DOI : 10.1007/978-0-387-09597-4_2
URL : https://hal.archives-ouvertes.fr/hal-00653322

A. Lardenois, A. Gattiker, O. Collin, F. Chalmel, and M. Primig, GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle, Database, vol.2010, issue.0, p.30, 2010.
DOI : 10.1093/database/baq030
URL : https://hal.archives-ouvertes.fr/hal-00639961

Y. Zhang, L. Zhong, B. Xu, Y. Yang, R. Ban et al., SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining, Nucleic Acids Research, vol.41, issue.D1, pp.1055-1062, 2013.
DOI : 10.1093/nar/gks1186
URL : http://doi.org/10.1093/nar/gks1186

T. L. Lee, H. H. Cheung, J. Claus, C. Sastry, S. Singh et al., GermSAGE: a comprehensive SAGE database for transcript discovery on male germ cell development, Nucleic Acids Research, vol.37, issue.Database, pp.891-897, 2009.
DOI : 10.1093/nar/gkn644

T. L. Lee, Y. Li, H. H. Cheung, J. Claus, S. Singh et al., GonadSAGE: a comprehensive SAGE database for transcript discovery on male embryonic gonad development, Bioinformatics, vol.26, issue.4, pp.585-586, 2010.
DOI : 10.1093/bioinformatics/btp695

A. J. Hsueh and R. Rauch, Ovarian Kaleidoscope Database: Ten Years and Beyond1, Biology of Reproduction, vol.86, issue.6, 0192.
DOI : 10.1095/biolreprod.112.099127
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3386152

J. A. Davies, M. H. Little, B. Aronow, J. Armstrong, J. Brennan et al., Access and Use of the GUDMAP Database of Genitourinary Development, Methods Mol. Biol, vol.886, pp.185-201, 2012.
DOI : 10.1007/978-1-61779-851-1_17

I. Merelli, H. Perez-sanchez, S. Gesing, D. Agostino, and D. , High-Performance Computing and Big Data in Omics-Based Medicine, BioMed Research International, vol.2014, p.825649, 2014.
DOI : 10.1155/2014/825649

J. Wang, L. Kong, G. Gao, and J. Luo, A brief introduction to web-based genome browsers, Briefings in Bioinformatics, vol.14, issue.2, pp.131-143, 2013.
DOI : 10.1093/bib/bbs029

K. R. Rosenbloom, J. Armstrong, G. P. Barber, J. Casper, H. Clawson et al., The UCSC Genome Browser database: 2015 update, Nucleic Acids Research, vol.43, issue.D1, pp.670-681, 2015.
DOI : 10.1093/nar/gku1177

J. Goecks, N. Coraor, A. Nekrutenko, and J. Taylor, NGS analyses by visualization with Trackster, Nature Biotechnology, vol.89, issue.11, pp.1036-1039, 2012.
DOI : 10.1074/jbc.M111.312280
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3889118

S. W. Choo, H. Heydari, T. K. Tan, C. C. Siow, C. Y. Beh et al., VibrioBase: A Model for Next-Generation Genome and Annotation Database Development, The Scientific World Journal, vol.42, p.569324, 2014.
DOI : 10.1111/j.1574-6968.1990.tb04883.x
URL : http://doi.org/10.1155/2014/569324

H. Heydari, W. Y. Wee, N. Lokanathan, R. Hari, M. Yusoff et al., MabsBase: A Mycobacterium abscessus Genome and Annotation Database, PLoS ONE, vol.23, issue.21, p.62443, 2013.
DOI : 10.1371/journal.pone.0062443.g003

H. Heydari, N. V. Mutha, M. I. Mahmud, C. C. Siow, W. Y. Wee et al., StaphyloBase: a specialized genomic resource for the staphylococcal research community, Database, vol.2014, issue.0, p.10, 2014.
DOI : 10.1093/database/bau010

S. W. Choo, M. Y. Ang, H. Fouladi, S. Y. Tan, C. C. Siow et al., HelicoBase: a Helicobacter genomic resource and analysis platform, BMC Genomics, vol.15, issue.1, p.600, 2014.
DOI : 10.1186/1471-2164-15-600

S. Geisen, G. Barturen, A. M. Alganza, M. Hackenberg, and J. L. Oliver, NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes, Nucleic Acids Research, vol.42, issue.D1, pp.53-59, 2014.
DOI : 10.1093/nar/gkt1202

M. Hackenberg, G. Barturen, and J. L. Oliver, NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data, Nucleic Acids Research, vol.39, issue.Database, pp.75-79, 2011.
DOI : 10.1093/nar/gkq942

M. E. Skinner, A. V. Uzilov, L. D. Stein, C. J. Mungall, and I. H. Holmes, JBrowse: A next-generation genome browser, Genome Research, vol.19, issue.9, 2009.
DOI : 10.1101/gr.094607.109

D. Blankenberg, V. Kuster, G. Coraor, N. Ananda, G. Lazarus et al., Galaxy: A Web-Based Genome Analysis Tool for Experimentalists, Curr. Protoc. Mol. Biol., Chapter, vol.19, pp.1-21, 2010.
DOI : 10.1002/0471142727.mb1910s89

B. Giardine, C. Riemer, R. C. Hardison, R. Burhans, L. Elnitski et al., Galaxy: A platform for interactive large-scale genome analysis, Genome Research, vol.15, issue.10, 2005.
DOI : 10.1101/gr.4086505

J. Goecks, A. Nekrutenko, and J. Taylor, Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences, Genome Biology, vol.11, issue.8, p.86, 2010.
DOI : 10.1186/gb-2010-11-8-r86

H. Gan, L. Wen, S. Liao, X. Lin, T. Ma et al., Dynamics of 5-hydroxymethylcytosine during mouse spermatogenesis, Nature Communications, vol.4, 1995.
DOI : 10.1073/pnas.1003953107

S. S. Hammoud, D. H. Low, C. Yi, D. T. Carrell, E. Guccione et al., Chromatin and Transcription Transitions of Mammalian Adult Germline Stem Cells and Spermatogenesis, Cell Stem Cell, vol.15, issue.2, pp.239-253, 2014.
DOI : 10.1016/j.stem.2014.04.006

J. Gaucher, F. Boussouar, E. Montellier, S. Curtet, T. Buchou et al., Bromodomain-dependent stage-specific male genome programming by Brdt, The EMBO Journal, vol.13, issue.19, pp.3809-3820, 2012.
DOI : 10.1038/emboj.2012.233

K. Brick, F. Smagulova, P. Khil, R. D. Camerini-otero, and G. V. Petukhova, Genetic recombination is directed away from functional genomic elements in mice, Nature, vol.9, issue.7400, pp.642-645, 2012.
DOI : 10.1038/nature11089
URL : https://hal.archives-ouvertes.fr/hal-00877666

S. Erkek, M. Hisano, C. Y. Liang, M. Gill, R. Murr et al., Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa, Nature Structural & Molecular Biology, vol.558, issue.7, pp.868-875, 2013.
DOI : 10.1093/bioinformatics/btl140

X. Z. Li, C. K. Roy, X. Dong, E. Bolcun-filas, J. Wang et al., An Ancient Transcription Factor Initiates the Burst of piRNA Production during Early Meiosis in Mouse Testes, Molecular Cell, vol.50, issue.1, pp.67-81, 2013.
DOI : 10.1016/j.molcel.2013.02.016

U. Brykczynska, M. Hisano, S. Erkek, L. Ramos, E. J. Oakeley et al., Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa, Nature Structural & Molecular Biology, vol.287, issue.6, pp.679-687, 2010.
DOI : 10.1038/nsmb.1821

A. Laiho, N. Kotaja, A. Gyenesei, and A. Sironen, Transcriptome Profiling of the Murine Testis during the First Wave of Spermatogenesis, PLoS ONE, vol.40, issue.4, p.61558, 2013.
DOI : 10.1371/journal.pone.0061558.s009

M. Soumillon, A. Necsulea, M. Weier, D. Brawand, X. Zhang et al., Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis, Cell Reports, vol.3, issue.6, pp.2179-2190, 2013.
DOI : 10.1016/j.celrep.2013.05.031
URL : https://hal.archives-ouvertes.fr/hal-00852777

F. Chalmel, A. Lardenois, B. Evrard, A. D. Rolland, O. Sallou et al., High-resolution profiling of novel transcribed regions during rat spermatogenesis, Biol. Reprod, vol.91, p.5, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01063924

S. Chocu, B. Evrard, R. Lavigne, A. D. Rolland, F. Aubry et al., Forty-four novel protein-coding loci discovered using a proteomics informed by transcriptomics (PIT) approach in rat male germ cells, Biol. Reprod, vol.91, p.123, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01121802

O. Meikar, V. V. Vagin, F. Chalmel, K. Sostar, A. Lardenois et al., An atlas of chromatoid body components, RNA, vol.20, issue.4, pp.483-495, 2014.
DOI : 10.1261/rna.043729.113
URL : https://hal.archives-ouvertes.fr/hal-00985894

A. Necsulea, M. Soumillon, M. Warnefors, A. Liechti, T. Daish et al., The evolution of lncRNA repertoires and expression patterns in tetrapods, Nature, vol.39, issue.7485, pp.635-640, 2014.
DOI : 10.1038/nature12943

T. Barrett, S. E. Wilhite, P. Ledoux, C. Evangelista, I. F. Kim et al., NCBI GEO: archive for functional genomics data sets--update, Nucleic Acids Research, vol.41, issue.D1, pp.991-995, 2013.
DOI : 10.1093/nar/gks1193

A. Lardenois, Y. Liu, T. Walther, F. Chalmel, B. Evrard et al., Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6, Proceedings of the National Academy of Sciences, vol.108, issue.3, pp.1058-1063, 2011.
DOI : 10.1073/pnas.1016459108
URL : https://hal.archives-ouvertes.fr/hal-00682830

R. Lavigne, E. Becker, Y. Liu, B. Evrard, A. Lardenois et al., Direct Iterative Protein Profiling (DIPP) - an Innovative Method for Large-scale Protein Detection Applied to Budding Yeast Mitosis, Molecular & Cellular Proteomics, vol.11, issue.2, pp.111-012682, 2012.
DOI : 10.1074/mcp.M111.012682
URL : https://hal.archives-ouvertes.fr/hal-00682837

Z. Xu, W. Wei, J. Gagneur, F. Perocchi, S. Clauder-munster et al., Bidirectional promoters generate pervasive transcription in yeast, Nature, vol.35, issue.7232, pp.1033-1037, 2009.
DOI : 10.1038/nature07728

M. V. Granovskaia, L. J. Jensen, M. E. Ritchie, J. Toedling, Y. Ning et al., High-resolution transcription atlas of the mitotic cell cycle in budding yeast, Genome Biology, vol.11, issue.3, p.24, 2010.
DOI : 10.1186/gb-2010-11-3-r24

J. J. Johnston, W. S. Rubinstein, F. M. Facio, D. Ng, L. N. Singh et al., Secondary Variants in Individuals Undergoing Exome Sequencing: Screening of 572 Individuals Identifies High-Penetrance Mutations in Cancer-Susceptibility Genes, The American Journal of Human Genetics, vol.91, issue.1, pp.97-108, 2012.
DOI : 10.1016/j.ajhg.2012.05.021

D. Welter, J. Macarthur, J. Morales, T. Burdett, P. Hall et al., The NHGRI GWAS Catalog, a curated resource of SNP-trait associations, Nucleic Acids Research, vol.42, issue.D1, pp.1001-1006, 2014.
DOI : 10.1093/nar/gkt1229

R. M. Kuhn, D. Haussler, and W. J. Kent, The UCSC genome browser and associated tools, Briefings in Bioinformatics, vol.14, issue.2, pp.144-161, 2013.
DOI : 10.1093/bib/bbs038

A. R. Quinlan, BEDTools: The Swiss-Army Tool for Genome Feature Analysis, Curr. Protoc. Bioinform, vol.42, pp.11-12, 2014.
DOI : 10.1002/0471250953.bi1112s47

H. Zhao, Z. Sun, J. Wang, H. Huang, J. P. Kocher et al., CrossMap: a versatile tool for coordinate conversion between genome assemblies, Bioinformatics, vol.30, issue.7, pp.1006-1007, 2014.
DOI : 10.1093/bioinformatics/btt730

W. J. Kent, BLAT---The BLAST-Like Alignment Tool, Genome Research, vol.12, issue.4, pp.656-664, 2002.
DOI : 10.1101/gr.229202

J. P. Dadoune, Expression of mammalian spermatozoal nucleoproteins, Microscopy Research and Technique, vol.61, issue.1, pp.56-75, 2003.
DOI : 10.1002/jemt.10317

R. Balhorn, The protamine family of sperm nuclear proteins, Genome Biology, vol.8, issue.9, p.227, 2007.
DOI : 10.1186/gb-2007-8-9-227

C. Trapnell, A. Roberts, L. Goff, G. Pertea, D. Kim et al., Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nature Protocols, vol.7, issue.3, pp.562-578, 2012.
DOI : 10.1038/nbt0710-691