The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community

We report the development of the ReproGenomics Viewer (RGV), a multi- and cross-species working environment for the visualization, mining and comparison of published omics data sets for the reproductive science community. The system currently embeds 15 published data sets related to gametogenesis from nine model organisms. Data sets have been curated and conveniently organized into broad categories including biological topics, technologies, species and publications. RGV's modular design for both organisms and genomic tools enables users to upload and compare their data with that from the data sets embedded in the system in a cross-species manner. The RGV is freely available at http://rgv.genouest.org.

[1]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[2]  Mia Yang Ang,et al.  StaphyloBase: a specialized genomic resource for the staphylococcal research community , 2014, Database J. Biol. Databases Curation.

[3]  J. Dadoune Expression of mammalian spermatozoal nucleoproteins , 2003, Microscopy research and technique.

[4]  Rami Rauch,et al.  Ovarian Kaleidoscope Database: Ten Years and Beyond1 , 2012, Biology of reproduction.

[5]  M. Primig,et al.  High-Resolution Profiling of Novel Transcribed Regions During Rat Spermatogenesis1 , 2014, Biology of reproduction.

[6]  Antoine H. F. M. Peters,et al.  Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa , 2010, Nature Structural &Molecular Biology.

[7]  Hamed Heydari,et al.  MabsBase: A Mycobacterium abscessus Genome and Annotation Database , 2013, PloS one.

[8]  Frédéric Chalmel,et al.  GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle , 2010, Database J. Biol. Databases Curation.

[9]  Frédéric Chalmel,et al.  Forty-Four Novel Protein-Coding Loci Discovered Using a Proteomics Informed by Transcriptomics (PIT) Approach in Rat Male Germ Cells1 , 2014, Biology of reproduction.

[10]  Maureen J Donlin,et al.  Using the Generic Genome Browser (GBrowse) , 2007, Current protocols in bioinformatics.

[11]  Saher Sue Hammoud,et al.  Chromatin and transcription transitions of mammalian adult germline stem cells and spermatogenesis. , 2014, Cell stem cell.

[12]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.

[13]  J. Toppari,et al.  An atlas of chromatoid body components , 2014, RNA.

[14]  C. Pineau,et al.  Testicular development and spermatogenesis: harvesting the postgenomics bounty. , 2008, Advances in experimental medicine and biology.

[15]  Jun Zhu,et al.  SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining , 2012, Nucleic Acids Res..

[16]  Rod Balhorn,et al.  The protamine family of sperm nuclear proteins , 2007, Genome Biology.

[17]  Mia Yang Ang,et al.  VibrioBase: A Model for Next-Generation Genome and Annotation Database Development , 2014, TheScientificWorldJournal.

[18]  Michael Hackenberg,et al.  NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes , 2013, Nucleic Acids Res..

[19]  D. Wolgemuth,et al.  Bromodomain‐dependent stage‐specific male genome programming by Brdt , 2012, The EMBO journal.

[20]  David Haussler,et al.  The UCSC genome browser and associated tools , 2012, Briefings Bioinform..

[21]  L. Stein,et al.  JBrowse: a next-generation genome browser. , 2009, Genome research.

[22]  L. Steinmetz,et al.  Bidirectional promoters generate pervasive transcription in yeast , 2009, Nature.

[23]  C. Pineau,et al.  Testicular postgenomics: targeting the regulation of spermatogenesis , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

[24]  Daniel J. Blankenberg,et al.  Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists , 2010, Current protocols in molecular biology.

[25]  Peggy Hall,et al.  The NHGRI GWAS Catalog, a curated resource of SNP-trait associations , 2013, Nucleic Acids Res..

[26]  Ge Gao,et al.  A brief introduction to web-based genome browsers , 2013, Briefings Bioinform..

[27]  Frédéric Chalmel,et al.  Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6 , 2010, Proceedings of the National Academy of Sciences.

[28]  Owen M. Rennert,et al.  GermSAGE: a comprehensive SAGE database for transcript discovery on male germ cell development , 2008, Nucleic Acids Res..

[29]  Larry N. Singh,et al.  Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes. , 2012, American journal of human genetics.

[30]  Jing Wang,et al.  CrossMap: a versatile tool for coordinate conversion between genome assemblies , 2014, Bioinform..

[31]  Sean R. Davis,et al.  NCBI GEO: archive for functional genomics data sets—update , 2012, Nucleic Acids Res..

[32]  Mia Yang Ang,et al.  HelicoBase: a Helicobacter genomic resource and analysis platform , 2014, BMC Genomics.

[33]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[34]  Michael Hackenberg,et al.  NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data , 2010, Nucleic Acids Res..

[35]  C. Pineau,et al.  Direct Iterative Protein Profiling (DIPP) - an Innovative Method for Large-scale Protein Detection Applied to Budding Yeast Mitosis* , 2011, Molecular & Cellular Proteomics.

[36]  Ivan Merelli,et al.  High-Performance Computing and Big Data in Omics-Based Medicine , 2014, BioMed research international.

[37]  Anton Nekrutenko,et al.  NGS analyses by visualization with Trackster , 2012, Nature Biotechnology.

[38]  Daniel J. Blankenberg,et al.  Galaxy: a platform for interactive large-scale genome analysis. , 2005, Genome research.

[39]  Zhiping Weng,et al.  An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes. , 2013, Molecular cell.

[40]  A. Quinlan BEDTools: The Swiss‐Army Tool for Genome Feature Analysis , 2014, Current protocols in bioinformatics.

[41]  A. Gyenesei,et al.  Transcriptome Profiling of the Murine Testis during the First Wave of Spermatogenesis , 2013, PloS one.

[42]  Richard Baldock,et al.  Access and use of the GUDMAP database of genitourinary development. , 2012, Methods in molecular biology.

[43]  Matthew E Ritchie,et al.  High-resolution transcription atlas of the mitotic cell cycle in budding yeast , 2010, Genome Biology.

[44]  Frank Grützner,et al.  The evolution of lncRNA repertoires and expression patterns in tetrapods , 2014, Nature.

[45]  Owen M. Rennert,et al.  GonadSAGE: a comprehensive SAGE database for transcript discovery on male embryonic gonad development , 2010, Bioinform..

[46]  Kevin Brick,et al.  Genetic recombination is directed away from functional genomic elements in mice , 2012, Nature.

[47]  D. Karolchik,et al.  The UCSC Genome Browser database: 2016 update , 2015, bioRxiv.

[48]  Antoine H. F. M. Peters,et al.  Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa , 2013, Nature Structural &Molecular Biology.

[49]  F. Tang,et al.  Dynamics of 5-hydroxymethylcytosine during mouse spermatogenesis , 2013, Nature Communications.

[50]  T. Mikkelsen,et al.  Cellular source and mechanisms of high transcriptome complexity in the mammalian testis. , 2013, Cell reports.