Transcript abundance of equine spermatozoa
Ontology highlight
ABSTRACT:
ORGANISM(S): Equus caballus
PROVIDER: GSE75350 | GEO | 2016/11/01
SECONDARY ACCESSION(S): PRJNA303992
REPOSITORIES: GEO
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2015-04-01 | GSE61984 | GEO
Project description:MicroRNAs (miRNAs) are involved in nearly every biological process examined to date. Mounting evidence show that some spermatozoa specific miRNAs play important roles in the regulation of spermatogenesis and germ cells development, but little is known of the exact identity and function of miRNA in sperm cells or their potential involvement in spermatogenesis and germ cells development. Here, we investigated the spermatozoa miRNA profiles using illumina deep sequencing combined with bioinformatic analysis using zebrafish as a model system. Deep sequencing of small RNAs yielded 12 million raw reads from zebrafish spermatozoa. Analysis showed that the noncoding RNA of the spermatozoa included tRNA, rRNA, snRNA, snoRNA and miRNA. By mapping to the zebrafish genome, we identified 400 novel and 204 conserved miRNAs which could be grouped into 104 families, including zebrafish specific families, such as mir-731, mir-724, mir-725, mir-729 and mir-2185. We report the first characterization of the miRNAs profiling in zebrafish spermatozoa. The obtained spermatozoa miRNAs profiling will serve as valuable resources to systematically study spermatogenesis in fish and vertebrate. Examination of small RNA populations in zebrafish spermatozoa
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Project description:We reported RNA profiles of mice spermatozoa, a total of 35,288,825 reads matching 33,039 transcripts, including 27,310 coding transcripts, were obtained. RNA profiles of the spermatozoa of 9-10 weeks adult mice were sequenced by RNA-seq,using Illumina GAIIx.
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Project description:Proteins play an important role in many reproductive functions such as sperm maturation and physiology, sperm transit in the female genital tract or sperm-oocyte interaction. However, little information concerning reproductive features is available in the case of aquatic animals. The present study aims to characterize the proteome of both spermatozoa and seminal plasma of bottlenose dolphins (Tursiops truncatus) as a model organism for cetaceans. Ejaculate samples were obtained voluntarily from two trained dolphins housed in an aquarium. Spermatozoa and seminal plasma were analyzed by means of proteomic analyses using a LC-MS/MS and a list with the gene symbols corresponding to each protein was submitted to DAVID database. A total of 423 and 307 proteins were identified in spermatozoa and seminal plasma, respectively, and the samples shared 111 proteins. Furthermore, 70 proteins were identified as involved in reproductive processes, 39 in spermatozoa, and 31 in seminal plasma. The top-5 most abundant proteins were also identified in these samples: AKAP3, ODF2, TUBB, GST3, ROPN1 for spermatozoa and CST11, LTF, ALB, HSP90B1, PIGR for seminal plasma. In conclusion, this proteomic study provides the first characterization of proteomic expression patterns in cetacean sperm and seminal plasma, opening a window to future research on the discovery of biomarkers, analysis of conservation capacity or additional applications in the field of assisted reproduction technologies.
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Project description:Genome-wide DNA methylation profile of human spermatozoa using the meDIP technique and massively parallel sequencing. DNA methylation is an indispensible epigenetic modification required for regulating the expression of mammalian genomes. Immunoprecipitation-based methods for DNA methylome analysis are rapidly shifting the bottleneck in this field from data generation to data analysis, necessitating the development of better analytical tools. In particular, an inability to estimate absolute methylation levels remains a major analytical difficulty associated with immunoprecipitation-based DNA methylation profiling. To address this issue, we developed a cross-platform algorithm-Bayesian tool for methylation analysis (Batman)-for analyzing methylated DNA immunoprecipitation (MeDIP) profiles generated using oligonucleotide arrays (MeDIP-chip) or next-generation sequencing (MeDIP-seq). We developed the latter approach to provide a high-resolution whole-genome DNA methylation profile (DNA methylome) of a mammalian genome. Strong correlation of our data, obtained using mature human spermatozoa, with those obtained using bisulfite sequencing suggest that combining MeDIP-seq or MeDIP-chip with Batman provides a robust, quantitative and cost-effective functional genomic strategy for elucidating the function of DNA methylation. ArrayExpress Release Date: 2008-06-10 Publication Title: A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis Publication Author List: Thomas A Down; Vardhman K Rakyan; Daniel J Turner; Paul Flicek; Heng Li; Eugene Kulesha; Stefan Gräf; Nathan Johnson; Javier Herrero; Eleni M Tomazou; Natalie P Thorne; Liselotte Bäckdahl; Marlis Herberth; Kevin L Howe; David K Jackson; Marcos M Miretti; John C Marioni; Ewan Birney; Tim J P Hubbard; Richard Durbin; Simon Tavaré; Stephan Beck Person Roles: submitter; investigator Person Last Name: Flicek Person First Name: Paul Person Mid Initial Person Email: flicek@ebi.ac.uk Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Person Affiliation: European Bioinformatics Institute
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