Project description:We investigated the transcriptome obtained from microarray analysis of human ejaculates used in an IVF programme. The gene expression profiles are to be correlated with successful/failed induction of oocyte fertilisation and/or pregnancy. Since human ejaculates are often contaminated with so-called 'round cells' (mostly somatic cells such as leukocytes and macrophages, but also immature germ cells), a considerable part of the gene expression pertains not to spermatozoa. Rigorous statistical analysis of the data is to be used to extract genes that correlate with fertilization success. A set of 25 human ejaculates (12 pregnancy; 3 biochemical pregnancy; 7 oocyte fertilization; 3 no oocyte fertilization) from an IVF procedure were used for RNA extraction and microarray hybridization.
Project description:We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3’ and/or 5’ end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5’ differences and in support of this we report that a 5’ isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis of miRBase shows that 5’ isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes
Project description:We investigated the transcriptome obtained from microarray analysis of human ejaculates used in an IVF programme. The gene expression profiles are to be correlated with successful/failed induction of oocyte fertilisation and/or pregnancy. Since human ejaculates are often contaminated with so-called 'round cells' (mostly somatic cells such as leukocytes and macrophages, but also immature germ cells), a considerable part of the gene expression pertains not to spermatozoa. Rigorous statistical analysis of the data is to be used to extract genes that correlate with fertilization success.
Project description:Transcriptomic profiling of granulosa and cumulus cells for prediction of successful embryo implantation in human in-vitro fertilization procedures
Project description:Single-nucleus RNA sequencing (snRNA-seq) was used to profile the transcriptome of 16,015 nuclei in human adult testis. This dataset includes five samples from two different individuals. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.
