Project description:Accessing endometrial tissue during the early phases of the menstrual cycle is challenging. With this experiment we are capturing the dynamic epithelial cell states after breakdown using endometrial organoids (EOs) subjected to the in vitro menstrual cycle (IVMC) protocol. EOs are collected for scRNAseq analysis before breakdown (Hormonal Withdrawal 48h), 12h after breakdown (Post-breakdown 12h), 24h after breakdown (Post-breakdown 24h), 48h after breakdown (Post-breakdown 48h) as well as 24h (E2 differentiation 24h) and 48h after estrogen treatment (E2 differentiation 48h).
Project description:Six independent endometrial organoid cultures were subjected to the in vitro menstrual cycle protocol (IVMC), which recapitulates the events of differentiation, hormonal withdrawal, breakdown, repair and regeneration. Samples were collected at various timepoints (Pre-diff, P4-diff, Horm Withdr 24h, Horm Withdr 48h, Repair 24h, E2-diff 24h, E2-diff 48h) and analysed with bulk RNAseq to validate the protocol and investigate the dynamic transcriptomic changes across timepoints.
Project description:Asthma is a chronic inflammatory airway disease characterized by airway inflammation and remodeling. The role of 15-oxo-5Z,8Z,11Z,13E-eicosatetraenoic acid (15-oxoETE), a 15-HETE metabolite catalyzed by 15-prostaglandin dehydrogenase (15-PGDH), has been relatively unexplored in asthma. In this study, we used RNA-seq to explore the effect of 15-KETE on the transcriptome of airway epithelial cells, aiming to identify its potential downstream targets and mechanisms of action.
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:Gene expression profiling of immortalized human mesenchymal stem cells with hTERT/E6/E7 transfected MSCs. hTERT may change gene expression in MSCs. Goal was to determine the gene expressions of immortalized MSCs.
Project description:Gene methylation profiling of immortalized human mesenchymal stem cells comparing HPV E6/E7-transfected MSCs cells with human telomerase reverse transcriptase (hTERT)- and HPV E6/E7-transfected MSCs. hTERT may increase gene methylation in MSCs. Goal was to determine the effects of different transfected genes on global gene methylation in MSCs.
