Project description:Single-cell transcriptomics, reliant on the incorporation of barcodes and unique molecular identifiers (UMIs) into captured polyA+ mRNA, faces a significant challenge due to synthesis errors in oligonucleotide capture sequences. These inaccuracies, which are especially problematic in long-read sequencing, impair the precise identification of sequences and result in inaccuracies in UMI deduplication. To mitigate this issue, we have modified the oligonucleotide capture design, which integrates an interposed anchor between the barcode and UMI, and a 'V' base anchor adjacent to the polyA capture region. This configuration is devised to ensure compatibility with both short and long-read sequencing technologies, facilitating improved UMI recovery and enhanced feature detection, thereby improving the efficacy of droplet-based sequencing methods.
Project description:Aging and COVID-19 are known to influence DNA methylation, potentially affecting the rate of aging and the risk of disease. The physiological functions of 54 volunteers—including maximal oxygen uptake (VO₂ max), grip strength, and vertical jump—were assessed just before the COVID-19 pandemic and again three years later. Of these volunteers, 27 had contracted COVID-19. Eight epigenetic clocks were used to assess the rate of aging during the three-year period: DNAmAge showed accelerated aging and five clocks showed slowed aging (DNAmAgeSkinBlood, DNAmAgeHannum, DNAmFitAge, PhenoAge, and DNAmTL). When we considered only females, we observed a stronger effect in the increase of DNAmAge acceleration, while we observed slowed aging in the case of SkinBloodClock, and DNAmTL. The methylation of the promoter region of the H1FNT genes, which encodes testis-specific histone H1 family member N (H1fnt) and plays a crucial role in spermatogenesis decreased the most significantly. In contrast, the promoter of CSTL1, which encodes Cystatin-like 1, showed the most significant increase. We found that having COVID-19 during the 3-year study period significantly increased the progress of aging assessed by DNAmGrimAge, DNAmGrimAge2, and DNAmFitAge (p=0.024, 0.047, 0.032, respectively after we adjusted the analysis for baseline variables). The data suggest that COVID-19 may have a mild long-term effect on epigenetic aging.
Project description:Glycoarrays are used to identify differences in the expression of enzymes involved in gag synthesis and degradation in cartilage aging and arthritis. This experiment includes 3 samples from donors with and without growth factor stimulation. Samples are from human biopsy/necropsy origin. Human knee chondrocytes were grown in monolayer culture from 3 donors unstimulated or stimulated with TGFß1 (10ng/ml) for 6 hours.