Archived formalin-fixed and paraffin-embedded (FFPE) heart tissue from autopsied individuals represents an important resource for investigating the DNA methylation of heart tissue of deceased individuals. The DNA quality of FFPE tissue from autopsies may be decreased, affecting the DNA methylation measurements. Therefore, inexpensive screening methods for estimating DNA quality are valuable. We investigated the correlation between the DNA quality of archived FFPE heart tissue examined with the Illumina Infinium HD FFPE QC assay (Infinium QC) and Thermo Fisher's Quantifiler Trio DNA Quantification kit (QuantifilerTrio), respectively, and the amount of usable DNA methylation data as measured by the probe detection rate (probe DR) obtained with the Illumina Infinium MethylationEPIC array. We observed a high correlation (r = 0.75; p < 10) between the QuantifilerTrio degradation index, DI, and the amount of usable DNA methylation data analysed with SeSAMe, whereas a much weaker correlation was observed between the Infinium QC and SeSAMe probe DR (r = 0.17; p < 0.05). Based on the results, QuantifilerTrio DI seems to predict the proportion of usable DNA methylation data analysed with the Illumina Infinium MethylationEPIC array and SeSAMe by a linear model: SeSAMe probe DR = 0.80-log(DI) × 0.25.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9898234 | PMC |
| http://dx.doi.org/10.1038/s41598-023-29120-y | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Efficient and Rapid Enrichment of Extracellular Vesicles Using DNA Nanotechnology-Enabled Synthetic Nano-Glue.
Anal Chem
January 2025
The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China.
Swift and efficient enrichment and isolation of extracellular vesicles (EVs) are crucial for enhancing precise disease diagnostics and therapeutic strategies, as well as elucidating the complex biological roles of EVs. Conventional methods of isolating EVs are often marred by lengthy and laborious processes. In this study, we introduce an innovative approach to enrich and isolate EVs by leveraging the capabilities of DNA nanotechnology.
View Article and Find Full Text PDFCritical considerations and computational tools in plant genome editing.
Heliyon
January 2025
Biotechnology Unit, ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, West Bengal, 700121, India.
Recent advances in genome editing tools and CRISPR-Cas technologies have enabled plant genome engineering reach new heights. The current regulatory exemptions for certain categories of genome edited products, such as those derived from SDN-1 and SDN-2, which are free of any transgene, have significantly accelerated genome editing research in a number of agricultural crop plants in different countries. Although CRISPR-Cas technology is becoming increasingly popular, it is still important to carefully consider a number of factors before planning and carrying conducting CRISPR-Cas studies.
View Article and Find Full Text PDFShort and long-term effects of experimental varicocele.
Andrology
January 2025
Department of Surgery, Division of Urology, Human Reproduction Section, São Paulo Federal University, São Paulo, Brazil.
Background: Varicocele is associated with a progressive decrease in male fertile potential, but it has yet to be determined if the duration of varicocele is associated with altered sperm functional quality.
Objectives: This experimental study investigated the time-dependent effects of varicocele on spermatogenesis, sperm parameters, and sperm functional traits.
Materials And Methods: Thirty-five mature male Wistar rats (200 ± 25 g) were included.
[Development of DNA molecular identity cards for germplasm of Murraya paniculata based on SSR markers].
Zhongguo Zhong Yao Za Zhi
December 2024
Experimental Research Center,China Academy of Chinese Medical Sciences Beijing 100700, China.
To promote the conservation and utilization of the germplasm resources and provide a basis for the breeding of new varieties of Murraya paniculata, this study analyzed the genetic diversity of the germplasm resources and developed the molecular identity(ID) card of M. paniculata. Multiple fluorescence PCR-capillary electrophoresis was performed for 65 germplasm accessions of M.
View Article and Find Full Text PDF[Molecular authentication of calcined oyster (Ostrea gigas) and its processed products].
Zhongguo Zhong Yao Za Zhi
December 2024
Experimental Research Center, China Academy of Chinese Medical Sciences Beijing 100700, China.
Calcined oyster is a commonly used shellfish traditional Chinese medicine in clinical practice in China. During the processing of oysters, their microscopic characteristics are destroyed, and open-fire calcination can damage the DNA of oysters, making it difficult to identify the primary source. The establishment of a specific polymerase chain reaction(PCR) method for the identification of calcined oysters can provide a guarantee for the safety and clinical efficacy of the medicine and its processed products.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!