Long and ultra-long read DNA sequencing technologies require high molecular weight DNA with high quality and sufficient quantity, which could be challenging to obtain from recalcitrant plant tissues. We describe a protocol to isolate ultra-long DNA from 12 species for ultra-long read genome sequencing. A suitable nuclei lysis buffer is critical for DNA quality and yield. This protocol will enable individual labs to isolate high molecular weight DNA at a rapid pace with low cost from a variety of plant species. For complete information on the use and execution of this protocol, please refer to: Zhang et al. (2020).
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http://dx.doi.org/10.1016/j.xpro.2021.100343 | DOI Listing |
DNA Repair (Amst)
January 2025
School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel; Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel; Department of Biomedical Engineering, Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel. Electronic address:
Quantitative genomic mapping of DNA damage may provide insights into the underlying mechanisms of damage and repair. Sequencing based approaches are bound to the limitations of PCR amplification bias and read length which hamper both the accurate quantitation of damage events and the ability to map them to structurally complex genomic regions. Optical Genome mapping in arrays of parallel nanochannels allows physical extension and genetic profiling of millions of long genomic DNA fragments, and has matured to clinical utility for characterization of complex structural aberrations in cancer genomes.
View Article and Find Full Text PDFEpigenetics Chromatin
December 2024
Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.
DNA methylation is an essential epigenetic mechanism for regulation of gene expression, through which many physiological (X-chromosome inactivation, genetic imprinting, chromatin structure and miRNA regulation, genome defense, silencing of transposable elements) and pathological processes (cancer and repetitive sequences-associated diseases) are regulated. Nanopore sequencing has emerged as a novel technique that can analyze long strands of DNA (long-read sequencing) without chemically treating the DNA. Interestingly, nanopore sequencing can also extract epigenetic status of the nucleotides (including both 5-Methylcytosine and 5-hydroxyMethylcytosine), and a large variety of bioinformatic tools have been developed for improving its detection properties.
View Article and Find Full Text PDFGenome Biol
December 2024
Laboratory of Human Genomics, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
PeerJ Comput Sci
July 2024
Department of Electronic Engineering, Information School, Yunnan University, Kunming, Yunnan, China.
Long reads generated by third-generation sequencing (3GS) technologies are involved in many biological analyses and play a vital role due to their ultra-long read length. However, the high error rate affects the downstream process. DeepCorr, a novel error correction algorithm for data from both PacBio and ONT platforms based on deep learning is proposed.
View Article and Find Full Text PDFGenet Med Open
January 2024
Department of Genetics, Harvard Medical School, Boston, MA.
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