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Protocol for mitochondrial variant enrichment from single-cell RNA sequencing using MAESTER.
STAR Protoc
January 2025
Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA. Electronic address:
Single-cell RNA sequencing (scRNA-seq) enables detailed characterization of cell states but often lacks insights into tissue clonal structures. Here, we present a protocol to probe cell states and clonal information simultaneously by enriching mitochondrial DNA (mtDNA) variants from 3'-barcoded full-length cDNA. We describe steps for input library preparation, mtDNA enrichment, PCR product cleanup, and paired-end sequencing.
View Article and Find Full Text PDFDeciphering mixed infections by plant RNA virus and reconstructing complete genomes simultaneously present within-host.
PLoS One
January 2025
PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France.
Local co-circulation of multiple phylogenetic lineages is particularly likely for rapidly evolving pathogens in the current context of globalisation. When different phylogenetic lineages co-occur in the same fields, they may be simultaneously present in the same host plant (i.e.
View Article and Find Full Text PDFClair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data.
bioRxiv
January 2025
Department of Computer Science, School of Computing and Data Science, University of Hong Kong, Hong Kong, China.
Variant calling using long-read RNA sequencing (lrRNA-seq) can be applied to diverse tasks, such as capturing full-length isoforms and gene expression profiling. It poses challenges, however, due to higher error rates than DNA data, the complexities of transcript diversity, RNA editing events, etc. In this paper, we propose Clair3-RNA, the first deep learning-based variant caller tailored for lrRNA-seq data.
View Article and Find Full Text PDFBrassica rapa receptor-like cytoplasmic kinase BrRLCK1 negatively regulates freezing tolerance in transgenic Arabidopsis via the CBF pathway.
Gene
January 2025
Crop Research Institute, Gansu Academy of Agriculture Sciences, Lanzhou 730070, China.
Some winter rapeseed (Brassica rapa) varieties can endure extremely low temperatures (-20°C to -32°C). However, because of a lack of mutant resources, the molecular mechanisms underlying cold tolerance in B. rapa remain unclear.
View Article and Find Full Text PDFViperin and Its Effect on SVCV Replication in Common Carp, .
Animals (Basel)
January 2025
Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
is an interferon-stimulated gene (ISG) that plays an important role in the congenital antiviral immunity of vertebrates. In this study, the common carp () gene is characterized, and we determine whether it has the ability to inhibit spring viremia of carp virus (SVCV) replication in EPC cells. The results showed that the full-length cDNA of the gene was 1044 bp and it encoded 348 amino acids.
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