Paired-end sequencing has enabled a variety of new methods for high-throughput interrogation of both genome structure and chromatin architecture. Here, we discuss how the paired-end paradigm can be used to interpret sequencing data as biophysical measurements of in vivo chromatin structure that report on single molecules in single cells.
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http://dx.doi.org/10.1016/j.tcb.2015.08.004 | DOI Listing |
Food Chem (Oxf)
June 2025
Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China.
The clear molecular characterization of genetically modified (GM) plants and animals is a prerequisite for obtaining regulatory approval and safety certification for commercial cultivation. This characterization includes the identification of the transferred DNA (T-DNA) insertion site, its flanking sequences, the copy number of inserted genes, and the detection of any unintended genomic alterations accompanying the transformation process. In this study, we performed a comprehensive molecular characterization of the well-known GM soybean event FG72 using paired-end whole-genome sequencing (PE-WGS).
View Article and Find Full Text PDFSTAR 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 PDFFront Parasitol
April 2024
Centre for Malaria Elimination, Institute of Tropical Medicine, Mount Kenya University, Thika, Kenya.
The Circumsporozoite Protein (PfCSP) has been used in developing the RTS,S, and R21 malaria vaccines. However, genetic polymorphisms within compromise the effectiveness of the vaccine. Thus, it is essential to continuously assess the genetic diversity of , especially when deploying it across different geographical regions.
View Article and Find Full Text PDFMicrobiol Resour Announc
January 2025
The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA.
A draft genome was generated for a strain of closely related to sp. ENV421 isolated from plants of smooth cordgrass germinated from seeds collected in a salt marsh in Cape Cod (USA). Genomic DNA was sequenced using paired-end Illumina technologies.
View Article and Find Full Text PDFRespir Res
January 2025
Department of Obstetrics and Gynecology, C.S. Mott Center for Human Growth and Development, School of Medicine, Wayne State University, 275 E Hancock St, Rm 195, Detroit, MI, 48201, USA.
Current fetal alcohol spectrum disorders (FASD) studies primarily focus on alcohol's actions on the fetal brain although respiratory infections are a leading cause of morbidity/mortality in newborns. The limited studies examining the pulmonary adaptations in FASD demonstrate decreased surfactant protein A and alveolar macrophage phagocytosis, impaired differentiation, and increased risk of Group B streptococcal pneumonia with no study examining sexual dimorphism in adaptations. We hypothesized that developmental alcohol exposure in pregnancy will lead to sexually dimorphic fetal lung morphological and immune adaptations.
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