Beyond the Linear Genome: Paired-End Sequencing as a Biophysical Tool.

Trends Cell Biol

Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA. Electronic address:

Published: December 2015

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.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5540433PMC
http://dx.doi.org/10.1016/j.tcb.2015.08.004DOI Listing

Publication Analysis

Top Keywords

paired-end sequencing
8
linear genome
4
genome paired-end
4
sequencing biophysical
4
biophysical tool
4
tool paired-end
4
sequencing enabled
4
enabled variety
4
variety methods
4
methods high-throughput
4

Similar Publications

Deciphering the complex molecular architecture of the genetically modified soybean FG72 through paired-end whole genome sequencing.

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 PDF

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 PDF

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 PDF

Draft genome sequence of sp. SA01 isolated from seedlings collected in Cape Cod (USA).

Microbiol 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 PDF

Sexual dimorphism in lung transcriptomic adaptations in fetal alcohol spectrum disorders.

Respir 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.

View Article and Find Full Text PDF

Want 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!