Results 21 to 30 of about 721,346 (281)

Direct RNA sequencing [PDF]

Nature, 2009
Our understanding of human biology and disease is ultimately dependent on a complete understanding of the genome and its functions. The recent application of microarray and sequencing technologies to transcriptomics has changed the simplistic view of transcriptomes to a more complicated view of genome-wide transcription where a large fraction of ...
Fatih, Ozsolak, Adam R, Platt, Dan R, Jones, Jeffrey G, Reifenberger, Lauryn E, Sass, Peter, McInerney, John F, Thompson, Jayson, Bowers, Mirna, Jarosz, Patrice M, Milos   +9 more
openaire   +3 more sources

Native RNA or cDNA Sequencing for Transcriptomic Analysis: A Case Study on Saccharomyces cerevisiae

Frontiers in Bioengineering and Biotechnology, 2022
Direct sequencing of single molecules through nanopores allows for accurate quantification and full-length characterization of native RNA or complementary DNA (cDNA) without amplification.
Thidathip Wongsurawat, Piroon Jenjaroenpun, Visanu Wanchai, Intawat Nookaew   +3 more
doaj   +1 more source

RNA sequencing by direct tagmentation of RNA/DNA hybrids [PDF]

Proceedings of the National Academy of Sciences, 2019
Transcriptome profiling by RNA sequencing (RNA-seq) has been widely used to characterize cellular status, but it relies on second-strand complementary DNA (cDNA) synthesis to generate initial material for library preparation. Here we use bacterial transposase Tn5, which has been increasingly used in various high-throughput DNA analyses, to construct ...
Lin Di, Yusi Fu, Yue Sun, Jie Li, Lu Liu, Jiacheng Yao, Guanbo Wang, Yalei Wu, Kaiqin Lao, Raymond W. Lee, Genhua Zheng, Jun Xu, Juntaek Oh, Dong Wang, X. Sunney Xie, Yanyi Huang, Jianbin Wang   +16 more
openaire   +4 more sources

Adaptive sampling for nanopore direct RNA-sequencing

RNA, 2023
Nanopore long-read sequencing enables real-time monitoring and controlling of individual nanopores. This allows us to enrich or deplete specific sequences in DNA sequencing in a process called “adaptive sampling.” So far, adaptive sampling (AS) was not applicable to the direct sequencing of RNA.
Naarmann-de Vries, Isabel S., Gjerga, Enio, Gandor, Catharina L.A., Dieterich, Christoph   +3 more
openaire   +2 more sources

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification [PDF]

, 2020
Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. We adapted nanopore direct RNA sequencing to examine RNA from a wild-type accession of the model plant Arabidopsis thaliana and a ...
Barton, Geoffrey J., Gould, Peter D., Hall, Anthony J. W., Knop, Katarzyna, Mackinnon, Katarzyna, Parker, Matthew T., Schurch, Nicholas J., Sherwood, Anna V., Simpson, Gordon G.   +8 more
core   +3 more sources

The microglial sensome revealed by direct RNA sequencing [PDF]

Nature Neuroscience, 2013
Microglia, the principal neuroimmune sentinels of the brain, continuously sense changes in their environment and respond to invading pathogens, toxins and cellular debris. Microglia exhibit plasticity and can assume neurotoxic or neuroprotective priming states that determine their responses to danger.
Hickman, Suzanne E., Ohsumi, Toshiro, Wang, Li-chong, Kingery, Nathan D., Borowsky, Mark L, Means, Terry K., Khoury, Joseph   +6 more
openaire   +3 more sources

Pervasive effects of RNA degradation on Nanopore direct RNA sequencing

NAR Genomics and Bioinformatics, 2022
Abstract Oxford Nanopore direct RNA sequencing (DRS) is capable of sequencing complete RNA molecules and accurately measuring gene and isoform expression. However, as DRS is designed to profile intact RNA, expression quantification may be more heavily dependent upon RNA integrity than alternative RNA sequencing methodologies.
Yair D J Prawer, Josie Gleeson, Ricardo De Paoli-Iseppi, Michael B Clark   +3 more
openaire   +3 more sources

Determining the Suitability of MinION’s Direct RNA and DNA Amplicon Sequencing for Viral Subtype Identification

Viruses, 2020
The MinION sequencer is increasingly being used for the detection and outbreak surveillance of pathogens due to its rapid throughput. For RNA viruses, MinION’s new direct RNA sequencing is the next significant development.
Deborah M. Leigh, Christopher Schefer, Carolina Cornejo   +2 more
doaj   +1 more source

Epidermal Growth Factor Receptor Mutation and Anaplastic Lymphoma Kinase Gene Fusion: Detection in Malignant Pleural Effusion by RNA or PNA Analysis. [PDF]

PLoS ONE, 2016
Analyzing EGFR mutations and detecting ALK gene fusion are indispensable when planning to treat pulmonary adenocarcinoma. Malignant pleural effusion (MPE) is a devastating complication of lung cancer and sometimes the only source for mutation analysis ...
Yi-Lin Chen, Chung-Ta Lee, Cheng-Chan Lu, Shu-Ching Yang, Wan-Li Chen, Yang-Cheng Lee, Chung-Hsien Yang, Shu-Ling Peng, Wu-Chou Su, Nan-Haw Chow, Chung-Liang Ho   +10 more
doaj   +1 more source

Systematic Comparison of Nanopore and Illumina Sequencing for the Detection of Plant Viruses and Viroids Using Total RNA Sequencing Approach

Frontiers in Microbiology, 2022
High-throughput sequencing (HTS) has become an important tool for plant virus detection and discovery. Nanopore sequencing has been rapidly developing in the recent years and offers new possibilities for fast diagnostic applications of HTS.
Anja Pecman, Anja Pecman, Ian Adams, Ion Gutiérrez-Aguirre, Adrian Fox, Neil Boonham, Maja Ravnikar, Denis Kutnjak   +7 more
doaj   +1 more source