Results 1 to 10 of about 1,474,283 (156)

From bulk, single-cell to spatial RNA sequencing

International Journal of Oral Science, 2021
RNA sequencing (RNAseq) can reveal gene fusions, splicing variants, mutations/indels in addition to differential gene expression, thus providing a more complete genetic picture than DNA sequencing.
Xinmin Li, Cun-Yu Wang
doaj   +2 more sources

A gene-specific RNA enrichment protocol for nanopore direct-RNA sequencing. [PDF]

PLoS ONE
Oxford Nanopore direct-RNA sequencing, a third-generation sequencing technology, allows for the analysis of native RNA molecules in their natural cellular state.
Maja Bele Dyrendalsli, Cecilie Løkke, Christer Einvik   +2 more
doaj   +2 more sources

Quantification of substoichiometric modification reveals global tsRNA hypomodification, preferences for angiogenin-mediated tRNA cleavage, and idiosyncratic epitranscriptomes of human neuronal cell-lines

Computational and Structural Biotechnology Journal, 2023
Modification of tRNA is an integral part of the epitranscriptome with a particularly pronounced potential to generate diversity in RNA expression. Eukaryotic tRNA contains modifications in up to 20% of their nucleotides, but not all sites are always ...
Florian Pichot, Marion C. Hogg, Virginie Marchand, Valérie Bourguignon, Elisabeth Jirström, Cliona Farrell, Hesham A. Gibriel, Jochen H.M. Prehn, Yuri Motorin, Mark Helm   +9 more
doaj   +1 more source

Holistic Optimization of Bioinformatic Analysis Pipeline for Detection and Quantification of 2′-O-Methylations in RNA by RiboMethSeq

Frontiers in Genetics, 2020
A major trend in the epitranscriptomics field over the last 5 years has been the high-throughput analysis of RNA modifications by a combination of specific chemical treatment(s), followed by library preparation and deep sequencing.
Florian Pichot, Florian Pichot, Florian Pichot, Virginie Marchand, Lilia Ayadi, Lilia Ayadi, Valérie Bourguignon-Igel, Valérie Bourguignon-Igel, Mark Helm, Yuri Motorin, Yuri Motorin   +10 more
doaj   +1 more source

Advances in Non-Coding RNA Sequencing

Non-Coding RNA, 2021
Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules. Since the discovery of the first ncRNA in the 1960s, ncRNAs have been shown to be involved in nearly all steps of the central dogma of molecular biology.
Julia Micheel, Aram Safrastyan, Damian Wollny   +2 more
doaj   +1 more source

Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees. [PDF]

, 2014
BackgroundOne of the great advantages of next generation sequencing is the ability to generate large genomic datasets for virtually all species, including non-model organisms.
Filkov, Vladimir, Groover, Andrew, Liu, Lijun, Missirian, Victor, Zinkgraf, Matthew   +4 more
core   +5 more sources

On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments [PDF]

, 2020
Background: In gene expression studies, RNA sample pooling is sometimes considered because of budget constraints or lack of sufficient input material. Using microarray technology, RNA sample pooling strategies have been reported to optimize both the cost
Assefa, Alemu Takele, Thas, Olivier, Vandesompele, Jo   +2 more
core   +2 more sources

HCC: RNA-Sequencing in Cirrhosis

Biomolecules, 2023
Hepatocellular carcinoma (HCC) ranks the most common types of cancer worldwide. As the fourth leading cause of cancer-related deaths, its prognosis remains poor. Most patients developed HCC on the basis of chronic liver disease. Cirrhosis is an important
Haoyu Wang, Wenjie Shi, Jing Lu, Yuan Liu, Wei Zhou, Zekun Yu, Shengying Qin, Junwei Fan   +7 more
doaj   +1 more source

Utility of nanopore sequencing for detecting pathogens in bronchoalveolar lavage fluid from pediatric patients with respiratory failure

Journal of Clinical Virology Plus, 2023
RNA viruses are the most frequent pathogens responsible for respiratory infections, particularly in pediatric patients. Next-generation sequencing, represented by Illumina sequencing, is one of the most comprehensive methods for identifying pathogens ...
Makoto Yamaguchi, Kazuhiro Horiba, Kazunori Haruta, Suguru Takeuchi, Takako Suzuki, Yuka Torii, Shinji Kawabe, Sho Wada, Takanari Ikeyama, Yoshinori Ito, Tomoo Ogi, Jun-ichi Kawada   +11 more
doaj   +1 more source

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