13 papers · ranked by Valyu relevance
Rohan Lowe, Neil Shirley, Mark Bleackley, Stephen Dolan + 1 more
'Thomas Shafee'] Transcriptomics technologies are the techniques used to study an organism’s [transcriptome](), the sum of all of its [RNA transcripts](). The information content of an organism is recorded in the DNA of its [genome]() and [expressed]() through [transcription](). Here, [mRNA]() serves as a transient…
Parul Tyagi, Deeksha Singh, Shivangi Mathur, Ayushi Singh + 1 more
'Rajiv Ranjan'] Transcriptome sequencing or RNA-Sequencing is a high-resolution, sensitive and high-throughput next-generation sequencing (NGS) approach used to study non-model plants and other organisms. In other words, it is an assembly of RNA transcripts from individual or whole samples of functional and…
Tamer Butto, Stefan Pastore, Max Müller, Kaushik Viswanathan Iyer + 6 more
Nanopore technology offers real-time sequencing opportunities, providing rapid access to sequenced data and allowing researchers to manage the sequencing process efficiently, resulting in cost-effective strategies. Here, we present focused case studies demonstrating the versatility of real-time transcriptomics analysis…
Tanner Stokes, Haoning Howard Cen, Philipp Kapranov, Iain J Gallagher + 7 more
'Iain J Gallagher' 'Andrew A. Pitsillides' 'Claude‐Henry Volmar' 'William E Kraus' 'James D. Johnson' 'Stuart M. Phillips' 'Claes Wahlestedt' 'James A. Timmons'] Title: Abstract Sequencing the human genome empowers translational medicine, facilitating transcriptome-wide molecular diagnosis, pathway biology, and drug…
Gabriel Dorado, Sergio Gálvez, Teresa E. Rosales, Víctor F. Vásquez + 1 more
'Pilar Hernández'] Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing…
Adam D Hargreaves, John F Mulley
Portable DNA sequencers such as the Oxford Nanopore MinION device have the potential to be truly disruptive technologies, facilitating new approaches and analyses and, in some cases, taking sequencing out of the lab and into the field. However, the capabilities of these technologies are still being revealed. Here we…
Daniel J. Kliebenstein
Transcriptomics is a major platform to study organismal biology. The advent of new parallel sequencing technologies has opened up a new avenue of transcriptomics with ever deeper and deeper sequencing to identify and quantify each and every transcript in a sample. However, this may not be the best usage of the parallel…
Jonathan S. Abebe, Yasmine Alwie, Erik Fuhrmann, Jonas Leins + 5 more
High-resolution annotations of transcriptomes from all domains of life are essential for many sequencing-based RNA analyses, including Nanopore direct RNA sequencing (DRS), which would otherwise be hindered by misalignments and other analysis artefacts. DRS allows the capture and full-length sequencing of native RNAs…
Wen Jiang, Zhanyong Guo, Nuno Lages, W. Jim Zheng + 3 more
To understand cellular coordination of multiple transcriptome regulation mechanisms, we simultaneously measured three parameters – transcription rate (TR), mRNA abundance (RA) and translation activity (TA) – and assessed mRNA stability with the RA to TR ratio. This revealed multiple quantitative insights. First, the…
Ya-Hui Lin, Jennifer E. Dodd, Luisa Cutillo, Lydia M. Castelli + 14 more
Transcriptomes and translatomes measure genome-wide levels of total and ribosome-associated RNAs. A few hundred translatomes were reported over >250,000 transcriptomes highlighting the challenges of identifying translating RNAs. Here, we used a human isogenic inducible model of TDP-43-linked amyotrophic lateral…
Oskar Bruning, Han Rauwerda, Rob J Dekker, Wim C de Leeuw + 4 more
'Paul F K Wackers' 'Wim A Ensink' 'Martijs J Jonker' 'Timo M Breit'] We have collected several valuable lessons that will help improve transcriptomics experimentation. These lessons relate to experiment design, execution, and analysis. The cautions, but also the pointers, may help biologists avoid common pitfalls in…
Gloria M. Sheynkman, Katharine S. Tuttle, Elizabeth Tseng, Jason G. Underwood + 8 more
Most human protein-coding genes are expressed as multiple isoforms. This in turn greatly expands the functional repertoire of the encoded proteome. While at least one reliable open reading frame (ORF) model has been assigned for every gene, the majority of alternative isoforms remains uncharacterized experimentally.…
Jorge Ruiz-Orera, Pol Verdaguer-Grau, José Luis Villanueva-Cañas, Xavier Messeguer + 1 more
Cells express thousands of transcripts that show weak coding potential. Known as long non-coding RNAs (lncRNAs), they typically contain short open reading frames (ORFs) having no homology with known proteins. Recent studies show that a significant proportion of lncRNAs are translated, challenging the view that they are…