Results 41 to 50 of about 721,346 (281)

Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice

Genomics, Proteomics & Bioinformatics, 2023
Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic studies. However, the cDNA dependence of most RNA sequencing techniques constrains their ability to detect base modifications on ...
Feng Yu, Huanhuan Qi, Li Gao, Sen Luo, Rebecca Njeri Damaris, Yinggen Ke, Wenhua Wu, Pingfang Yang   +7 more
doaj   +1 more source

CircRM: profiling circular RNA modifications from nanopore direct RNA sequencing. [PDF]

Brief Bioinform
Abstract Circular RNA (circRNA) represents a critical class of regulatory RNAs with distinctive structural and functional features. The functions of circRNAs are modulated by various RNA modifications. Here, we present CircRM, a nanopore direct RNA sequencing-based computational method for profiling RNA modifications in circRNAs at ...
Li J, Chen S, Wu Z, Wang H, Xia R, Meng J, Zhang Y.   +6 more
europepmc   +4 more sources

Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-seq and ESTs [PDF]

, 2013
The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct annotation is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped ...
A Derti, A Dobin, A Sherstnev, AI Reid, Alexander Sherstnev, B Langmead, BJ Haas, BJ Haas, BS Yoon, C Burge, C Cole, C Luo, C Trapnell, CE Joyce, CH Jan, Christian Cole, Céline Duc, D Brawand, DM Church, F Ozsolak, F Ozsolak, F Ozsolak, Geoffrey J. Barton, Gordon G. Simpson, H Stroud, H Zou, HK Saini, I Ulitsky, J Bracht, J Harrow, JE Collins, JH Yang, Junfang Song, Kate G. Storey, L Jiang, M Fujii, M Garber, M Yandell, MB Gerstein, Nicholas J. Schurch, P Lamesch, PE Boardman, Sara J. Brown, T Pelissier, Thomas Preiss, TS Becker, V Curwen, V Hamburger, W. H. Irwin McLean, X Cai, Y Kurihara, Y Lee, Z Moqtaderi   +52 more
core   +5 more sources

Capturing the ‘ome’ : the expanding molecular toolbox for RNA and DNA library construction [PDF]

, 2018
All sequencing experiments and most functional genomics screens rely on the generation of libraries to comprehensively capture pools of targeted sequences.
Boone, Morgane, Callewaert, Nico, De Koker, Andries   +2 more
core   +2 more sources

Transgene silencing and transgene-derived siRNA production in tobacco plants homozygous for an introduced AtMYB90 construct [PDF]

, 2015
Transgenic tobacco (Nicotiana tabacum) lines were engineered to ectopically over-express AtMYB90 (PAP2), an R2-R3 Myb gene associated with regulation of anthocyanin production in Arabidopsis thaliana. Independently transformed transgenic lines, Myb27 and
Cakir, Cahid, Cazzonelli, Christopher I., Chen, Junping, Velten, Jeff, Youn, Eunseog   +4 more
core   +1 more source

Mapping of RNA Modifications by Direct Nanopore Sequencing and JACUSA2

, 2023
RNA modifications exist in all kingdom of life. Several different types of base or ribose modifications are now summarized under the term the ”epitranscriptome”. With the advent of high-throughput sequencing technologies, much progress has been made in understanding RNA modification biology and how these modifications can influence many aspects of RNA ...
Amina, Lemsara, Christoph, Dieterich, Isabel S, Naarmann-de Vries   +2 more
openaire   +3 more sources

A novel method for the capture-based purification of whole viral native RNA genomes

AMB Express, 2019
Current technologies for targeted characterization and manipulation of viral RNA primarily involve amplification or ultracentrifugation with isopycnic gradients of viral particles to decrease host RNA background. The former strategy is non-compatible for
Cedric Chih Shen Tan, Sebastian Maurer-Stroh, Yue Wan, October Michael Sessions, Paola Florez de Sessions   +4 more
doaj   +1 more source

Direct RNA sequencing in plants: Practical applications and future perspectives [PDF]

Plant Communications
Muhammad Tahir ul Qamar, Ling-Ling Chen, Xi-Tong Zhu   +2 more
exaly   +2 more sources

MicroRNAs in the stressed heart: Sorting the signal from the noise [PDF]

, 2014
The short noncoding RNAs, known as microRNAs, are of undisputed importance in cellular signaling during differentiation and development, and during adaptive and maladaptive responses of adult tissues, including those that comprise the heart.
Matkovich, Scot J
core   +3 more sources

Common CHD8 Genomic Targets Contrast With Model-Specific Transcriptional Impacts of CHD8 Haploinsufficiency. [PDF]

, 2018
The packaging of DNA into chromatin determines the transcriptional potential of cells and is central to eukaryotic gene regulation. Case sequencing studies have revealed mutations to proteins that regulate chromatin state, known as chromatin remodeling ...
Catta-Preta, Rinaldo, Lim, Kenneth, Nord, Alex S, Wade, A Ayanna   +3 more
core   +6 more sources