26 papers · ranked by Valyu relevance
Malachi Griffith, Jason R. Walker, Nicholas C. Spies, Benjamin J. Ainscough + 2 more
'Benjamin J. Ainscough' 'Obi L. Griffith' 'Francis Ouellette'] Massively parallel RNA sequencing (RNA-seq) has rapidly become the assay of choice for interrogating RNA transcript abundance and diversity. This article provides a detailed introduction to fundamental RNA-seq molecular biology and informatics concepts. We…
Charlotte Gustafsson, Julia Hauenstein, Nicolai Frengen, Aleksandra Krstic + 2 more
RNA sequencing has become the mainstay for studies of gene expression. Still, analysis of rare cells with random hexamer priming – to allow analysis of a broader range of transcripts – remains challenging. We here describe a tagmentation-based, rRNA blocked, random hexamer primed RNAseq approach (T-RHEX-RNAseq) for…
Charlotte Gustafsson, Julia Hauenstein, Nicolai Frengen, Aleksandra Krstic + 2 more
'Aleksandra Krstic' 'Sidinh Luc' 'Robert Månsson'] Background RNA sequencing has become the mainstay for studies of gene expression. Still, analysis of rare cells with random hexamer priming - to allow analysis of a broader range of transcripts - remains challenging. Results We here describe a tagmentation-based, rRNA…
Xian Adiconis, Lin Fan, David DeLuca, Andrey Sivachenko + 8 more
'Nathalie Pochet' 'Aaron Berlin' 'Sarah Young' 'Gad Getz' 'Aviv Regev' 'Chad Nusbaum' 'Andreas Gnirke' 'Joshua Z Levin'] Next-generation sequencing of RNA (RNA-Seq) is a powerful tool that can be applied to a wide range of biological questions. RNA-Seq provides insight at multiple levels into the transcription of the…
Marie-Ange Palomares, Cyril Dalmasso, Eric Bonnet, Céline Derbois + 5 more
High-throughput RNA-sequencing has become the gold standard method for whole-transcriptome gene expression analysis, and is widely used in numerous applications to study cell and tissue transcriptomes. It is also being increasingly used in a number of clinical applications, including expression profiling for…
Wei Vivian Li, Jingyi Jessica Li
Background: Since the invention of next-generation RNA sequencing (RNA-seq) technologies, they have become a powerful tool to study the presence and quantity of RNA molecules in biological samples and have revolutionized transcriptomic studies. The analysis of RNA-seq data at four different levels (samples, genes…
Dhrithi Deshpande, Karishma Chhugani, Yutong Chang, Aaron Karlsberg + 12 more
'Caitlin Loeffler' 'Jinyang Zhang' 'Agata Muszyńska' 'Jeremy Rotman' 'Laura Tao' 'Brunilda Balliu' 'Elizabeth Tseng' 'Eleazar Eskin' 'Fangqing Zhao' 'Pejman Mohammadi' 'Paweł P. Łabaj' 'Serghei Mangul'] Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA 90095, USA…
Kuan-Hao Chao, Yi-Wen Hsiao, Yi-Fang Lee, Chien‐Yueh Lee + 4 more
'Liang‐Chuan Lai' 'Mong‐Hsun Tsai' 'Tzu‐Pin Lu' 'Eric Y. Chuang'] Abstract—RNA-Seq analysis has revolutionized researchers' understanding of the transcriptome in biological research. Assessing the differences in transcriptomic profiles between tissue samples or patient groups enables researchers to explore the…
Yan Guo, Chung-I Li, Fei Ye, Yu Shyr
Background RNAseq technology is replacing microarray technology as the tool of choice for gene expression profiling. While providing much richer data than microarray, analysis of RNAseq data has been much more challenging. To date, there has not been a consensus on the best approach for conducting robust RNAseq…
Brian K Lohman, Jesse N Weber, Daniel I Bolnick
RNAseq is a relatively new tool for ecological genetics that offers researchers insight into changes in gene expression in response to a myriad of natural or experimental conditions. However, standard RNAseq methods (e.g., Illumina TruSeq^®^ or NEBNext^®^) can be cost prohibitive, especially when study designs require…
Weisheng Wu, Jennie L. Lovett, Kerby Shedden, Beverly I. Strassmann + 1 more
Genomic imprinting is an epigenetic mechanism that results in allele specific expression (ASE) based on parent of origin. It is known to play a role in the prenatal and postnatal allocation of maternal resources in mammals. ASE detected by whole transcriptome RNA-seq (wht-RNAseq) has been widely used to analyze…
Yan Guo, Quanhu Sheng, Jiang Li, Fei Ye + 3 more
'Paolo Provero'] RNAseq and microarray methods are frequently used to measure gene expression level. While similar in purpose, there are fundamental differences between the two technologies. Here, we present the largest comparative study between microarray and RNAseq methods to date using The Cancer Genome Atlas (TCGA)…
Yan Guo, Shilin Zhao, Fei Ye, Quanhu Sheng + 1 more
Background. After a decade of microarray technology dominating the field of high-throughput gene expression profiling, the introduction of RNAseq has revolutionized gene expression research. While RNAseq provides more abundant information than microarray, its analysis has proved considerably more complicated. To date…
Muhamad Fachrul, Abhilasha Karkey, Mila Shakya, Louise Judd + 14 more
RNAseq data can be used to infer genetic variants, yet its use for estimating genetic population structure remains underexplored. Here, we construct a freely available computational tool (RGStraP) to estimate RNAseq-based genetic principal components (RG-PCs) and assess whether RG-PCs can be used to control for…
Ye Wang, Michael Mashock, Zhuang Tong, Xiaofeng Mu + 6 more
'Xin Zhou' 'Hong Zhang' 'Gexin Zhao' 'Bin Liu' 'Xinmin Li'] RNA sequencing (RNAseq) is one of the most commonly used techniques in life sciences, and has been widely used in cancer research, drug development, and cancer diagnosis and prognosis. Driven by various biological and technical questions, the techniques of…
Botond Sipos, Greg Slodkowicz, Tim Massingham, Nick Goldman
In line with the importance of RNA-seq, the bioinformatics community has produced numerous data analysis tools incorporating methods to correct sample-specific biases. However, few advanced simulation tools exist to enable benchmarking of competing correction methods. We introduce the first framework to reproduce the…
Weisheng Wu, Jennie L Lovett, Kerby Shedden, Beverly I Strassmann + 2 more
Genomic imprinting is an epigenetic mechanism that results in allele-specific expression (ASE) based on the parent of origin. It is known to play a role in the prenatal and postnatal allocation of maternal resources in mammals. ASE detected by whole transcriptome RNA-seq (wht-RNAseq) has been widely used to analyze…
Lathan Liou, Milena Hornburg, D. S. Robertson
Motivation: While the analysis of a single RNA sequencing (RNAseq) dataset has been well described in the literature, modern research workflows often have additional complexity in that related RNAseq experiments are performed sequentially over time. The simplest and most widely used analysis strategy ignores the…
Ahmed Ibrahem Hafez, Beatriz Soriano, Aya Allah Elsayed, Ricardo Futami + 14 more
'Ricardo Futami' 'Raquel Ceprián' 'Ricardo Ramos' 'Genís Martínez' 'Francisco J. Roig' 'Miguel Angel Torres-Font' 'Fernando Naya-Català' 'Josep À. Calduch-Giner' 'Lucía Trilla‐Fuertes' 'Angelo Gámez‐Pozo' 'Vicente Arnau' 'José M. Sempere' 'Jaume Pérez‐Sánchez' 'Toni Gabaldón' 'Carlos Lloréns'] Hafez, A. 1,2,3# …
Michael Lanzillotti, Jennifer Brodbelt
Recent progress in top-down mass spectrometry analysis of progressively larger nucleic acids has enabled in-depth characterization of intact, modified RNA molecules. Development of methods for desalting and MS/MS fragmentation allows rapid acquisition of high-quality top-down MS/MS spectra of nucleic acids up to 100…
Michael Lanzillotti, Jennifer Brodbelt
Mass spectrometry has proven to be a highly effective tool for characterization of RNA post-transcriptional modifications. For both synthetic RNAs and ones from biological sources, mass spectrometry can interrogate multiple, co-occurring covalent modifications at the nucleotide level simultaneously. To expand the…
Janet Sasso, Barbara Ambrose, Rumiana Tenchov, Ruchira Datta + 3 more
In the last decade, there has been a shift in research, clinical development, and commercial activity to exploit the many roles of RNA in physiology for use in medicine. With the rapid success in the development of lipid-RNA nanoparticles for mRNA vaccines against COVID-19 and with several approved RNA-based drugs, RNA…
Authors not listed
Large-scale de novo nucleic acid synthesis is a powerful tool enabling researchers to better understand and engineer biological systems. Fields ranging from genomics to nucleic acid therapeutics to synthetic biology make use of high-throughput experimental approaches requiring access to large pools or libraries of DNA…
Authors not listed
Oligonucleotides offer a powerful class of new therapeutic modalities, which requires the support of robust and sensitive analytical methods. The primary structure of RNA-based therapeutic drugs is considered a critical quality attribute by regulatory agencies, and must be empirically confirmed to ensure quality…
Authors not listed
mRNA-based technology has emerged as a new class of medicines with a wide range of applications, including viral vaccines, cancer vaccines, and therapeutics for the treatment of metabolic diseases and cardiovascular conditions. Impurities, including double-stranded RNA (dsRNA), mRNA fragments, and mRNA multimers…
Juerg Straubhaar, Alexandria D’Souza, Zachary Niziolek, Bogdan Budnik
Single-cell analysis has clearly established itself in biology and biomedical fields as an invaluable tool that allows one to comprehensively understand the relationship between cells, including their types, states, transitions, trajectories, and spatial position. Scientific methods such as fluorescence labeling…