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RNA-Seq optimization with eQTL gold standards. [PDF]
, 2013 BackgroundRNA-Sequencing (RNA-Seq) experiments have been optimized for library preparation, mapping, and gene expression estimation. These methods, however, have revealed weaknesses in the next stages of analysis of differential expression, with results ...
Arking, Dan E +5 more
core +2 more sources
An RNA-seq primer for pulmonologists [PDF]
European Respiratory Journal, 2019 With the evolution of high throughput sequencing technologies, the past decade has seen an exponential rise in the use of RNA sequencing (RNA-seq). RNA-seq has deepened our understanding of biological systems to unprecedented levels of resolution, identifying not only gene expression signatures but also regulatory RNA molecules that may play critical ...
Sarah G. Chu +3 more
openaire +2 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 +2 more
core +2 more sources
Bioinformatics, 2011 Abstract Summary: RNA-Seq is an exciting methodology that leverages the power of high-throughput sequencing to measure RNA transcript counts at an unprecedented accuracy. However, the data generated from this process are extremely large and biologist-friendly tools with which to analyze it are sorely lacking. MultiExperiment Viewer (MeV)
Howe, Eleanor A. +3 more
openaire +2 more sources
SCRABBLE: single-cell RNA-seq imputation constrained by bulk RNA-seq data
Genome Biology, 2019 Single-cell RNA-seq data contain a large proportion of zeros for expressed genes. Such dropout events present a fundamental challenge for various types of data analyses. Here, we describe the SCRABBLE algorithm to address this problem. SCRABBLE leverages
Tao Peng, Qin Zhu, Penghang Yin, Kai Tan
doaj +1 more source
Detecting differential usage of exons from RNA-Seq data [PDF]
, 2012 RNA-Seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression. Understanding the regulation of these processes requires comparisons between treatments, tissues or conditions.
Alejandro Reyes +2 more
core +3 more sources
Prime-seq, efficient and powerful bulk RNA sequencing
Genome Biology, 2022 Cost-efficient library generation by early barcoding has been central in propelling single-cell RNA sequencing. Here, we optimize and validate prime-seq, an early barcoding bulk RNA-seq method.
Aleksandar Janjic +11 more
doaj +1 more source
Frontiers in Bioinformatics, 2023 Introduction: The application of RNA-sequencing has led to numerous breakthroughs related to investigating gene expression levels in complex biological systems.
Ryan S. McClure +4 more
doaj +1 more source
RNA-Seq Assembly – Are We There Yet? [PDF]
Frontiers in Plant Science, 2012 Transcriptomic sequence resources represent invaluable assets for research, in particular for non-model species without a sequenced genome. To date, the Next Generation Sequencing technologies 454/Roche and Illumina have been used to generate transcriptome sequence databases by mRNA-Seq for more than fifty different plant species.
Schliesky, Simon +3 more
openaire +4 more sources
intePareto: an R package for integrative analyses of RNA-Seq and ChIP-Seq data
BMC Genomics, 2020 Background RNA-Seq, the high-throughput sequencing (HT-Seq) of mRNAs, has become an essential tool for characterizing gene expression differences between different cell types and conditions.
Yingying Cao +2 more
doaj +1 more source