MOTIVATION Gene expression profiling using RNA-seq is a powerful technique for screening RNA species' landscapes and their dynamics in an unbiased way. While several advanced methods exist for differential expression analysis of RNA-seq data, proper tools to anal.yze RNA-seq time-course have not been proposed. RESULTS In this study, we use RNA-seq to measure gene expression during the early h...

Summary: Differential expression analysis using high-throughput RNA sequencing (RNA-seq) data is widely applied in transcriptomic studies and many software tools have been developed for this purpose. Active development of existing popular tools, together with emergence of new tools means that studies comparing the performance of differential expression analysis methods become rapidly out-of-dat...

MOTIVATION Isoform quantification is an important goal of RNA-seq experiments, yet it remains problematic for genes with low expression or several isoforms. These difficulties may in principle be ameliorated by exploiting correlated experimental designs, such as time series or dosage response experiments. Time series RNA-seq experiments, in particular, are becoming increasingly popular, yet the...

Standard RNA-seq has a well know tendency to generate "ghost" antisense reads due to formation of spurious second strand cDNA in the sequencing process. We recently reported on a novel variant of RNA-seq coined "tagRNA-seq" introduced for the purpose of distinguishing primary from processed transcripts in bacteria. Incidentally, the additional information provided by the tags is also very suita...

RNA-seq analysis involves multiple steps from processing raw sequencing data to identifying, organizing, annotating, and reporting differentially expressed genes. bcbio is an open source, community-maintained framework providing automated and scalable RNA-seq methods for identifying gene abundance counts. We have developed bcbioRNASeq, a Bioconductor package that provides ready-to-render templa...

AnAlysis of RnA-seq dAtA Profiling the transcriptome has been a central application of NGS technologies. Since the sequencing technology generates short reads, the first step is to map the reads onto the source genome, genes, and transcripts. Despite development of many algorithms and tools for mapping reads to the reference genomes, accurately mapping RNA-seq reads remains a tough problem due ...

Summary Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes in RNA-seq data. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses. Availability and implementation...

Abstract DDX39B is a member of the DEAD box (DDX) RNA helicase family required for nearly all cellular metabolic processes. The exact role and potential molecular mechanism in progression human colorectal cancer (CRC) remain to be investigated. In present study, we demonstrate that expression higher CRC tissues than adjacent normal tissues. Gain- loss-of-function assays revealed facilitates met...

Despite significant advances of the bovine epigenome investigation, new evidence for epigenetic basis fetal cartilage development remains lacking. In this study, chondrocytes were isolated from long bone tissues fetuses at 90 days. The Assay Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) and transcriptome (RNA-seq) used to characterize gene expression chromatin acce...