The deep sequencing of an mRNA population, RNA-seq, is a very successful application of next-generation sequencing technologies (NGSTs). RNA-seq takes advantage of two key NGST features: (1) samples can be mixtures of different DNA pieces, and (2) sequencing provides both qualitative and quantitative information about each DNA piece analyzed. We recently used RNA-seq to study the transcriptome ...

MOTIVATION RNA-Seq experiments have shown great potential for transcriptome profiling. While sequencing increases the level of biological detail, integrative data analysis is also important. One avenue is the construction of coexpression networks. Because the capacity of RNA-Seq data for network construction has not been previously evaluated, we constructed a coexpression network using striatal...

Abstract Background The flesh pigmentation of farmed Atlantic salmon is formed by accumulation carotenoids derived from commercial diets. In the gastrointestinal system, hindgut considered critical in processes uptake and metabolism. Tasmania, color depletion can noticeably affect at different levels severity following extremely hot summers. this study, RNA sequencing (RNA-Seq) was performed to...

MOTIVATION RNA-seq has become the method of choice to quantify genes and exons, discover novel transcripts and detect fusion genes. However, reliable variant identification from RNA-seq data remains challenging because of the complexities of the transcriptome, the challenges of accurately mapping exon boundary spanning reads and the bias introduced during the sequencing library preparation. M...

Rationale: circular RNAs (circRNAs) have been demonstrated to play a crucial role in cancer progression. KIAA1429, key component of the m6A methyltransferase complex, has recently reported promote hepatocellular carcinoma (HCC) progression by regulating methylation. The aim present study is investigate KIAA1429-mediated HCC Methods: RNA sequencing (RNA-seq) and methylated immunoprecipitation (m...

Unlike population-level approaches, single-cell RNA sequencing enables transcriptomic analysis of an individual cell. Through the combination of high-throughput sequencing and bioinformatic tools, single-cell RNA-seq can detect more than 10,000 transcripts in one cell to distinguish cell subsets and dynamic cellular changes. After several years' development, single-cell RNA-seq can now achieve ...

salinization of crop lands is one of the most important reasons for reduction in productivity and threats food security. activation of signaling process in plants is the first step during sense environmental cues and stress signals. identification of the components of plant intracellular signaling mechanisms, pathways, and networks in response to salt stress in aegilops tauschii (the d genome d...

In eukaryotic cells, alternative cleavage of 3' untranslated regions (UTRs) can affect transcript stability, transport and translation. For polyadenylated (poly(A)) transcripts, cleavage sites can be characterized with short-read sequencing using specialized library construction methods. However, for large-scale cohort studies as well as for clinical sequencing applications, it is desirable to ...

C57BL/6J (B6) and DBA/2J (D2) are two of the most commonly used inbred mouse strains in neuroscience research. However, the only currently available mouse genome is based entirely on the B6 strain sequence. Subsequently, oligonucleotide microarray probes are based solely on this B6 reference sequence, making their application for gene expression profiling comparisons across mouse strains dubiou...