RNA sequencing (RNA-seq) has become a powerful tool to understand molecular mechanisms and/or developmental programs. It provides a fast, reliable and cost-effective method to access sets of expressed elements in a qualitative and quantitative manner. Especially for non-model organisms and ...
Read More »The Pitfalls of RNA-Seq Methodology
TP53 undergoes multiple RNA-splicing events, resulting in at least nine mRNA transcripts encoding at least 12 functionally different protein isoforms. Antibodies specific to p53 protein isoforms have proven difficult to develop, thus researchers must rely on the transcript information to ...
Read More »InFusion – Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data
Analysis of fusion transcripts has become increasingly important due to their link with cancer development. Since high-throughput sequencing approaches survey fusion events exhaustively, several computational methods for the detection of gene fusions from RNA-seq data have been developed. This kind ...
Read More »ChimPipe – Accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data
Chimeric transcripts are commonly defined as transcripts linking two or more different genes in the genome, and can be explained by various biological mechanisms such as genomic rearrangement, read-through or trans-splicing, but also by technical or biological artefacts. Several studies ...
Read More »RNA-Seq reveals to what extent splice-variant transcripts are translated into protein products
High-throughput RNA sequencing (RNA-seq) has revealed an enormous complexity of alternative splicing (AS) across diverse cell and tissue types. However, it is currently unknown to what extent repertoires of splice-variant transcripts are translated into protein products. Here, University of Toronto ...
Read More »Phenotype prediction from alternative splicing and gene expression data
A central task of bioinformatics is to develop sensitive and specific means of providing medical prognoses from biomarker patterns. Common methods to predict phenotypes in RNA-Seq datasets utilize machine learning algorithms trained via gene expression. Isoforms, however, generated from alternative ...
Read More »Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
High-throughput sequencing of mRNA (RNA-seq) has become the standard method for measuring and comparing the levels of gene expression in a wide variety of species and conditions. RNA-seq experiments generate very large, complex data sets that demand fast, accurate and ...
Read More »A High Resolution Map of the Arabidopsis thaliana Developmental Transcriptome Based on RNA-seq Profiling
Arabidopsis thaliana is a long established model species for plant molecular biology, genetics and genomics, and studies of A.thaliana gene function provide the basis for formulating hypotheses and designing experiments involving other plants, including economically important species. A comprehensive understanding ...
Read More »RACE-Seq – extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing
Long non-coding RNAs (lncRNAs) constitute a large, yet mostly uncharacterized fraction of the mammalian transcriptome. Such characterization requires a comprehensive, high-quality annotation of their gene structure and boundaries, which is currently lacking. Here researchers from the Barcelona Institute of Science ...
Read More »Spliced synthetic genes as internal controls in RNA sequencing experiments
RNA sequencing (RNA-seq) can be used to assemble spliced isoforms, quantify expressed genes and provide a global profile of the transcriptome. However, the size and diversity of the transcriptome, the wide dynamic range in gene expression and inherent technical biases ...
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