RNA-Seq Blog Transcriptome Research & Industry News
Transposable elements (TEs) regulate diverse biological processes, from early development to cancer. Expression of young TEs is difficult to...
Read More »CELLO-seq – locus-specific expression of transposable elements in single cells
GeneTEFlow – A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data
Transposable elements (TEs) are mobile genetic elements in eukaryotic genomes. Recent research highlights the important role of TEs in the embryogenesis, neurodevelopment, and immune functions...
Read More »TEffectR – an R package for studying the potential effects of transposable elements on gene expression
Recent studies highlight the crucial regulatory roles of transposable elements (TEs) on proximal gene expression in distinct biological contexts such as disease and development. However, computational tools...
Read More »TEcandidates – prediction of genomic origin of expressed transposable elements using RNA-seq data
In recent years, Transposable Elements (TEs) have been related to gene regulation. However, estimating the origin of expression of TEs through RNA-seq is complicated by multimapping reads coming from their repetitive sequences. Current approaches that address multimapping reads are focused ...
Read More »SalmonTE – An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data
Transposable elements (TEs) are DNA sequences which are capable of moving from one location to another and represent a large proportion (45%) of the human genome. TEs have functional roles in a variety of biological phenomena such as cancer, neurodegenerative ...
Read More »Identification of Non-coding RNAs by High-Throughput Sequencing
Non-coding RNA transcripts, such as long non-coding RNAs, miRNAs, siRNAs, and transposon-originating transcripts, are involved in the regulation of RNA stability, protein translation, and/or the modulation of chromatin states. RNA-Seq can be used to catalog this diversity of novel transcripts ...
Read More »Considerations and complications of mapping small RNA high-throughput data to transposable elements
High-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. When coupled with fully-sequenced genomes, millions of small RNA (sRNA) reads are mapped to regions of interest and the results scrutinized for clues about epigenetic mechanisms. However, ...
Read More »TEtools – facilitates big data expression analysis of transposable elements
Over recent decades, substantial efforts have been made to understand the interactions between host genomes and transposable elements (TEs). The impact of TEs on the regulation of host genes is well known, with TEs acting as platforms of regulatory sequences. ...
Read More »TEtranscripts – A package for including transposable elements in differential expression analysis of RNA-Seq datasets
Most RNA-seq data analysis software packages are not designed to handle the complexities involved in properly apportioning short sequencing reads to highly repetitive regions of the genome. These regions are often occupied by transposable elements (TEs), which make up between ...
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