Existing methods for detecting RNA intermediates resulting from exonuclease degradation are low-throughput and laborious. In addition, mapping the 3' ends of RNA molecules to the genome after high-throughput sequencing is challenging, particularly if the 3' ends contain post-transcriptional modifications. To address these problems, we developed EnD-Seq, a high-throughput sequencing protocol tha...

Abstract Introduction Gastric mesenchymal tumours are a rare group of neoplasms, which include gastrointestinal stromal (GISTs) and leiomyomas. To date, there is limited information on the tumour microenvironment (TME) in these despite TME widely known to influence hallmarks cancer. In this study we used single cell RNA sequencing (scRNAseq) profile individual cells GIST leiomyoma. Method The t...

MOTIVATION RNA-seq is replacing microarrays as the primary tool for gene expression studies. Many RNA-seq studies have used insufficient biological replicates, resulting in low statistical power and inefficient use of sequencing resources. RESULTS We show the explicit trade-off between more biological replicates and deeper sequencing in increasing power to detect differentially expressed (DE)...

RNA-binding proteins (RBPs) are key mediators of posttranscriptional gene expression control. However, the links between cell signaling on one hand and RBP function other understudied. While thousands posttranslational modification (PTM) sites RBPs have been identified, their functional roles only poorly characterized. RNA-interactome capture (RIC) cross-linking immunoprecipitation (CLIP) attra...

Construction of next-generation sequencing (NGS) libraries involves RNA manipulation, which often creates noisy, biased, and artifactual data that contribute to errors in transcriptome analysis. In this study, a total of 19 whole transcriptome termini site sequencing (WTTS-seq) and seven RNA sequencing (RNA-seq) libraries were prepared from Xenopus tropicalis adult and embryo samples to determi...

RNA sequencing approaches to transcriptome analysis require a large amount of input total RNA to yield sufficient mRNA using either poly-A selection or depletion of rRNA. This feature makes it difficult to miniaturize transcriptome analysis for greater efficiency. To address this challenge, we devised and validated a simple procedure for the preparation of whole-transcriptome cDNA libraries fro...

Next-generation sequencing (NGS) and mass spectrometry technologies bring unprecedented throughput, scalability and speed, facilitating the studies of biological systems. These technologies allow to sequence and analyze heterogeneous RNA populations rather than single sequences. In particular, they provide the opportunity to implement massive viral surveillance and transcriptome quantification....

The transcriptome plays an important role in the life of a cell. Detailed analysis of the transcriptome enables interpretation of its structure and functionality. High throughput sequencing technology signi cantly enhanced the understanding of transcriptome activity. The RNA-sequencing process currently provides the most accurate estimation of gene expression levels. Moreover, RNA-seq allows de...

Single-cell RNA sequencing is a promising and robust technique that has been widely applied in the field of dermatology to study transcriptional profile each cell at very high resolution. Here we tested compatibility novel instrument-free single-cell RNA-sequencing kit, recently developed by Scipio bioscience, on human skin cells. Human punch biopsy was first mechanically treated for separation...