RNA binding proteins (RBPs) play key roles in determining cellular behavior by manipulating the processing of target RNAs. Robust methods are required to detect the numerous binding sites of RBPs across the transcriptome. RNA-immunoprecipitation followed by sequencing (RIP-seq) and crosslinking followed by immunoprecipitation and sequencing (CLIP-seq) are state-of-the-art methods used to identi...

A rapid method for determining nucleotide sequences in RNA is described. It employs the 3'-deoxy analogues of the ribonucleoside triphosphates as specific chain terminators during RNA synthesis. For example, the inclusion of 3'-deoxyuridine 5'-triphosphate in an RNA synthesis reaction in addition to the four usual ribonucleoside triphosphate precursors results in the synthesis of a set of diffe...

This article includes supplemental data. Please visit http://www.fasebj.org to obtain this information.Multiple recent publications on RNA sequencing (RNA-seq) have demonstrated the power of next-generation sequencing technologies in whole-transcriptome analysis. Vendor-specific protocols used for RNA library construction often require at least 100 ng total RNA. However, under certain condition...

This study aimed to get a better understanding of molecular epidemiology and genetic variation in the spike glycoprotein as key viral component involved entrance into host cells potential vaccination target. Three Iraqi SARS-CoV-2 strains were investigated using whole-genome sequencing, with two them clustering 20A (GH) clade, remaining strain is clustered 20E (GV) belonging B.1.36.1 B.1.177.80...

Malaria parasites introduce outstanding life-phase variations as they grow across multiple atmospheres of the mosquito vector. There are transcriptomes several thousand different parasites. (RNA-seq) Ribonucleic acid sequencing is a prevalent gene expression tool leading to better understanding genetic interrogations. RNA-seq measures transcriptions expressions genes. Data from necessitate proc...

RNA-sequencing is a powerful tool in studying RNomics. However, the highly abundance of ribosomal RNAs (rRNA) and transfer RNA (tRNA) have predominated in the sequencing reads, thereby hindering the study of lowly expressed genes. Therefore, rRNA depletion prior to sequencing is often performed in order to preserve the subtle alteration in gene expression especially those at relatively low expr...

BACKGROUND Lung cancer is the most common cause of cancer related death. Alterations in gene sequence, structure, and expression have an important role in the pathogenesis of lung cancer. Fusion genes and alternative splicing of cancer-related genes have the potential to be oncogenic. In the current study, we performed RNA-sequencing (RNA-seq) to investigate potential fusion genes and alternati...

The ability to extract RNA and prepare RNA sequencing (RNA-Seq) libraries from Formalin Fixed Paraffin Embedded (FFPE) tissues allows researchers to identify and validate new biomarkers of disease onset, progression, and therapy resistance. However, the typically poor quality of RNA derived from FFPE samples has previously limited use of this tissue source as a resource for transcriptome profil...

RNA sequencing (RNA-seq) has emerged as the method of choice for measuring the expression of RNAs in a given cell population. In most RNA-seq technologies, sequencing the full length of RNA molecules requires fragmentation into smaller pieces. Unfortunately, the issue of nonuniform sequencing coverage across a genomic feature has been a concern in RNA-seq and is attributed to biases for certain...

Prior to the advent of new, deep sequencing methods, small RNA (sRNA) discovery was dependent on Sanger sequencing, which was time-consuming and limited knowledge to only the most abundant sRNA. The innovation of large-scale, next-generation sequencing has exponentially increased knowledge of the biology, diversity and abundance of sRNA populations. In this review, we discuss issues involved in...