RNA cleavage by some endoribonucleases and self-cleaving ribozymes produces RNA fragments with 5'-hydroxyl (5'-OH) and 2',3'-cyclic phosphate termini. To identify 5'-OH RNA fragments produced by these cleavage events, we exploited the unique ligation mechanism of Escherichia coli RtcB RNA ligase to attach an oligonucleotide linker to RNAs with 5'-OH termini, followed by steps for library constr...

The advent of Next Generation Sequencing (NGS) technology has enabled a new major approach for micro RNAs (miRNAs) expression profiling through the so called RNA-Sequencing (RNA-Seq). Different tools have been developed in the last years in order to detect and quantify miRNAs, especially in pathological samples, starting from the big amount of data deriving from RNA sequencing. These tools, usu...

Acknowledgments First and foremost, I want to thank my advisor Dr. Christopher Taylor. His endless support and wisdom helped me finish this dissertation. His enthusiasm for Bioinformatics was contagious—and I definitely caught it. His depth of knowledge and very precise academic guidance brought me to develop a web-based GUI distributed computational pipeline, which provides all-in-one function...

conclusions overall, results of present study were consistent with the data reported earlier base on 5’ ntr in iranian isolates and revealed genotype ir2 is major genotype in iranian hgv-positive patient. it means there are higher similarities between iranian and europe-usa in hgv ns3 gene. results nucleotide blast results emphasized that most similar sequences to ir ns3 sequences were those fr...

The standard method for the storage and preservation of RNA has been at ultra-low temperatures. However, reliance on liquid nitrogen and freezers for storage of RNA has multiple downsides. Recently new techniques have been developed for storing RNA at room temperature utilizing desiccation and are reported to be an effective alternative for preserving RNA integrity. In this study we compared fr...

RNA modifications play pivotal roles in the life cycle and fate, are now appreciated as a major posttranscriptional regulatory layer cell. In last few years, direct nanopore sequencing (dRNA-seq) has emerged promising technology that can provide single-molecule resolution maps of their native context. While be successfully sequenced using this technology, detection is still challenging. Here, w...

Preserving the original RNA orientation information in RNA-Sequencing (RNA-Seq) experiment is essential to the analysis and understanding of the complexity of mammalian transcriptomes. We describe herein a simple, robust, and time-effective protocol for generating strand-specific RNA-seq libraries suited for the Illumina sequencing platform. We modified the Illumina TruSeq RNA sample preparatio...