Comprehensive comparative analysis of strand-specific RNA sequencing methods

Comparative analysis of strand-specific RNA sequencing approaches

Background Standard RNA sequencing approaches generally require double-stranded cDNA synthesis, which erases RNA strand information. Synthesis of a randomly primed double-stranded cDNA followed by addition of adaptors for next-generation sequencing leads to the loss of information about which strand was present in the original mRNA template. The polarity of the transcript is important for corre...

Comparative Analysis of Single-Cell RNA Sequencing Methods.

Single-cell RNA sequencing (scRNA-seq) offers new possibilities to address biological and medical questions. However, systematic comparisons of the performance of diverse scRNA-seq protocols are lacking. We generated data from 583 mouse embryonic stem cells to evaluate six prominent scRNA-seq methods: CEL-seq2, Drop-seq, MARS-seq, SCRB-seq, Smart-seq, and Smart-seq2. While Smart-seq2 detected t...

A strand-specific library preparation protocol for RNA sequencing.

The analysis of transcriptome, which was over the past decade based mostly on microarray technologies, is now being superseded by so-called next generation sequencing (NGS) systems that changed the way to explore entire transcriptome. RNA sequencing (RNA-Seq), one application of NGS, is a powerful tool, providing information not only about the expression level of genes but also further about th...

High-throughput illumina strand-specific RNA sequencing library preparation.

RNA CoMPASS: RNA Comprehensive Multi-Processor Analysis System for Sequencing

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...