Understanding biological systems using state-of-the-art genomics methods require, among other approaches, the gene expression profiling of different tissues, states, or conditions. RNA-seq is the method of choice to study gene expression with little background noise and a large dynamic range for detection of differentially expressed genes. This laboratory course will provide hands-on training on bulk MARS-seq, a method for digital gene expression analysis developed in Ido Amit lab at the Weizmann Institute. This protocol is designed for preparation of 3’ RNA sequencing libraries from low input RNA material in a simple, cost-effective fashion, due to early multiplexing of the samples. Libraries prepared in the course will be sequenced and analyzed. In order to enable fast and user-friendly data analysis, the LSCF Bioinformatics unit developed an intuitive and scalable transcriptome pipeline (UTAP) that executes the full process on Weizmann computer cluster (WEXAC), starting from sequences and ending with a comprehensive report. The sequenced data analysis part will be included in a session (3 hours) that will cover the theoretical basis for the analysis steps UTAP performs and a hands-on session to run the pipeline and understand the outputs it produces.
During the course, we will also present and discuss key aspects of genomics research, the power of unbiased gene expression profiling and Next Generation Sequencing (NGS), as well as quality control evaluation of input material, libraries and sequenced samples.