Whole Transcriptome Sequencing Evaluation Case Study

This case study presents an evaluation of whole transcriptome sequencing as an alternative to targeted RNA sequencing, particularly focusing on the Watchmaker RNA Library Prep Kit with Polaris Depletion. The study aims to address the technical challenges associated with RNA sequencing from clinical specimens, such as limited input material and RNA degradation. Conducted in two phases, the first phase compared the performance of the Watchmaker workflow against a standard RNA library prep into exome capture method using various sample types, including whole blood and FFPE samples. Key metrics assessed included turnaround time, library complexity, and gene detection rates. The second phase further evaluated the robustness of the Watchmaker workflow across different RNA input amounts and qualities. Results indicated that the Watchmaker workflow significantly reduced turnaround time and improved data quality, demonstrating high reproducibility and effective depletion of non-informative transcripts. The findings suggest that whole transcriptome sequencing can effectively recover biologically meaningful information from challenging clinical samples.