UC Santa Cruz

Sequencing technologies are incredibly versatile and have been adapted to measure a wide range of biological phenomena. Using sequencing data, scientists can decipher the genetic makeup of species, and provide understandings into genomics, transcriptomics, and epigenetics. Traditionally, sequencing has been done on Illumina short-read sequencers, but larger Illumina sequencing machines are expensive, and only the best-equipped labs can afford them. As a result, most labs send their libraries out to sequencing cores which could take weeks or months to get their data back. Additionally, traditional sequencing methods face limitations due to their short read lengths. For example, short-read based RNA-seq can’t resolve transcript isoforms and are therefore limited to less detailed gene level analysis. My work addresses both of these issues - expensive hardware and limited read lengths - using Oxford Nanopore Technologies (ONT) affordable long-read sequencers. My first project involved developing a workflow for converting short-read libraries into nanopore libraries while also increasing the low raw accuracy of ONT sequencers. I show that this workflow can be used to replace expensive illumina sequencers and allows labs to sequence their short read libraries at high accuracy on ONT sequencers. For my second project I developed and applied a workflow for using long read sequencing to investigate the isoform landscape of mouse livers over a circadian time course. Together, my projects push the capabilities of ONT sequencers and uncover the nuances of the circadian control of the transcriptional landscape of mouse liver.