Project description:The delta smelt (Hypomesus transpacificus) is a pelagic fish species endemic to the Sacramento-San Joaquin Estuary in Northern California, listed as endangered under both the USA Federal and Californian State Endangered Species Acts and acts as an indicator of ecosystem health in its habitat range. Interrogative tools are required to successfully monitor effects of contaminants upon the delta smelt, and to research potential causes of population decline in this species. We used microarray technology to investigate genome-wide effects in 47-day old larvae after a 7-day exposure to ambient water samples from the Sacramento River at a monitoring field station (Hood) situated 8 miles downstream of the Sacramento regional Wastewater Treatment Plant. Genomic assessments were carried out on surviving organisms and contrasted to laboratory controls.
Project description:Raw data for our manuscript in prep, titled: "Real time health monitoring through urine analysis: A preliminary observational study."
Project description:Whole-genome bisulfite sequencing (WGBS) is currently the gold standard for DNA methylation (5-methylcytosine, 5mC) profiling, however the destructive nature of sodium bisulfite results in DNA fragmentation and subsequent biases in sequencing data. Such issues have led to the development of bisulfite-free methods for 5mC detection. Nanopore sequencing is a long read non-destructive approach that directly analyzes DNA and RNA fragments in real time. Recently, computational tools have been developed that enable base-resolution detection of 5mC from Oxford Nanopore sequencing data. In this chapter we provide a detailed protocol for preparation, sequencing, read assembly and analysis of genome-wide 5mC using Nanopore sequencing technologies.
